From 90507a970b4f9264a212eb24792fe6143c1e6e17 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 6 Jun 2023 12:00:01 -0400
Subject: [PATCH 01/69] feat: use pydantic-zarr for representing multiscale
 groups

---
 poetry.lock                                 | 219 ++++++++++++++++----
 pyproject.toml                              |   1 +
 src/pydantic_ome_ngff/latest/multiscales.py |  49 ++---
 src/pydantic_ome_ngff/tree.py               |  76 -------
 src/pydantic_ome_ngff/v04/multiscales.py    |  47 ++---
 tests/test_latest.py                        |  73 +++----
 tests/test_v04.py                           |  72 +++----
 7 files changed, 285 insertions(+), 252 deletions(-)
 delete mode 100644 src/pydantic_ome_ngff/tree.py

diff --git a/poetry.lock b/poetry.lock
index d2c7039..ac84f79 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,16 @@
 # This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
+[[package]]
+name = "asciitree"
+version = "0.3.3"
+description = "Draws ASCII trees."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"},
+]
+
 [[package]]
 name = "attrs"
 version = "22.2.0"
@@ -219,6 +230,18 @@ files = [
     {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"},
 ]
 
+[[package]]
+name = "entrypoints"
+version = "0.4"
+description = "Discover and load entry points from installed packages."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "entrypoints-0.4-py3-none-any.whl", hash = "sha256:f174b5ff827504fd3cd97cc3f8649f3693f51538c7e4bdf3ef002c8429d42f9f"},
+    {file = "entrypoints-0.4.tar.gz", hash = "sha256:b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4"},
+]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.1.1"
@@ -234,6 +257,18 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "fasteners"
+version = "0.18"
+description = "A python package that provides useful locks"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "fasteners-0.18-py3-none-any.whl", hash = "sha256:1d4caf5f8db57b0e4107d94fd5a1d02510a450dced6ca77d1839064c1bacf20c"},
+    {file = "fasteners-0.18.tar.gz", hash = "sha256:cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953"},
+]
+
 [[package]]
 name = "filelock"
 version = "3.10.0"
@@ -401,6 +436,77 @@ files = [
 [package.dependencies]
 setuptools = "*"
 
+[[package]]
+name = "numcodecs"
+version = "0.11.0"
+description = "A Python package providing buffer compression and transformation codecs for use"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "numcodecs-0.11.0-cp310-cp310-win_amd64.whl", hash = "sha256:0fabc7dfdf64a9555bf8a34911e05b415793c67a1377207dc79cd96342291fa1"},
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+]
+
+[package.dependencies]
+entrypoints = "*"
+numpy = ">=1.7"
+
+[package.extras]
+docs = ["mock", "numpydoc", "sphinx", "sphinx-issues"]
+msgpack = ["msgpack"]
+test = ["coverage", "flake8", "pytest", "pytest-cov"]
+zfpy = ["zfpy (>=1.0.0)"]
+
+[[package]]
+name = "numpy"
+version = "1.24.3"
+description = "Fundamental package for array computing in Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
 [[package]]
 name = "packaging"
 version = "23.0"
@@ -466,48 +572,48 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "pydantic"
-version = "1.10.6"
+version = "1.10.8"
 description = "Data validation and settings management using python type hints"
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 python-versions = ">=3.7"
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-    {file = "pydantic-1.10.6.tar.gz", hash = "sha256:cf95adb0d1671fc38d8c43dd921ad5814a735e7d9b4d9e437c088002863854fd"},
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+    {file = "pydantic-1.10.8-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:17aef11cc1b997f9d574b91909fed40761e13fac438d72b81f902226a69dac01"},
+    {file = "pydantic-1.10.8-cp39-cp39-win_amd64.whl", hash = "sha256:66a703d1983c675a6e0fed8953b0971c44dba48a929a2000a493c3772eb61a5a"},
+    {file = "pydantic-1.10.8-py3-none-any.whl", hash = "sha256:7456eb22ed9aaa24ff3e7b4757da20d9e5ce2a81018c1b3ebd81a0b88a18f3b2"},
+    {file = "pydantic-1.10.8.tar.gz", hash = "sha256:1410275520dfa70effadf4c21811d755e7ef9bb1f1d077a21958153a92c8d9ca"},
 ]
 
 [package.dependencies]
@@ -517,6 +623,22 @@ typing-extensions = ">=4.2.0"
 dotenv = ["python-dotenv (>=0.10.4)"]
 email = ["email-validator (>=1.0.3)"]
 
+[[package]]
+name = "pydantic-zarr"
+version = "0.1.3"
+description = ""
+category = "main"
+optional = false
+python-versions = ">=3.9,<4.0"
+files = [
+    {file = "pydantic_zarr-0.1.3-py3-none-any.whl", hash = "sha256:6975055557ba9bec873693bc0d47e100d52f54cf8cde4eebae83b5c7ee34e61e"},
+    {file = "pydantic_zarr-0.1.3.tar.gz", hash = "sha256:ded6a41744670e1f992a858e26efcf4a02e834da7d94e66153edb070ee844b85"},
+]
+
+[package.dependencies]
+pydantic = ">=1.10.8,<2.0.0"
+zarr = ">=2.14.2,<3.0.0"
+
 [[package]]
 name = "pyrsistent"
 version = "0.19.3"
@@ -748,7 +870,28 @@ platformdirs = ">=2.4,<4"
 docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
 test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
 
+[[package]]
+name = "zarr"
+version = "2.14.2"
+description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
+    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+]
+
+[package.dependencies]
+asciitree = "*"
+fasteners = "*"
+numcodecs = ">=0.10.0"
+numpy = ">=1.20"
+
+[package.extras]
+jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "8f9c860337789e81ded8ae4a32435c60b9be73f28993b839a0c8bf304b4af637"
+content-hash = "4d1e5c2217e358fbade28531c262f70bf716a876f8d6222c3c8643ef34a9efef"
diff --git a/pyproject.toml b/pyproject.toml
index 1aa8fd8..e95fe13 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 [tool.poetry.dependencies]
 python = "^3.9"
 pydantic = "^1.10.4"
+pydantic-zarr = "^0.1.3"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 00c05e2..df7116b 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,15 +1,15 @@
 from collections import Counter
-from typing import Any, Dict, List, Optional, Tuple, Union, cast
+from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import conlist, root_validator, validator, Field
+from pydantic import BaseModel, conlist, root_validator, validator, Field
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
-from pydantic_ome_ngff.tree import Array, Attrs, Group
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.axes import AxisType
 from pydantic_ome_ngff.latest.axes import Axis
+from pydantic_zarr import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(StrictBase):
@@ -154,7 +154,7 @@ def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         return axes
 
 
-class MultiscaleAttrs(Attrs):
+class MultiscaleAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -163,42 +163,36 @@ class MultiscaleAttrs(Attrs):
     multiscales: List[Multiscale]
 
 
-class MultiscaleGroup(Group):
-    attrs: MultiscaleAttrs
-
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
     @root_validator
     def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        children: List[Union[Array, Group]] = values["children"]
-        child_arrays = []
-        child_groups = []
-
-        for child in children:
-            if isinstance(child, Group):
-                child_groups.append(child)
-            else:
-                child_arrays.append(child)
-        child_array_names = [a.name for a in child_arrays]
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
+
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in child_array_names:
+                if (dpath := dataset.path) not in array_items:
                     raise ValueError(
                         f"""
                     Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the children of that group. All 
-                    arrays in multiscale metadata must be children of the group.
+                    array with that name was found in the items of that group. All 
+                    arrays in multiscale metadata must be items of the group.
                     """
                     )
         return values
 
     @root_validator
     def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        array_children: Tuple[Array, ...] = tuple(
-            filter(lambda v: hasattr(v, "shape"), values["children"])
-        )
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
 
-        ndims = [len(a.shape) for a in array_children]
+        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             raise ValueError(
                 f"""
@@ -209,12 +203,13 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
-            tforms: List[ctx.CoordinateTransform] = []
+            tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
             for dataset in multiscale.datasets:
                 tforms.extend(dataset.coordinateTransformations)
             for tform in tforms:
+
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
                         Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
diff --git a/src/pydantic_ome_ngff/tree.py b/src/pydantic_ome_ngff/tree.py
deleted file mode 100644
index f821737..0000000
--- a/src/pydantic_ome_ngff/tree.py
+++ /dev/null
@@ -1,76 +0,0 @@
-from typing import (
-    Union,
-    Protocol,
-    Tuple,
-    Dict,
-    Any,
-    Iterable,
-    Literal,
-    List,
-    runtime_checkable,
-)
-from pydantic import BaseModel, Field
-from pydantic_ome_ngff.base import StrictBase
-
-NodeType = Literal["array", "group"]
-
-
-class Attrs(BaseModel):
-    ...
-
-
-class Node(StrictBase):
-    node_type: NodeType
-    name: str
-    attrs: Attrs = Attrs()
-
-
-class Array(Node):
-    node_type: NodeType = Field("array", const=True)
-    shape: Tuple[int, ...]
-    dtype: str
-
-
-class Group(Node):
-    node_type: NodeType = Field("group", const=True)
-    children: List[Union["Group", Array]]
-
-
-class NodeLike(Protocol):
-    basename: str
-    attrs: Dict[str, Any]
-
-
-@runtime_checkable
-class ArrayLike(NodeLike, Protocol):
-    shape: Tuple[int, ...]
-    dtype: Any
-
-
-@runtime_checkable
-class GroupLike(NodeLike, Protocol):
-    def values(self) -> Iterable[Union["GroupLike", ArrayLike]]:
-        """
-        Iterable of the children of this group
-        """
-        ...
-
-
-def build_tree(element: Union[GroupLike, ArrayLike]) -> Union[Group, Array]:
-    """
-    Recursively parse an array-like or group-like into an Array or Group.
-    """
-    result: Union[Group, Array]
-    name = element.basename
-    attrs = Attrs(**element.attrs)
-
-    if isinstance(element, ArrayLike):
-        result = Array(
-            shape=element.shape, name=name, dtype=str(element.dtype), attrs=attrs
-        )
-    elif isinstance(element, GroupLike):
-        children = list(map(build_tree, element.values()))
-        result = Group(name=name, attrs=attrs, children=children)
-    else:
-        raise ValueError(f"Object of type {type(element)} cannot be processed.")
-    return result
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 916833e..809e81e 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,12 +1,11 @@
 from collections import Counter
 import warnings
-from typing import Any, Dict, List, Optional, Union, Tuple, cast
-
-from pydantic import Field, conlist, root_validator, validator
+from typing import Any, Dict, List, Optional, Union, cast
 
+from pydantic import BaseModel, Field, conlist, root_validator, validator
+from pydantic_zarr import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
-from pydantic_ome_ngff.tree import Group, Attrs, Array
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axes import Axis, AxisType
 import pydantic_ome_ngff.v04.coordinateTransformations as ctx
@@ -157,7 +156,7 @@ def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         return axes
 
 
-class MultiscaleAttrs(Attrs):
+class MultiscaleAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -166,42 +165,36 @@ class MultiscaleAttrs(Attrs):
     multiscales: List[Multiscale]
 
 
-class MultiscaleGroup(Group):
-    attrs: MultiscaleAttrs
-
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
     @root_validator
     def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        children: List[Union[Array, Group]] = values["children"]
-        child_arrays = []
-        child_groups = []
-
-        for child in children:
-            if isinstance(child, Group):
-                child_groups.append(child)
-            else:
-                child_arrays.append(child)
-        child_array_names = [a.name for a in child_arrays]
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
+
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in child_array_names:
+                if (dpath := dataset.path) not in array_items:
                     raise ValueError(
                         f"""
                     Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the children of that group. All 
-                    arrays in multiscale metadata must be children of the group.
+                    array with that name was found in the items of that group. All 
+                    arrays in multiscale metadata must be items of the group.
                     """
                     )
         return values
 
     @root_validator
     def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        array_children: Tuple[Array, ...] = tuple(
-            filter(lambda v: hasattr(v, "shape"), values["children"])
-        )
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
 
-        ndims = tuple(len(a.shape) for a in array_children)
+        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             raise ValueError(
                 f"""
diff --git a/tests/test_latest.py b/tests/test_latest.py
index 45e51bf..86ad9d8 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -2,9 +2,10 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_ome_ngff.tree import Array
+from pydantic_zarr import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
+    MultiscaleAttrs,
     MultiscaleDataset,
     MultiscaleGroup,
 )
@@ -276,64 +277,52 @@ def test_coordinate_transforms_invalid_elements(
 
 
 def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1, 1, 1, 1), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the children of that group.",
+        match="array with that name was found in the items of that group.",
     ):
-        bad_children = [
-            Array(name=d.path + "bla", shape=(1, 1, 1, 1), dtype="")
+        bad_items = {
+            d.path
+            + "x": ArraySpec(
+                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+            )
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
 
 def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1, 1, 1, 1), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
         # arrays with varying rank
-        bad_children = [
-            Array(name=d.path, shape=(1,) * (idx + 1), dtype="")
+        bad_items = {
+            d.path: ArraySpec(
+                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+            )
             for idx, d in enumerate(default_multiscale.datasets)
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
-        bad_children = [
-            Array(name=d.path, shape=(1,), dtype="")
+        bad_items = {
+            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
diff --git a/tests/test_v04.py b/tests/test_v04.py
index 6cfd989..7070e48 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -2,10 +2,11 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_ome_ngff.tree import Array
+from pydantic_zarr import ArraySpec
 from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
+    MultiscaleAttrs,
     MultiscaleDataset,
     MultiscaleGroup,
 )
@@ -278,64 +279,51 @@ def test_coordinate_transforms_invalid_elements(
 
 
 def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1, 1, 1, 1), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the children of that group.",
+        match="array with that name was found in the items of that group.",
     ):
-        bad_children = [
-            Array(name=d.path + "bla", shape=(1, 1, 1, 1), dtype="")
+        bad_items = {
+            d.path
+            + "x": ArraySpec(
+                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+            )
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
 
 def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1, 1, 1, 1), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
         # arrays with varying rank
-        bad_children = [
-            Array(name=d.path, shape=(1,) * (idx + 1), dtype="")
+        bad_items = {
+            d.path: ArraySpec(
+                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+            )
             for idx, d in enumerate(default_multiscale.datasets)
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
-        bad_children = [
-            Array(name=d.path, shape=(1,), dtype="")
+        bad_items = {
+            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)

From 7295c2618109ee2deba68492ddb8fbcab11eb6c2 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 6 Jun 2023 12:16:35 -0400
Subject: [PATCH 02/69] chore: update type signature of version in latest
 multiscale, although the version is still untyped. also use conlist for axes.

---
 src/pydantic_ome_ngff/latest/multiscales.py | 10 +++++-----
 src/pydantic_ome_ngff/v04/multiscales.py    |  4 ++--
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index df7116b..d4edd93 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -2,7 +2,7 @@
 from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, root_validator, validator, Field
+from pydantic import BaseModel, conlist, root_validator, validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
@@ -68,10 +68,10 @@ class Multiscale(StrictVersionedBase):
     """
 
     # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # is not properly typed by the spec...
     _version = version
-    # SPEC: why is this optional? why is it untyped?
-    version: Optional[Any] = version
+    # SPEC: why is this untyped?
+    version: Any = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
     name: Optional[Any]
@@ -83,7 +83,7 @@ class Multiscale(StrictVersionedBase):
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: List[Axis] = Field(..., min_items=2, max_items=5)
+    axes: conlist(Axis, min_items=2, max_items=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 809e81e..38b05f5 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -2,7 +2,7 @@
 import warnings
 from typing import Any, Dict, List, Optional, Union, cast
 
-from pydantic import BaseModel, Field, conlist, root_validator, validator
+from pydantic import BaseModel, conlist, root_validator, validator
 from pydantic_zarr import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
@@ -85,7 +85,7 @@ class Multiscale(StrictVersionedBase):
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: List[Axis] = Field(..., min_items=2, max_items=5)
+    axes: conlist(Axis, min_items=2, max_items=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[

From 20c4a8ce0a373121bb40f6e2f57ad5c9906de41b Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 8 Nov 2023 15:36:50 +0100
Subject: [PATCH 03/69] feat: update to pydantic 2 / pydantic-zarr 0.5.2

---
 poetry.lock                                   | 1823 ++++++++++++-----
 pyproject.toml                                |    6 +-
 src/pydantic_ome_ngff/latest/axes.py          |   73 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |   74 +-
 src/pydantic_ome_ngff/v04/axes.py             |   73 +-
 src/pydantic_ome_ngff/v04/cli.py              |   15 +
 .../v04/coordinateTransformations.py          |   10 +-
 src/pydantic_ome_ngff/v04/imageLabel.py       |    6 +-
 src/pydantic_ome_ngff/v04/multiscales.py      |  119 +-
 src/pydantic_ome_ngff/v04/plate.py            |   21 +-
 tests/test_latest.py                          |   45 +-
 tests/test_v04.py                             |   51 +-
 12 files changed, 1603 insertions(+), 713 deletions(-)
 create mode 100644 src/pydantic_ome_ngff/v04/cli.py

diff --git a/poetry.lock b/poetry.lock
index ac84f79..a0e0775 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,149 +1,359 @@
-# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+
+[[package]]
+name = "aiobotocore"
+version = "2.7.0"
+description = "Async client for aws services using botocore and aiohttp"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "aiobotocore-2.7.0-py3-none-any.whl", hash = "sha256:aec605df77ce4635a0479b50fd849aa6b640900f7b295021ecca192e1140e551"},
+    {file = "aiobotocore-2.7.0.tar.gz", hash = "sha256:506591374cc0aee1bdf0ebe290560424a24af176dfe2ea7057fe1df97c4f0467"},
+]
+
+[package.dependencies]
+aiohttp = ">=3.7.4.post0,<4.0.0"
+aioitertools = ">=0.5.1,<1.0.0"
+botocore = ">=1.31.16,<1.31.65"
+wrapt = ">=1.10.10,<2.0.0"
+
+[package.extras]
+awscli = ["awscli (>=1.29.16,<1.29.65)"]
+boto3 = ["boto3 (>=1.28.16,<1.28.65)"]
+
+[[package]]
+name = "aiohttp"
+version = "3.8.6"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1"},
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+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2817b2f66ca82ee699acd90e05c95e79bbf1dc986abb62b61ec8aaf851e81c93"},
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@@ -220,38 +430,24 @@ toml = ["tomli"]
 
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 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
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 python-versions = ">=3.7"
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@@ -259,42 +455,145 @@ test = ["pytest (>=6)"]
 
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 [package.extras]
@@ -304,7 +603,6 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -316,7 +614,6 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -328,7 +625,6 @@ files = [
 name = "isort"
 version = "5.12.0"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -342,78 +638,220 @@ pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"
 plugins = ["setuptools"]
 requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
+[[package]]
+name = "jmespath"
+version = "1.0.1"
+description = "JSON Matching Expressions"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"},
+    {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
+]
+
 [[package]]
 name = "jsonschema"
-version = "4.17.3"
+version = "4.19.2"
 description = "An implementation of JSON Schema validation for Python"
-category = "dev"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.19.2-py3-none-any.whl", hash = "sha256:eee9e502c788e89cb166d4d37f43084e3b64ab405c795c03d343a4dbc2c810fc"},
+    {file = "jsonschema-4.19.2.tar.gz", hash = "sha256:c9ff4d7447eed9592c23a12ccee508baf0dd0d59650615e847feb6cdca74f392"},
 ]
 
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-pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+attrs = ">=22.2.0"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
 
 [package.extras]
 format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
 format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
 
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+optional = false
+python-versions = ">=3.8"
+files = [
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+
+[package.dependencies]
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+
+[[package]]
+name = "markdown-it-py"
+version = "3.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = false
+python-versions = ">=3.8"
+files = [
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+
+[package.dependencies]
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+
+[package.extras]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+optional = false
+python-versions = ">=3.7"
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 mypy-extensions = ">=1.0.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
-typing-extensions = ">=3.10"
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 [package.extras]
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 install-types = ["pip"]
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 python-versions = ">=3.5"
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@@ -423,14 +861,13 @@ files = [
 
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 description = "Node.js virtual environment builder"
-category = "dev"
 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
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 [package.dependencies]
@@ -438,113 +875,113 @@ setuptools = "*"
 
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 name = "numcodecs"
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-description = "A Python package providing buffer compression and transformation codecs for use"
-category = "main"
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 description = "Core utilities for Python packages"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
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 optional = false
 python-versions = ">=3.7"
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 [[package]]
 name = "pluggy"
-version = "1.0.0"
+version = "1.3.0"
 description = "plugin and hook calling mechanisms for python"
-category = "dev"
 optional = false
-python-versions = ">=3.6"
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 files = [
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 [package.extras]
@@ -553,14 +990,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
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+version = "3.5.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -572,124 +1008,183 @@ virtualenv = ">=20.10.0"
 
 [[package]]
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 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
@@ -698,18 +1193,17 @@ pluggy = ">=0.12,<2.0"
 tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
-version = "4.0.0"
+version = "4.1.0"
 description = "Pytest plugin for measuring coverage."
-category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 [package.dependencies]
@@ -719,100 +1213,292 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
+[[package]]
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+description = "Extensions to the standard Python datetime module"
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+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
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+]
+
+[package.dependencies]
+six = ">=1.5"
+
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+    {file = "yarl-1.9.2.tar.gz", hash = "sha256:04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
 
 [[package]]
 name = "zarr"
-version = "2.14.2"
+version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
-    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
+    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
 ]
 
 [package.dependencies]
 asciitree = "*"
 fasteners = "*"
 numcodecs = ">=0.10.0"
-numpy = ">=1.20"
+numpy = ">=1.20,<1.21.0 || >1.21.0"
 
 [package.extras]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "4d1e5c2217e358fbade28531c262f70bf716a876f8d6222c3c8643ef34a9efef"
+content-hash = "d6ba84447520a466cb6cd52278784c5dfdac4c3ac0622619ac0306a55dec74c6"
diff --git a/pyproject.toml b/pyproject.toml
index e95fe13..3ec75f7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,8 +9,10 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
 python = "^3.9"
-pydantic = "^1.10.4"
-pydantic-zarr = "^0.1.3"
+pydantic-zarr = "0.5.2"
+fsspec = "^2023.10.0"
+s3fs = "^2023.10.0"
+rich = "^13.6.0"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/src/pydantic_ome_ngff/latest/axes.py b/src/pydantic_ome_ngff/latest/axes.py
index 848a8b3..822f478 100644
--- a/src/pydantic_ome_ngff/latest/axes.py
+++ b/src/pydantic_ome_ngff/latest/axes.py
@@ -1,8 +1,8 @@
 import warnings
-from pydantic import validator
+from pydantic import model_validator
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-from typing import Any, Dict, Optional
+from typing import Any, Optional
 from pydantic_ome_ngff.v04.axes import AxisType, SpaceUnit, TimeUnit
 
 
@@ -18,53 +18,44 @@ class Axis(StrictVersionedBase):
     type: Optional[str]
     unit: Optional[str]
 
-    @validator("unit")
-    def check_unit(cls, unit: str, values: Dict[str, AxisType]) -> str:
-        type = values["type"]
-        if type == AxisType.space:
+    @model_validator(mode="after")
+    def check_units(self) -> "Axis":
+        typ = self.type
+        unit = self.unit
+        if typ == AxisType.space:
             if unit not in SpaceUnit.__members__:
-                warnings.warn(
-                    f"""
-                Unit "{unit}" is not recognized as a standard unit for an axis with 
-                type "{type}".
-                """,
-                    UserWarning,
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit for "
+                    f" an axis with type '{typ}''."
                 )
-        elif type == AxisType.time:
+                warnings.warn(msg)
+        elif typ == AxisType.time:
             if unit not in TimeUnit.__members__:
-                warnings.warn(
-                    f"""
-                Unit "{unit}" is not recognized as a standard unit for an axis with 
-                type "{type}".
-                """,
-                    UserWarning,
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                    f"with type '{typ}'."
                 )
-        elif type == AxisType.channel:
+                warnings.warn(msg)
+        elif typ == AxisType.channel:
             pass
-        elif type is None:
-            warnings.warn(
-                f"""
-             Null axis type. Version {cls._version} of the OME-NGFF spec states that 
-             the "type" field of an axis should be set to a string.
-            """,
-                UserWarning,
+        elif typ is None:
+            msg = (
+                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
+                "that the 'type' field of an axis should be set to a string."
             )
+            warnings.warn(msg, UserWarning)
         else:
-            warnings.warn(
-                f"""
-            Unknown axis type "{type}". Version {cls._version} of the OME-NGFF spec 
-            states that the "type" field of an axis should be one of 
-            {AxisType._member_names_}.
-            """,
-                UserWarning,
+            msg = (
+                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
+                " spec states that the 'type' field of an axis should be one of "
+                f"{AxisType._member_names_}."
             )
+            warnings.warn(msg)
 
         if unit is None:
-            warnings.warn(
-                f"""
-            Null unit. Version {cls._version} of the OME-NGFF spec states
-            that the `unit` field of an axis should be set to a string.
-            """,
-                UserWarning,
+            msg = (
+                f"Null unit. Version {self._version} of the OME-NGFF spec states "
+                "that the `unit` field of an axis should be set to a string."
             )
-        return unit
+            warnings.warn(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index d4edd93..7d000ed 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -2,23 +2,23 @@
 from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, root_validator, validator
+from pydantic import BaseModel, conlist, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.axes import AxisType
 from pydantic_ome_ngff.latest.axes import Axis
-from pydantic_zarr import GroupSpec, ArraySpec
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(StrictBase):
     path: str
     coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_items=1, max_items=2
+        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
     )
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_dimensionality(
         cls,
         transforms: List[
@@ -39,7 +39,7 @@ def check_transforms_dimensionality(
             )
         return transforms
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_types(
         cls, transforms: List[ctx.CoordinateTransform]
     ) -> List[ctx.CoordinateTransform]:
@@ -74,23 +74,23 @@ class Multiscale(StrictVersionedBase):
     version: Any = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
-    name: Optional[Any]
+    name: Any = None
     # SPEC: not clear what this field is for, given the existence of .metadata
     # SPEC: untyped!
-    type: Optional[Any]
+    type: Any = None
     # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_items=2, max_items=5)
+    axes: conlist(Axis, min_length=2, max_length=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[
         List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
     ]
 
-    @validator("name")
+    @field_validator("name")
     def check_name(cls, name: Optional[str]) -> Optional[str]:
         if name is None:
             warnings.warn(
@@ -101,7 +101,7 @@ def check_name(cls, name: Optional[str]) -> Optional[str]:
             )
         return name
 
-    @validator("axes")
+    @field_validator("axes")
     def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         name_dupes = duplicates(a.name for a in axes)
         if len(name_dupes) > 0:
@@ -164,42 +164,40 @@ class MultiscaleAttrs(BaseModel):
 
 
 class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @root_validator
-    def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_arrays_exist(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if hasattr(v, "shape")
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
-                    raise ValueError(
-                        f"""
-                    Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the items of that group. All 
-                    arrays in multiscale metadata must be items of the group.
-                    """
+                    msg = (
+                        f"Dataset {dpath} was specified in multiscale metadata, but no "
+                        "array with that name was found in the items of that group. "
+                        "All arrays in multiscale metadata must be items of the group."
                     )
-        return values
+                    raise ValueError(msg)
+        return self
 
-    @root_validator
-    def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_array_ndim(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if hasattr(v, "shape")
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
-            raise ValueError(
-                f"""
-            All arrays must have the same dimensionality. Got arrays with dimensionality
-            {ndims}. 
-            """
+            msg = (
+                "All arrays must have the same dimensionality. "
+                f"Got arrays with dimensionality {ndims}."
             )
+            raise ValueError(msg)
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
@@ -216,12 +214,12 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                         tform,
                     )
                     if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
-                        raise ValueError(
-                            f"""
-                        Transform {tform} has dimensionality {tform_dims} which does not
-                        match the dimensionality of the arrays in this group ({ndims}). 
-                        Transform dimensionality must match array 
-                        dimensionality.
-                        """
+                        msg = (
+                            f"Transform {tform} has dimensionality {tform_dims} "
+                            "which does not match the dimensionality "
+                            f"of the arrays in this group ({ndims}). "
+                            "Transform dimensionality must match array "
+                            "dimensionality."
                         )
-        return values
+                        raise ValueError(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/axes.py b/src/pydantic_ome_ngff/v04/axes.py
index a99a308..ba13c64 100644
--- a/src/pydantic_ome_ngff/v04/axes.py
+++ b/src/pydantic_ome_ngff/v04/axes.py
@@ -2,8 +2,8 @@
 from pydantic_ome_ngff.v04.base import version
 import warnings
 from enum import Enum
-from typing import Any, Dict, Optional
-from pydantic import validator
+from typing import Any, Optional
+from pydantic import model_validator
 
 
 class AxisType(str, Enum):
@@ -79,53 +79,44 @@ class Axis(StrictVersionedBase):
     type: Optional[str]
     unit: Optional[str]
 
-    @validator("unit")
-    def check_unit(cls, unit: str, values: Dict[str, AxisType]) -> str:
-        type = values["type"]
-        if type == AxisType.space:
+    @model_validator(mode="after")
+    def check_units(self) -> "Axis":
+        typ = self.type
+        unit = self.unit
+        if typ == AxisType.space:
             if unit not in SpaceUnit.__members__:
-                warnings.warn(
-                    f"""
-                Unit "{unit}" is not recognized as a standard unit for an axis with 
-                type "{type}".
-                """,
-                    UserWarning,
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit "
+                    f"for an axis with type '{typ}'."
                 )
-        elif type == AxisType.time:
+                warnings.warn(msg)
+        elif typ == AxisType.time:
             if unit not in TimeUnit.__members__:
-                warnings.warn(
-                    f"""
-                Unit "{unit}" is not recognized as a standard unit for an axis with 
-                type "{type}".
-                """,
-                    UserWarning,
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                    f"with type '{typ}'."
                 )
-        elif type == AxisType.channel:
+                warnings.warn(msg)
+        elif typ == AxisType.channel:
             pass
-        elif type is None:
-            warnings.warn(
-                f"""
-             Null axis type. Version {cls._version} of the OME-NGFF spec states that 
-             the "type" field of an axis should be set to a string.
-            """,
-                UserWarning,
+        elif typ is None:
+            msg = (
+                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
+                "that the 'type' field of an axis should be set to a string."
             )
+            warnings.warn(msg, UserWarning)
         else:
-            warnings.warn(
-                f"""
-            Unknown axis type "{type}". Version {cls._version} of the OME-NGFF spec 
-            states that the "type" field of an axis should be one of 
-            {AxisType._member_names_}.
-            """,
-                UserWarning,
+            msg = (
+                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
+                " spec states that the 'type' field of an axis should be one of "
+                f"{AxisType._member_names_}."
             )
+            warnings.warn(msg)
 
         if unit is None:
-            warnings.warn(
-                f"""
-            Null unit. Version {cls._version} of the OME-NGFF spec states
-            that the `unit` field of an axis should be set to a string.
-            """,
-                UserWarning,
+            msg = (
+                f"Null unit. Version {self._version} of the OME-NGFF spec states "
+                "that the `unit` field of an axis should be set to a string."
             )
-        return unit
+            warnings.warn(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/cli.py b/src/pydantic_ome_ngff/v04/cli.py
new file mode 100644
index 0000000..6d9af11
--- /dev/null
+++ b/src/pydantic_ome_ngff/v04/cli.py
@@ -0,0 +1,15 @@
+import sys
+from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+import zarr
+from pydantic import ValidationError
+from rich import print_json, print
+
+if __name__ == "__main__":
+    path: str = sys.argv[1]
+    group = zarr.open(path, mode="r")
+    try:
+        result = MultiscaleGroup.from_zarr(group).model_dump_json(indent=2)
+        print_json(result)
+    except ValidationError as e:
+        result = e
+        print(result)
diff --git a/src/pydantic_ome_ngff/v04/coordinateTransformations.py b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
index 32af137..3c8ba9f 100644
--- a/src/pydantic_ome_ngff/v04/coordinateTransformations.py
+++ b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
@@ -1,4 +1,4 @@
-from typing import List, Literal, Union
+from typing import Literal, Sequence, Union
 from pydantic_ome_ngff.base import StrictBase
 
 
@@ -33,8 +33,8 @@ class VectorTranslationTransform(StrictBase):
     """
 
     type: Literal["translation"] = "translation"
-    translation: List[
-        float
+    translation: Sequence[
+        Union[float, int]
     ]  # SPEC: redundant field name -- we already know it's translation
 
 
@@ -45,7 +45,9 @@ class VectorScaleTransform(StrictBase):
     """
 
     type: Literal["scale"] = "scale"
-    scale: List[float]  # SPEC: redundant field name -- we already know it's scale
+    scale: Sequence[
+        Union[float, int]
+    ]  # SPEC: redundant field name -- we already know it's scale
 
 
 def get_transform_ndim(
diff --git a/src/pydantic_ome_ngff/v04/imageLabel.py b/src/pydantic_ome_ngff/v04/imageLabel.py
index 4de07b9..e86412b 100644
--- a/src/pydantic_ome_ngff/v04/imageLabel.py
+++ b/src/pydantic_ome_ngff/v04/imageLabel.py
@@ -1,7 +1,7 @@
 import warnings
 from typing import List, Optional, Tuple
 
-from pydantic import BaseModel, Field, validator
+from pydantic import BaseModel, Field, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.utils import duplicates
 
@@ -37,7 +37,7 @@ class ImageLabel(VersionedBase):
     properties: Optional[Properties]
     source: Optional[Source]
 
-    @validator("version")
+    @field_validator("version")
     def check_version(cls, ver: str) -> str:
         if ver is None:
             warnings.warn(
@@ -49,7 +49,7 @@ def check_version(cls, ver: str) -> str:
             )
         return ver
 
-    @validator("colors")
+    @field_validator("colors")
     def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
             warnings.warn(
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 38b05f5..d632042 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -2,8 +2,8 @@
 import warnings
 from typing import Any, Dict, List, Optional, Union, cast
 
-from pydantic import BaseModel, conlist, root_validator, validator
-from pydantic_zarr import GroupSpec, ArraySpec
+from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -14,10 +14,10 @@
 class MultiscaleDataset(StrictBase):
     path: str
     coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_items=1, max_items=2
+        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
     )
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_dimensionality(
         cls,
         transforms: List[
@@ -30,15 +30,14 @@ def check_transforms_dimensionality(
             if type(tx) in (ctx.VectorScaleTransform, ctx.VectorTranslationTransform):
                 ndims.append(ctx.get_transform_ndim(tx))
         if len(set(ndims)) > 1:
-            raise ValueError(
-                f"""
-            Elements of coordinateTransformations must have the same dimensionality. Got
-            elements with dimensionality = {ndims}.
-            """
+            msg = (
+                "Elements of coordinateTransformations must have the same "
+                f"dimensionality. Got elements with dimensionality = {ndims}."
             )
+            raise ValueError(msg)
         return transforms
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_types(
         cls,
         transforms: List[
@@ -46,20 +45,18 @@ def check_transforms_types(
         ],
     ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
         if (tform := transforms[0].type) != "scale":
-            raise ValueError(
-                f"""
-            The first element of coordinateTransformations must be a scale transform.
-            Got {tform} instead.
-            """
+            msg = (
+                "The first element of coordinateTransformations must be a scale "
+                f"transform. Got {tform} instead."
             )
+            raise ValueError(msg)
         if len(transforms) == 2:
             if (tform := transforms[1].type) != "translation":
-                raise ValueError(
-                    f"""
-                The second element of coordinateTransformations must be a translation 
-                transform. got {tform} instead.
-                """
+                msg = (
+                    "The second element of coordinateTransformations must be a "
+                    f"translation transform. got {tform} instead."
                 )
+                raise ValueError(msg)
         return transforms
 
 
@@ -76,34 +73,34 @@ class Multiscale(StrictVersionedBase):
     version: Optional[Any] = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
-    name: Optional[Any]
+    name: Optional[Any] = None
     # SPEC: not clear what this field is for, given the existence of .metadata
     # SPEC: untyped!
-    type: Optional[Any]
+    type: Any = None
     # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_items=2, max_items=5)
+    axes: conlist(Axis, min_length=2, max_length=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[
         List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ]
+    ] = None
 
-    @validator("name")
+    @field_validator("name")
     def check_name(cls, name: str) -> str:
         if name is None:
-            warnings.warn(
-                f"""
-            The name field was set to None. Version {cls._version} of the OME-NGFF spec 
-            states that the `name` field of a Multiscales object should not be None.
-            """
+            msg = (
+                f"The name field was set to None. Version {cls._version} "
+                "of the OME-NGFF spec states that the `name` field of a Multiscales "
+                "object should not be None."
             )
+            warnings.warn(msg)
         return name
 
-    @validator("axes")
+    @field_validator("axes")
     def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         name_dupes = duplicates(a.name for a in axes)
         if len(name_dupes) > 0:
@@ -162,46 +159,45 @@ class MultiscaleAttrs(BaseModel):
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: List[Multiscale]
+    multiscales: conlist(Multiscale, min_length=1)
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @root_validator
-    def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
+    @model_validator(mode="after")
+    def check_arrays_exist(self) -> "MultiscaleGroup":
+
+        attrs = self.attributes
+        array_items: dict[str, dict[str, Any]] = {
+            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
-                    raise ValueError(
-                        f"""
-                    Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the items of that group. All 
-                    arrays in multiscale metadata must be items of the group.
-                    """
+                    msg = (
+                        f"Dataset {dpath} was specified in multiscale metadata, but no "
+                        "array with that name was found in the items of that group. "
+                        "All arrays in multiscale metadata must be items of the group."
                     )
-        return values
+                    raise ValueError(msg)
+        return self
 
-    @root_validator
-    def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_array_ndim(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
-            raise ValueError(
-                f"""
-            All arrays must have the same dimensionality. Got arrays with dimensionality
-            {ndims}. 
-            """
+            msg = (
+                "All arrays must have the same dimensionality. "
+                f"Got arrays with dimensionality {ndims}."
             )
+            raise ValueError(msg)
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
@@ -218,12 +214,11 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                         tform,
                     )
                     if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
-                        raise ValueError(
-                            f"""
-                        Transform {tform} has dimensionality {tform_dims} which does not
-                        match the dimensionality of the arrays in this group ({ndims}). 
-                        Transform dimensionality must match array 
-                        dimensionality.
-                        """
+                        msg = (
+                            f"Transform {tform} has dimensionality {tform_dims} "
+                            "which does notmatch the dimensionality of the arrays "
+                            f"in this group ({ndims}). Transform dimensionality "
+                            "must match array dimensionality."
                         )
-        return values
+                        raise ValueError(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index bcbc6f1..1ccda2f 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -2,13 +2,14 @@
 
 from pydantic import BaseModel, PositiveInt
 from pydantic_ome_ngff.base import VersionedBase
-
 from pydantic_ome_ngff.v04.base import version
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
+from typing import Union
 
 
 class Acquisition(BaseModel):
     id: PositiveInt
-    name: Optional[str]
+    name: Optional[str] = None
     maximumfieldcount: PositiveInt
 
 
@@ -16,14 +17,14 @@ class Entry(BaseModel):
     name: str
 
 
-class Well(BaseModel):
+class WellMeta(BaseModel):
     # must be {rowName}/{columnName}
     path: str
     rowIndex: PositiveInt
     columnIndex: PositiveInt
 
 
-class Plate(VersionedBase):
+class PlateMeta(VersionedBase):
     """
     Plate metadata
     see https://ngff.openmicroscopy.org/0.4/#plate-md
@@ -33,9 +34,17 @@ class Plate(VersionedBase):
     # is not required by the spec...
     _version = version
     version: Optional[str] = version
-    name: Optional[str]
+    name: Optional[str] = None
     acquisitions: List[Acquisition]
     columns: List[Entry]
     rows: List[Entry]
     field_count: PositiveInt
-    wells: List[Well]
+    wells: List[WellMeta]
+
+
+class PlateAttributes(BaseModel):
+    plate: PlateMeta
+
+
+class PlateGroup(GroupSpec[PlateAttributes, Union[GroupSpec, ArraySpec]]):
+    ...
diff --git a/tests/test_latest.py b/tests/test_latest.py
index 86ad9d8..9d3b176 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -2,7 +2,7 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_zarr import ArraySpec
+from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
     MultiscaleAttrs,
@@ -175,7 +175,7 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
 
 
 @pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
-def test_multiscale_axis_length(num_axes: int):
+def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
@@ -197,7 +197,7 @@ def test_multiscale_axis_length(num_axes: int):
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="type=value_error.list"):
+    with pytest.raises(ValidationError, match="List should have"):
         Multiscale(
             name="foo",
             axes=axes,
@@ -243,10 +243,10 @@ def test_coordinate_transforms_invalid_ndims():
         ],
     ),
 )
-def test_coordinate_transforms_invalid_lenght(
+def test_coordinate_transforms_invalid_length(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
-    with pytest.raises(ValidationError, match="ensure this value has at most 2 items"):
+) -> None:
+    with pytest.raises(ValidationError, match="List should have at most 2 items"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -269,20 +269,22 @@ def test_coordinate_transforms_invalid_lenght(
 )
 def test_coordinate_transforms_invalid_elements(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
+) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -291,21 +293,23 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
         bad_items = {
             d.path
             + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
 
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -313,16 +317,19 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
         # arrays with varying rank
         bad_items = {
             d.path: ArraySpec(
-                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+                shape=(1,) * (idx + 1),
+                dtype="uint8",
+                chunks=(1,) * (idx + 1),
+                attributes={},
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
+            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
diff --git a/tests/test_v04.py b/tests/test_v04.py
index 7070e48..cb0751e 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -2,7 +2,7 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_zarr import ArraySpec
+from pydantic_zarr.v2 import ArraySpec
 from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
@@ -133,7 +133,7 @@ def test_multiscale_unique_axis_names():
         ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
+def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes = [
         Axis(name=str(idx), type=t, unit=units_map.get(t, None))
@@ -177,7 +177,7 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
 
 
 @pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
-def test_multiscale_axis_length(num_axes: int):
+def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
@@ -199,7 +199,7 @@ def test_multiscale_axis_length(num_axes: int):
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="type=value_error.list"):
+    with pytest.raises(ValidationError, match="List should have"):
         Multiscale(
             name="foo",
             axes=axes,
@@ -215,7 +215,7 @@ def test_multiscale_axis_length(num_axes: int):
         )
 
 
-def test_coordinate_transforms_invalid_ndims():
+def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
         VectorScaleTransform(scale=(1, 1)),
         VectorTranslationTransform(translation=(1, 1, 1)),
@@ -245,10 +245,12 @@ def test_coordinate_transforms_invalid_ndims():
         ],
     ),
 )
-def test_coordinate_transforms_invalid_lenght(
+def test_coordinate_transforms_invalid_length(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
-    with pytest.raises(ValidationError, match="ensure this value has at most 2 items"):
+) -> None:
+    with pytest.raises(
+        ValidationError, match="List should have at most 2 items after validation, not"
+    ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -271,20 +273,22 @@ def test_coordinate_transforms_invalid_lenght(
 )
 def test_coordinate_transforms_invalid_elements(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
+) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -293,20 +297,22 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
         bad_items = {
             d.path
             + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -314,16 +320,19 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
         # arrays with varying rank
         bad_items = {
             d.path: ArraySpec(
-                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+                shape=(1,) * (idx + 1),
+                dtype="uint8",
+                chunks=(1,) * (idx + 1),
+                attributes={},
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
+            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)

From 9c72f28752e48984ec43af14e96027dc12408246 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 8 Nov 2023 15:42:54 +0100
Subject: [PATCH 04/69] feat: pointless renaming

---
 src/pydantic_ome_ngff/latest/__init__.py |  4 ++--
 src/pydantic_ome_ngff/latest/plate.py    |  4 ++--
 src/pydantic_ome_ngff/latest/well.py     |  4 ++--
 src/pydantic_ome_ngff/v04/__init__.py    |  4 ++--
 src/pydantic_ome_ngff/v04/well.py        |  2 +-
 tests/test_latest.py                     | 10 +++++-----
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index aa98389..1f72baa 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,6 +1,6 @@
 from pydantic_ome_ngff.latest.axes import Axis  # noqa
 from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
 from pydantic_ome_ngff.latest.imageLabel import ImageLabel  # noqa
-from pydantic_ome_ngff.latest.well import Well  # noqa
-from pydantic_ome_ngff.latest.plate import Plate  # noqa
+from pydantic_ome_ngff.latest.well import WellMeta  # noqa
+from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.latest.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index 9dc7183..6a04eeb 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -2,10 +2,10 @@
 
 
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.plate import Plate as PlateV04
+from pydantic_ome_ngff.v04.plate import PlateMeta as PlateMetaV04
 
 
-class Plate(PlateV04):
+class PlateMeta(PlateMetaV04):
     """
     Plate metadata.
     See https://ngff.openmicroscopy.org/latest/#plate-md
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index 0111581..16fd610 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,9 +1,9 @@
 from typing import Optional
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.well import Well as WellV04
+from pydantic_ome_ngff.v04.well import WellMeta as WellMetaV04
 
 
-class Well(WellV04):
+class WellMeta(WellMetaV04):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/latest/#well-md
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index e69208d..da6b4d7 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -2,6 +2,6 @@
 from pydantic_ome_ngff.v04.coordinateTransformations import CoordinateTransform  # noqa
 from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
 from pydantic_ome_ngff.v04.imageLabel import ImageLabel  # noqa
-from pydantic_ome_ngff.v04.well import Well  # noqa
-from pydantic_ome_ngff.v04.plate import Plate  # noqa
+from pydantic_ome_ngff.v04.well import WellMeta  # noqa
+from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.v04.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 3dcfb9a..6abab21 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -11,7 +11,7 @@ class Image(BaseModel):
     acquisition: Optional[int]
 
 
-class Well(VersionedBase):
+class WellMeta(VersionedBase):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/0.4/#well-md
diff --git a/tests/test_latest.py b/tests/test_latest.py
index 9d3b176..c8d9e04 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -19,7 +19,7 @@
 
 
 @pytest.fixture
-def default_multiscale():
+def default_multiscale() -> Multiscale:
     axes = [
         Axis(name="c", type="channel", unit=None),
         Axis(name="z", type="space", unit="meter"),
@@ -65,12 +65,12 @@ def default_multiscale():
     return multi
 
 
-def test_multiscale(default_multiscale):
+def test_multiscale(default_multiscale: Multiscale) -> None:
     base_schema, strict_schema = fetch_schemas("latest", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
 
 
-def test_multiscale_unique_axis_names():
+def test_multiscale_unique_axis_names() -> None:
 
     axes = [
         Axis(name="y", type="space", unit="meter"),
@@ -131,7 +131,7 @@ def test_multiscale_unique_axis_names():
         ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
+def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes = [
         Axis(name=str(idx), type=t, unit=units_map.get(t, None))
@@ -213,7 +213,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
 
 
-def test_coordinate_transforms_invalid_ndims():
+def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
         VectorScaleTransform(scale=(1, 1)),
         VectorTranslationTransform(translation=(1, 1, 1)),

From 00ee0331899b2e9a46f3c56c582e3714ff2c1ac4 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Dec 2023 15:12:27 +0100
Subject: [PATCH 05/69] feat: big refactor: split validators into separate
 functions, rename transforms, etc

---
 .pre-commit-config.yaml                       |  14 +-
 src/pydantic_ome_ngff/latest/__init__.py      |   4 +-
 src/pydantic_ome_ngff/latest/axes.py          |  61 ----
 src/pydantic_ome_ngff/latest/axis.py          |  10 +
 .../latest/{imageLabel.py => label.py}        |   2 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |   7 +-
 ...dinateTransformations.py => transforms.py} |  23 +-
 src/pydantic_ome_ngff/v04/__init__.py         |   6 +-
 .../v04/{axes.py => axis.py}                  |  80 +++---
 src/pydantic_ome_ngff/v04/cli.py              |  15 -
 .../v04/coordinateTransformations.py          |  74 -----
 .../v04/{imageLabel.py => label.py}           |   0
 src/pydantic_ome_ngff/v04/multiscales.py      | 266 +++++++++---------
 src/pydantic_ome_ngff/v04/plate.py            |  21 +-
 src/pydantic_ome_ngff/v04/transforms.py       | 114 ++++++++
 src/pydantic_ome_ngff/v04/well.py             |  29 +-
 tests/test_latest.py                          |  12 +-
 tests/test_v04.py                             |  96 +++----
 18 files changed, 417 insertions(+), 417 deletions(-)
 delete mode 100644 src/pydantic_ome_ngff/latest/axes.py
 create mode 100644 src/pydantic_ome_ngff/latest/axis.py
 rename src/pydantic_ome_ngff/latest/{imageLabel.py => label.py} (84%)
 rename src/pydantic_ome_ngff/latest/{coordinateTransformations.py => transforms.py} (73%)
 rename src/pydantic_ome_ngff/v04/{axes.py => axis.py} (56%)
 delete mode 100644 src/pydantic_ome_ngff/v04/cli.py
 delete mode 100644 src/pydantic_ome_ngff/v04/coordinateTransformations.py
 rename src/pydantic_ome_ngff/v04/{imageLabel.py => label.py} (100%)
 create mode 100644 src/pydantic_ome_ngff/v04/transforms.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db3e79d..2c2a769 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,18 +5,16 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.12.0
-    hooks:
-    - id: black
-      language_version: python3.9
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
     - id: check-yaml
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.245'
+    rev: v0.1.8
     hooks:
+      # Run the linter.
       - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
\ No newline at end of file
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index 1f72baa..fb9e90e 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,6 +1,6 @@
-from pydantic_ome_ngff.latest.axes import Axis  # noqa
+from pydantic_ome_ngff.latest.axis import Axis  # noqa
 from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.latest.imageLabel import ImageLabel  # noqa
+from pydantic_ome_ngff.latest.label import ImageLabel  # noqa
 from pydantic_ome_ngff.latest.well import WellMeta  # noqa
 from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.latest.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/latest/axes.py b/src/pydantic_ome_ngff/latest/axes.py
deleted file mode 100644
index 822f478..0000000
--- a/src/pydantic_ome_ngff/latest/axes.py
+++ /dev/null
@@ -1,61 +0,0 @@
-import warnings
-from pydantic import model_validator
-from pydantic_ome_ngff.base import StrictVersionedBase
-from pydantic_ome_ngff.latest.base import version
-from typing import Any, Optional
-from pydantic_ome_ngff.v04.axes import AxisType, SpaceUnit, TimeUnit
-
-
-class Axis(StrictVersionedBase):
-    """
-    Axis metadata.
-    See https://ngff.openmicroscopy.org/latest/#axes-md
-    """
-
-    _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: Any
-    type: Optional[str]
-    unit: Optional[str]
-
-    @model_validator(mode="after")
-    def check_units(self) -> "Axis":
-        typ = self.type
-        unit = self.unit
-        if typ == AxisType.space:
-            if unit not in SpaceUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for "
-                    f" an axis with type '{typ}''."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.time:
-            if unit not in TimeUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                    f"with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.channel:
-            pass
-        elif typ is None:
-            msg = (
-                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
-                "that the 'type' field of an axis should be set to a string."
-            )
-            warnings.warn(msg, UserWarning)
-        else:
-            msg = (
-                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
-                " spec states that the 'type' field of an axis should be one of "
-                f"{AxisType._member_names_}."
-            )
-            warnings.warn(msg)
-
-        if unit is None:
-            msg = (
-                f"Null unit. Version {self._version} of the OME-NGFF spec states "
-                "that the `unit` field of an axis should be set to a string."
-            )
-            warnings.warn(msg)
-        return self
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
new file mode 100644
index 0000000..fbd8459
--- /dev/null
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -0,0 +1,10 @@
+from pydantic_ome_ngff.v04 import Axis as AxisV04
+
+
+class Axis(AxisV04):
+    """
+    Axis metadata.
+    See https://ngff.openmicroscopy.org/latest/#axes-md
+
+    Note: this metadata is unchanged from version 0.4 of the spec.
+    """
diff --git a/src/pydantic_ome_ngff/latest/imageLabel.py b/src/pydantic_ome_ngff/latest/label.py
similarity index 84%
rename from src/pydantic_ome_ngff/latest/imageLabel.py
rename to src/pydantic_ome_ngff/latest/label.py
index e0ff7bd..e48d93f 100644
--- a/src/pydantic_ome_ngff/latest/imageLabel.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -1,4 +1,4 @@
-from pydantic_ome_ngff.v04.imageLabel import ImageLabel as ImageLabelV04
+from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
 from pydantic_ome_ngff.latest.base import version
 from typing import Optional
 
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 7d000ed..f5e943c 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -5,10 +5,10 @@
 from pydantic import BaseModel, conlist, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.latest import coordinateTransformations as ctx
+from pydantic_ome_ngff.latest import transforms as ctx
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.v04.axes import AxisType
-from pydantic_ome_ngff.latest.axes import Axis
+from pydantic_ome_ngff.v04.axis import AxisType
+from pydantic_ome_ngff.latest.axis import Axis
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
@@ -207,7 +207,6 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for dataset in multiscale.datasets:
                 tforms.extend(dataset.coordinateTransformations)
             for tform in tforms:
-
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
                         Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
diff --git a/src/pydantic_ome_ngff/latest/coordinateTransformations.py b/src/pydantic_ome_ngff/latest/transforms.py
similarity index 73%
rename from src/pydantic_ome_ngff/latest/coordinateTransformations.py
rename to src/pydantic_ome_ngff/latest/transforms.py
index 5b22644..aa8a86b 100644
--- a/src/pydantic_ome_ngff/latest/coordinateTransformations.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,29 +1,36 @@
 from typing import Union
-import pydantic_ome_ngff.v04.coordinateTransformations as ctx
+import pydantic_ome_ngff.v04.transforms as ctx
 
 
-class IdentityTransform(ctx.IdentityTransform):
+class IdentityTransform(ctx.Identity):
     """
     An identity transform with no parameters.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathTransform(ctx.PathTransform):
+class PathScale(ctx.PathScale):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorTranslationTransform(ctx.VectorTranslationTransform):
+class PathTranslation(ctx.PathTranslation):
+    """ "
+    A coordinateTransform with at "path" field.
+    See https://ngff.openmicroscopy.org/latest/#trafo-md
+    """
+
+
+class VectorTranslationTransform(ctx.VectorTranslation):
     """
     A translation transform with a `translate` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorScaleTransform(ctx.VectorScaleTransform):
+class VectorScaleTransform(ctx.VectorScale):
     """
     A scale transform with a `scale` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
@@ -31,7 +38,7 @@ class VectorScaleTransform(ctx.VectorScaleTransform):
 
 
 def get_transform_ndim(
-    transform: Union[VectorScaleTransform, VectorTranslationTransform]
+    transform: Union[VectorScaleTransform, VectorTranslationTransform],
 ) -> int:
     """
     Get the dimensionality of a vector transform (scale or translation).
@@ -49,6 +56,6 @@ def get_transform_ndim(
         )
 
 
-ScaleTransform = Union[VectorScaleTransform, PathTransform]
-TranslationTransform = Union[VectorTranslationTransform, PathTransform]
+ScaleTransform = Union[VectorScaleTransform, PathScale]
+TranslationTransform = Union[VectorTranslationTransform, PathTranslation]
 CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index da6b4d7..ffd00cb 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -1,7 +1,7 @@
-from pydantic_ome_ngff.v04.axes import Axis  # noqa
-from pydantic_ome_ngff.v04.coordinateTransformations import CoordinateTransform  # noqa
+from pydantic_ome_ngff.v04.axis import Axis  # noqa
+from pydantic_ome_ngff.v04.transforms import Transform  # noqa
 from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.v04.imageLabel import ImageLabel  # noqa
+from pydantic_ome_ngff.v04.label import ImageLabel  # noqa
 from pydantic_ome_ngff.v04.well import WellMeta  # noqa
 from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.v04.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/v04/axes.py b/src/pydantic_ome_ngff/v04/axis.py
similarity index 56%
rename from src/pydantic_ome_ngff/v04/axes.py
rename to src/pydantic_ome_ngff/v04/axis.py
index ba13c64..e09ce91 100644
--- a/src/pydantic_ome_ngff/v04/axes.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,9 +1,9 @@
+from __future__ import annotations
+
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 import warnings
 from enum import Enum
-from typing import Any, Optional
-from pydantic import model_validator
 
 
 class AxisType(str, Enum):
@@ -75,48 +75,48 @@ class Axis(StrictVersionedBase):
 
     _version = version
     # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: Any
-    type: Optional[str]
-    unit: Optional[str]
+    name: str
+    type: str | None
+    unit: str | None
 
-    @model_validator(mode="after")
-    def check_units(self) -> "Axis":
-        typ = self.type
-        unit = self.unit
-        if typ == AxisType.space:
-            if unit not in SpaceUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit "
-                    f"for an axis with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.time:
-            if unit not in TimeUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                    f"with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.channel:
-            pass
-        elif typ is None:
-            msg = (
-                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
-                "that the 'type' field of an axis should be set to a string."
-            )
-            warnings.warn(msg, UserWarning)
-        else:
+
+def check_unit(model: Axis) -> "Axis":
+    typ = model.type
+    unit = model.unit
+    if typ == AxisType.space:
+        if unit not in SpaceUnit.__members__:
             msg = (
-                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
-                " spec states that the 'type' field of an axis should be one of "
-                f"{AxisType._member_names_}."
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
-
-        if unit is None:
+    elif typ == AxisType.time:
+        if unit not in TimeUnit.__members__:
             msg = (
-                f"Null unit. Version {self._version} of the OME-NGFF spec states "
-                "that the `unit` field of an axis should be set to a string."
+                f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                f"with type '{typ}'."
             )
             warnings.warn(msg)
-        return self
+    elif typ == AxisType.channel:
+        pass
+    elif typ is None:
+        msg = (
+            f"Null axis type. Version {model._version} of the OME-NGFF spec states "
+            "that the 'type' field of an axis should be set to a string."
+        )
+        warnings.warn(msg, UserWarning)
+    else:
+        msg = (
+            f"Unknown axis type '{typ}'. Version {model._version} of the OME-NGFF "
+            " spec states that the 'type' field of an axis should be one of "
+            f"{AxisType._member_names_}."
+        )
+        warnings.warn(msg)
+
+    if unit is None:
+        msg = (
+            f"Null unit. Version {model._version} of the OME-NGFF spec states "
+            "that the `unit` field of an axis should be set to a string."
+        )
+        warnings.warn(msg)
+    return model
diff --git a/src/pydantic_ome_ngff/v04/cli.py b/src/pydantic_ome_ngff/v04/cli.py
deleted file mode 100644
index 6d9af11..0000000
--- a/src/pydantic_ome_ngff/v04/cli.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import sys
-from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
-import zarr
-from pydantic import ValidationError
-from rich import print_json, print
-
-if __name__ == "__main__":
-    path: str = sys.argv[1]
-    group = zarr.open(path, mode="r")
-    try:
-        result = MultiscaleGroup.from_zarr(group).model_dump_json(indent=2)
-        print_json(result)
-    except ValidationError as e:
-        result = e
-        print(result)
diff --git a/src/pydantic_ome_ngff/v04/coordinateTransformations.py b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
deleted file mode 100644
index 3c8ba9f..0000000
--- a/src/pydantic_ome_ngff/v04/coordinateTransformations.py
+++ /dev/null
@@ -1,74 +0,0 @@
-from typing import Literal, Sequence, Union
-from pydantic_ome_ngff.base import StrictBase
-
-
-class IdentityTransform(StrictBase):
-    """
-    An identity transform with no parameters.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    # SPEC why does this exist, as opposed to translation by 0 or scale by 1?
-    type: str = "identity"
-
-
-class PathTransform(StrictBase):
-    """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    # SPEC: the existence of this type is a massive sinkhole in the spec
-    # translate and scale are both so simple that nobody should be using a path
-    # argument to refer to some remote resource representing a translation
-    # or a scale transform
-    type: Union[Literal["scale"], Literal["translation"]]
-    path: str
-
-
-class VectorTranslationTransform(StrictBase):
-    """
-    A translation transform with a `translate` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    type: Literal["translation"] = "translation"
-    translation: Sequence[
-        Union[float, int]
-    ]  # SPEC: redundant field name -- we already know it's translation
-
-
-class VectorScaleTransform(StrictBase):
-    """
-    A scale transform with a `scale` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    type: Literal["scale"] = "scale"
-    scale: Sequence[
-        Union[float, int]
-    ]  # SPEC: redundant field name -- we already know it's scale
-
-
-def get_transform_ndim(
-    transform: Union[VectorScaleTransform, VectorTranslationTransform]
-) -> int:
-    """
-    Get the dimensionality of a vector transform (scale or translation).
-    """
-    if transform.type == "scale" and hasattr(transform, "scale"):
-        return len(transform.scale)
-    elif transform.type == "translation" and hasattr(transform, "translation"):
-        return len(transform.translation)
-    else:
-        raise ValueError(
-            f"""
-        Transform must be either VectorScaleTransform or VectorTranslationTransform.
-        Got {type(transform)} instead.
-        """
-        )
-
-
-ScaleTransform = Union[VectorScaleTransform, PathTransform]
-TranslationTransform = Union[VectorTranslationTransform, PathTransform]
-CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
diff --git a/src/pydantic_ome_ngff/v04/imageLabel.py b/src/pydantic_ome_ngff/v04/label.py
similarity index 100%
rename from src/pydantic_ome_ngff/v04/imageLabel.py
rename to src/pydantic_ome_ngff/v04/label.py
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index d632042..62505e4 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,63 +1,135 @@
 from collections import Counter
-import warnings
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Annotated, Any, Dict, List, Optional, Sequence, Union, cast
 
-from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic import AfterValidator, BaseModel, conlist, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
-from pydantic_ome_ngff.v04.axes import Axis, AxisType
-import pydantic_ome_ngff.v04.coordinateTransformations as ctx
+from pydantic_ome_ngff.v04.axis import Axis, AxisType
+import pydantic_ome_ngff.v04.transforms as ctx
 
+VALID_NDIM = (2, 3, 4, 5)
 
-class MultiscaleDataset(StrictBase):
-    path: str
-    coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
-    )
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_dimensionality(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        ndims = []
-        for tx in transforms:
-            # this repeated conditional logic around transforms is so awful.
-            if type(tx) in (ctx.VectorScaleTransform, ctx.VectorTranslationTransform):
-                ndims.append(ctx.get_transform_ndim(tx))
-        if len(set(ndims)) > 1:
-            msg = (
-                "Elements of coordinateTransformations must have the same "
-                f"dimensionality. Got elements with dimensionality = {ndims}."
-            )
-            raise ValueError(msg)
-        return transforms
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_types(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        if (tform := transforms[0].type) != "scale":
+
+def ensure_scale_translation(
+    transforms: Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]],
+) -> Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]]:
+    """
+    Ensure that
+        - the first element is a scale transformation
+        - the second element is a translation transform
+    """
+    if len(transforms) == 0:
+        raise ValueError("Invalid transforms: got 0, expected 1 or 2")
+
+    maybe_scale = transforms[0]
+    if maybe_scale.type != "scale":
+        msg = (
+            "The first element of coordinateTransformations must be a scale "
+            f"transform. Got {maybe_scale} instead."
+        )
+        raise ValueError(msg)
+    if len(transforms) == 2:
+        maybe_trans = transforms[1]
+        if (maybe_trans.type) != "translation":
             msg = (
-                "The first element of coordinateTransformations must be a scale "
-                f"transform. Got {tform} instead."
+                "The second element of coordinateTransformations must be a "
+                f"translation transform. Got {maybe_trans} instead."
             )
             raise ValueError(msg)
-        if len(transforms) == 2:
-            if (tform := transforms[1].type) != "translation":
-                msg = (
-                    "The second element of coordinateTransformations must be a "
-                    f"translation transform. got {tform} instead."
-                )
-                raise ValueError(msg)
-        return transforms
+    else:
+        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        raise ValueError(msg)
+    return transforms
+
+
+def ensure_transforms_length(
+    transforms: Sequence[ctx.VectorScale | ctx.VectorTranslation],
+) -> Sequence[ctx.VectorScale | ctx.VectorTranslation]:
+    if (num_tx := len(transforms)) not in (1, 2):
+        msg = f"Invalid number of transforms: got {num_tx}, expected 1 or 2"
+        raise ValueError(msg)
+    return transforms
+
+
+class MultiscaleDataset(StrictBase):
+    """
+    A single entry in the multiscales.datasets list.
+    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+
+    Attributes:
+    ----------
+    path: str
+        The path to the zarr array that stores the image described by this metadata.
+        This path should be relative to the group that contains this metadata.
+    coordinateTransformations: Union[ctx.ScaleTransform, ctx.TranslationTransform]
+        The coordinate transformations for this image.
+    """
+
+    path: str
+    coordinateTransformations: Annotated[
+        List[ctx.Scale | ctx.Translation],
+        AfterValidator(ensure_transforms_length),
+        AfterValidator(ensure_scale_translation),
+        AfterValidator(ctx.ensure_dimensionality),
+    ]
+
+
+def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that there are between 2 and 5 axes (inclusive)
+    """
+    if (len_axes := len(axes)) not in VALID_NDIM:
+        msg = f"Incorrect number of axes provided ({len_axes}). Only 2, 3, 4, or 5 axes are allowed."
+        raise ValueError(msg)
+    return axes
+
+
+def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that the names of the axes are unique
+    """
+    name_dupes = duplicates(a.name for a in axes)
+    if len(name_dupes) > 0:
+        msg = f"Axis names must be unique. Axis names {tuple(name_dupes.keys())} are repeated."
+        raise ValueError(msg)
+    return axes
+
+
+def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that the following conditions hold:
+        - there are only 2 or 3 axes with type "space"
+        - the axes with type "space" are last in the list of axes
+        - there is only 1 axis with type "time"
+        - there is only 1 axis with type "channel"
+        - there is only 1 axis with a custom type
+    """
+    axis_types = [ax.type for ax in axes]
+    type_census = Counter(axis_types)
+    num_spaces = type_census["space"]
+    if num_spaces < 2 or num_spaces > 3:
+        msg = f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes are allowed."
+        raise ValueError(msg)
+
+    elif not all(a == "space" for a in axis_types[-num_spaces:]):
+        msg = f"Space axes must come last. Got axes with order: {axis_types}."
+        raise ValueError(msg)
+
+    if (num_times := type_census["time"]) > 1:
+        msg = f"Invalid number of time axes: {num_times}. Only 1 time axis is allowed."
+        raise ValueError(msg)
+
+    if (num_channels := type_census["channel"]) > 1:
+        msg = f"Invalid number of channel axes: {num_channels}. Only 1 channel axis is allowed."
+        raise ValueError(msg)
+
+    custom_axes = set(axis_types) - set(AxisType._member_names_)
+    if (num_custom := len(custom_axes)) > 1:
+        msg = f"Invalid number of custom axes: {num_custom}. Only 1 custom axis is allowed."
+        raise ValueError(msg)
+    return axes
 
 
 class Multiscale(StrictVersionedBase):
@@ -69,88 +141,19 @@ class Multiscale(StrictVersionedBase):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    # SPEC: why is this optional? why is it untyped?
-    version: Optional[Any] = version
-    # SPEC: why is this nullable instead of reserving the empty string
-    # SPEC: untyped!
-    name: Optional[Any] = None
-    # SPEC: not clear what this field is for, given the existence of .metadata
-    # SPEC: untyped!
+    version: Any = version
+    name: Any = None
     type: Any = None
-    # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
-    # SPEC: should not exist at top level and instead
-    # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_length=2, max_length=5)
-    # SPEC: should not live here, and if it is here,
-    # it should default to an empty list instead of being nullable
-    coordinateTransformations: Optional[
-        List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ] = None
-
-    @field_validator("name")
-    def check_name(cls, name: str) -> str:
-        if name is None:
-            msg = (
-                f"The name field was set to None. Version {cls._version} "
-                "of the OME-NGFF spec states that the `name` field of a Multiscales "
-                "object should not be None."
-            )
-            warnings.warn(msg)
-        return name
-
-    @field_validator("axes")
-    def check_axes(cls, axes: List[Axis]) -> List[Axis]:
-        name_dupes = duplicates(a.name for a in axes)
-        if len(name_dupes) > 0:
-            raise ValueError(
-                f"""
-                Axis names must be unique. Axis names {tuple(name_dupes.keys())} are 
-                repeated.
-                """
-            )
-        axis_types = [ax.type for ax in axes]
-        type_census = Counter(axis_types)
-        num_spaces = type_census["space"]
-        if num_spaces < 2 or num_spaces > 3:
-            raise ValueError(
-                f"""
-                Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes 
-                are allowed.
-                """
-            )
-
-        elif not all(a == "space" for a in axis_types[-num_spaces:]):
-            raise ValueError(
-                f"""
-                Space axes must come last. Got axes with order: {axis_types}
-                """
-            )
-
-        if (num_times := type_census["time"]) > 1:
-            raise ValueError(
-                f"""
-                Invalid number of time axes: {num_times}. Only 1 time axis is allowed.
-                """
-            )
+    axes: Annotated[
+        List[Axis],
+        AfterValidator(ensure_axis_length),
+        AfterValidator(ensure_axis_names),
+        AfterValidator(ensure_axis_types),
+    ]
 
-        if (num_channels := type_census["channel"]) > 1:
-            raise ValueError(
-                f"""
-                Invalid number of channel axes: {num_channels}. Only 1 channel axis is 
-                allowed.
-                """
-            )
-
-        custom_axes = set(axis_types) - set(AxisType._member_names_)
-        if len(custom_axes) > 1:
-            raise ValueError(
-                f"""Invalid number of custom axes: {custom_axes}. Only 1 custom axis is
-                allowed.
-                """
-            )
-        return axes
+    coordinateTransformations: List[ctx.Scale | ctx.Translation] | None = None
 
 
 class MultiscaleAttrs(BaseModel):
@@ -165,11 +168,11 @@ class MultiscaleAttrs(BaseModel):
 class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
-
         attrs = self.attributes
-        array_items: dict[str, dict[str, Any]] = {
+        array_items: dict[str, dict[str, ArraySpec]] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
+
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
@@ -207,13 +210,12 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for dataset in multiscale.datasets:
                 tforms.extend(dataset.coordinateTransformations)
             for tform in tforms:
-
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
-                        Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
+                        Union[ctx.VectorScale, ctx.VectorTranslation],
                         tform,
                     )
-                    if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
+                    if (tform_dims := ctx.ndim(tform)) not in set(ndims):
                         msg = (
                             f"Transform {tform} has dimensionality {tform_dims} "
                             "which does notmatch the dimensionality of the arrays "
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 1ccda2f..2b1c07e 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,11 +1,13 @@
 from typing import List, Optional
 
-from pydantic import BaseModel, PositiveInt
+from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
+from pydantic_ome_ngff.v04.well import WellGroup
+
 
 class Acquisition(BaseModel):
     id: PositiveInt
@@ -30,8 +32,7 @@ class PlateMeta(VersionedBase):
     see https://ngff.openmicroscopy.org/0.4/#plate-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # the version here as a private class attribute because the version is not required by the spec
     _version = version
     version: Optional[str] = version
     name: Optional[str] = None
@@ -46,5 +47,15 @@ class PlateAttributes(BaseModel):
     plate: PlateMeta
 
 
-class PlateGroup(GroupSpec[PlateAttributes, Union[GroupSpec, ArraySpec]]):
-    ...
+class PlateGroup(GroupSpec[PlateAttributes, Union[WellGroup, GroupSpec, ArraySpec]]):
+    @field_validator("members", mode="after")
+    @classmethod
+    def contains_well(
+        cls, members: Union[WellGroup, GroupSpec, ArraySpec]
+    ) -> Union[WellGroup, GroupSpec, ArraySpec]:
+        """
+        Check that .members contains a WellGroup
+        """
+        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+            raise ValidationError
+        return members
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
new file mode 100644
index 0000000..52c23a3
--- /dev/null
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -0,0 +1,114 @@
+from __future__ import annotations
+
+from typing import Literal, Sequence, Tuple, Union
+from pydantic_ome_ngff.base import StrictBase
+
+
+class Identity(StrictBase):
+    """
+    An identity transform. It has no parameters, and no valid use according to the spec.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: str = "identity"
+
+
+class PathTranslation(StrictBase):
+    """
+    A coordinateTransform with a `path` field.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"] = "translation"
+    path: str
+
+
+class PathScale(StrictBase):
+    """
+    A coordinateTransform with a `path` field.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"] = "scale"
+    path: str
+
+
+class VectorTranslation(StrictBase):
+    """
+    A translation transform with a `translate` field that is a vector.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"] = "translation"
+    translation: Sequence[float | int]
+
+
+class VectorScale(StrictBase):
+    """
+    A scale transform with a `scale` field that is a vector.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"] = "scale"
+    scale: Sequence[float | int]
+
+
+def ndim(
+    transform: Union[VectorScale, VectorTranslation],
+) -> int:
+    """
+    Get the dimensionality of a vector transform (scale or translation).
+    """
+    if hasattr(transform, "scale"):
+        return len(transform.scale)
+    elif hasattr(transform, "translation"):
+        return len(transform.translation)
+    else:
+        msg = (
+            "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
+            f"Got {type(transform)} instead."
+        )
+        raise ValueError(msg)
+
+
+def scale_translation(
+    scale: Sequence[float], translation: Sequence[float]
+) -> Tuple[Scale, Translation]:
+    """
+    Create a scale and transformation transformation from a scale and a translation parameter
+    """
+    len_scale = len(scale)
+    len_translation = len(translation)
+    if len_scale < 1:
+        msg = f"Not enough values in scale. Got {len_scale}"
+        raise ValueError(msg)
+    if len_translation < 1:
+        msg = f"Not enough values in `tranlsation`. Got {len_translation}"
+        raise ValueError(msg)
+    if len_translation != len_scale:
+        msg = (
+            f"Length of `scale` and `translation` do not match. `scale` has length = {len_scale}"
+            f"but `translation` has length = {len_translation}"
+        )
+        raise ValueError(msg)
+
+    return (VectorScale(scale=scale), VectorTranslation(translation=translation))
+
+
+Scale = VectorScale | PathScale
+Translation = VectorTranslation | PathTranslation
+Transform = Scale | Translation
+
+
+def ensure_dimensionality(
+    transforms: Sequence[VectorScale | VectorTranslation],
+) -> Sequence[VectorScale | VectorTranslation]:
+    ndims = tuple(ndim(tx) for tx in transforms)
+    ndims_set = set(ndims)
+    if len(ndims_set) > 1:
+        msg = (
+            "The transforms have inconsistent dimensionality. "
+            f"Got transforms with dimensionality = {ndims}."
+        )
+        raise ValueError(msg)
+    return transforms
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 6abab21..bf883d0 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,9 +1,11 @@
-from typing import List, Optional
+from typing import List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ValidationError, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 
 from pydantic_ome_ngff.v04.base import version
+from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class Image(BaseModel):
@@ -17,8 +19,27 @@ class WellMeta(VersionedBase):
     See https://ngff.openmicroscopy.org/0.4/#well-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # the version here as a private class attribute because the version is not required by the spec
     _version = version
     version: Optional[str] = version
     images: List[Image]
+
+
+class WellAttributes(BaseModel):
+    well: WellMeta
+
+
+class WellGroup(
+    GroupSpec[WellAttributes, Union[MultiscaleGroup, GroupSpec, ArraySpec]]
+):
+    @field_validator("members", mode="after")
+    @classmethod
+    def contains_well(
+        cls, members: Union[MultiscaleGroup, GroupSpec, ArraySpec]
+    ) -> Union[MultiscaleGroup, GroupSpec, ArraySpec]:
+        """
+        Check that .members contains a MultiscaleGroup
+        """
+        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+            raise ValidationError
+        return members
diff --git a/tests/test_latest.py b/tests/test_latest.py
index c8d9e04..746c4b8 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -9,12 +9,12 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
-from pydantic_ome_ngff.latest.coordinateTransformations import (
+from pydantic_ome_ngff.latest.transforms import (
     CoordinateTransform,
     VectorScaleTransform,
     VectorTranslationTransform,
 )
-from pydantic_ome_ngff.latest.axes import Axis
+from pydantic_ome_ngff.latest.axis import Axis
 from .conftest import fetch_schemas
 
 
@@ -71,7 +71,6 @@ def test_multiscale(default_multiscale: Multiscale) -> None:
 
 
 def test_multiscale_unique_axis_names() -> None:
-
     axes = [
         Axis(name="y", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -244,7 +243,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[CoordinateTransform, CoordinateTransform],
 ) -> None:
     with pytest.raises(ValidationError, match="List should have at most 2 items"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
@@ -268,7 +267,7 @@ def test_coordinate_transforms_invalid_length(
     ),
 )
 def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[CoordinateTransform, CoordinateTransform],
 ) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
@@ -291,8 +290,7 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
         match="array with that name was found in the items of that group.",
     ):
         bad_items = {
-            d.path
-            + "x": ArraySpec(
+            d.path + "x": ArraySpec(
                 shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
diff --git a/tests/test_v04.py b/tests/test_v04.py
index cb0751e..2862117 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -10,16 +10,16 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
-from pydantic_ome_ngff.v04.coordinateTransformations import (
-    CoordinateTransform,
-    VectorScaleTransform,
-    VectorTranslationTransform,
+from pydantic_ome_ngff.v04.transforms import (
+    Transform,
+    VectorScale,
+    VectorTranslation,
 )
-from pydantic_ome_ngff.v04.axes import Axis
+from pydantic_ome_ngff.v04.axis import Axis
 
 
 @pytest.fixture
-def default_multiscale():
+def default_multiscale() -> Multiscale:
     axes = [
         Axis(name="c", type="channel", unit=None),
         Axis(name="z", type="space", unit="meter"),
@@ -32,13 +32,13 @@ def default_multiscale():
         MultiscaleDataset(
             path=f"path{idx}",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -54,7 +54,7 @@ def default_multiscale():
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(
+            VectorScale(
                 scale=[
                     1,
                 ]
@@ -65,13 +65,12 @@ def default_multiscale():
     return multi
 
 
-def test_multiscale(default_multiscale):
+def test_multiscale(default_multiscale: Multiscale) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
+    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
 
-def test_multiscale_unique_axis_names():
-
+def test_multiscale_unique_axis_names() -> None:
     axes = [
         Axis(name="y", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -83,8 +82,8 @@ def test_multiscale_unique_axis_names():
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -94,7 +93,7 @@ def test_multiscale_unique_axis_names():
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(scale=[1, 1, 1]),
+            VectorScale(scale=[1, 1, 1]),
         ],
     )
 
@@ -107,8 +106,8 @@ def test_multiscale_unique_axis_names():
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -119,7 +118,7 @@ def test_multiscale_unique_axis_names():
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
+                VectorScale(scale=[1, 1, 1]),
             ],
         )
 
@@ -129,11 +128,9 @@ def test_multiscale_unique_axis_names():
     (
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-        (None, "space", "space", None),
-        ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes = [
         Axis(name=str(idx), type=t, unit=units_map.get(t, None))
@@ -144,13 +141,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -160,13 +157,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         )
     ]
     # TODO: make some axis-specifc exceptions
-    with pytest.raises(ValidationError):
+    with pytest.raises(ValidationError, match="Space axes must come last."):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -184,13 +181,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -199,13 +196,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="List should have"):
+    with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -217,12 +214,12 @@ def test_multiscale_axis_length(num_axes: int) -> None:
 
 def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
-        VectorScaleTransform(scale=(1, 1)),
-        VectorTranslationTransform(translation=(1, 1, 1)),
+        VectorScale(scale=(1, 1)),
+        VectorTranslation(translation=(1, 1, 1)),
     ]
     with pytest.raises(
         ValidationError,
-        match="Elements of coordinateTransformations must have the same dimensionality.",  # noqa
+        match="The transforms have inconsistent dimensionality.",  # noqa
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=tforms)
 
@@ -231,26 +228,20 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ]
-        * 3,
+            VectorScale(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+        ],
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-        [
-            VectorScaleTransform(scale=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ],
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: List[Transform],
 ) -> None:
-    with pytest.raises(
-        ValidationError, match="List should have at most 2 items after validation, not"
-    ):
+    with pytest.raises(ValidationError, match="expected 1 or 2"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -258,21 +249,21 @@ def test_coordinate_transforms_invalid_length(
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
 def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
@@ -295,8 +286,7 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
         match="array with that name was found in the items of that group.",
     ):
         bad_items = {
-            d.path
-            + "x": ArraySpec(
+            d.path + "x": ArraySpec(
                 shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets

From dd469b662d33bba0e87c2c61ceb9199fa3bbfea6 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 1 Jan 2024 17:56:08 +0100
Subject: [PATCH 06/69] feat: use python 3.10 as baseline, refactor the test
 suite a bit, use inheritance more for the latest classes, start looking at
 coverage and adjusting things accordingly

---
 poetry.lock                                   | 1473 +++++++++--------
 pyproject.toml                                |   32 +-
 src/pydantic_ome_ngff/base.py                 |    2 +-
 src/pydantic_ome_ngff/latest/axis.py          |    5 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |  229 +--
 src/pydantic_ome_ngff/latest/transforms.py    |   41 +-
 src/pydantic_ome_ngff/v04/axis.py             |   48 +-
 src/pydantic_ome_ngff/v04/label.py            |   64 +-
 src/pydantic_ome_ngff/v04/multiscales.py      |  103 +-
 src/pydantic_ome_ngff/v04/plate.py            |    1 +
 src/pydantic_ome_ngff/v04/transforms.py       |   18 +-
 src/pydantic_ome_ngff/v04/well.py             |    1 +
 tests/latest/__init__.py                      |    0
 .../test_multiscales.py}                      |  119 +-
 tests/v04/__init__.py                         |    0
 tests/v04/test_axis.py                        |   17 +
 tests/v04/test_label.py                       |   25 +
 .../{test_v04.py => v04/test_multiscales.py}  |   36 +-
 18 files changed, 1093 insertions(+), 1121 deletions(-)
 create mode 100644 tests/latest/__init__.py
 rename tests/{test_latest.py => latest/test_multiscales.py} (74%)
 create mode 100644 tests/v04/__init__.py
 create mode 100644 tests/v04/test_axis.py
 create mode 100644 tests/v04/test_label.py
 rename tests/{test_v04.py => v04/test_multiscales.py} (92%)

diff --git a/poetry.lock b/poetry.lock
index a0e0775..eeb582f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,133 +1,121 @@
-# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.7.0"
+version = "2.9.0"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.7.0-py3-none-any.whl", hash = "sha256:aec605df77ce4635a0479b50fd849aa6b640900f7b295021ecca192e1140e551"},
-    {file = "aiobotocore-2.7.0.tar.gz", hash = "sha256:506591374cc0aee1bdf0ebe290560424a24af176dfe2ea7057fe1df97c4f0467"},
+    {file = "aiobotocore-2.9.0-py3-none-any.whl", hash = "sha256:acf5e49644e6e434b9ecc26284ae7e05d557effbdcdd8185e2eb08925f011853"},
+    {file = "aiobotocore-2.9.0.tar.gz", hash = "sha256:4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.31.16,<1.31.65"
+botocore = ">=1.33.2,<1.33.14"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.29.16,<1.29.65)"]
-boto3 = ["boto3 (>=1.28.16,<1.28.65)"]
+awscli = ["awscli (>=1.31.2,<1.31.14)"]
+boto3 = ["boto3 (>=1.33.2,<1.33.14)"]
 
 [[package]]
 name = "aiohttp"
-version = "3.8.6"
+version = "3.9.1"
 description = "Async http client/server framework (asyncio)"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1"},
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1d84166673694841d8953f0a8d0c90e1087739d24632fe86b1a08819168b4566"},
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:253bf92b744b3170eb4c4ca2fa58f9c4b87aeb1df42f71d4e78815e6e8b73c9e"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3fd194939b1f764d6bb05490987bfe104287bbf51b8d862261ccf66f48fb4096"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6c5f938d199a6fdbdc10bbb9447496561c3a9a565b43be564648d81e1102ac22"},
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-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0fa375b3d34e71ccccf172cab401cd94a72de7a8cc01847a7b3386204093bb47"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9de50a199b7710fa2904be5a4a9b51af587ab24c8e540a7243ab737b45844543"},
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 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aioitertools"
@@ -140,9 +128,6 @@ files = [
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 ]
 
-[package.dependencies]
-typing_extensions = {version = ">=4.0", markers = "python_version < \"3.10\""}
-
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
@@ -191,53 +176,51 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "botocore"
-version = "1.31.64"
+version = "1.33.13"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
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 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = [
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-    {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""},
-]
+urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.16.26)"]
+crt = ["awscrt (==0.19.17)"]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -363,63 +346,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.3.2"
+version = "7.4.0"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -430,24 +413,24 @@ toml = ["tomli"]
 
 [[package]]
 name = "distlib"
-version = "0.3.7"
+version = "0.3.8"
 description = "Distribution utilities"
 optional = false
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 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -587,13 +586,13 @@ tqdm = ["tqdm"]
 
 [[package]]
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-version = "2.5.31"
+version = "2.5.33"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
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 [package.extras]
@@ -601,13 +600,13 @@ license = ["ukkonen"]
 
 [[package]]
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-version = "3.4"
+version = "3.6"
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 [[package]]
@@ -623,20 +622,17 @@ files = [
 
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+version = "5.13.2"
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-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jmespath"
@@ -651,13 +647,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.2"
+version = "4.20.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -672,17 +668,17 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
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 python-versions = ">=3.8"
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 [package.dependencies]
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "markdown-it-py"
@@ -804,38 +800,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.6.1"
+version = "1.8.0"
 description = "Optional static typing for Python"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -846,6 +842,7 @@ typing-extensions = ">=4.1.0"
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
 install-types = ["pip"]
+mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
 
 [[package]]
@@ -915,36 +912,47 @@ zfpy = ["zfpy (>=1.0.0)"]
 
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 [[package]]
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 [[package]]
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 python-versions = ">=3.8"
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@@ -1508,31 +1516,15 @@ files = [
 
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@@ -1552,19 +1544,19 @@ zstd = ["zstandard (>=0.18.0)"]
 
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+    {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
+    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
 ]
 
 [package.dependencies]
@@ -1764,5 +1767,5 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "d6ba84447520a466cb6cd52278784c5dfdac4c3ac0622619ac0306a55dec74c6"
+python-versions = "^3.10"
+content-hash = "ee46872069c5871528c57be240af3e1e784f1130e07bf77eff4c00621f71004e"
diff --git a/pyproject.toml b/pyproject.toml
index 3ec75f7..1f2df7c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ readme = "README.md"
 packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.10"
 pydantic-zarr = "0.5.2"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
@@ -47,4 +47,32 @@ disallow_untyped_defs = true
 init_forbid_extra = true
 init_typed = true
 warn_required_dynamic_aliases = true
-warn_untyped_fields = true
\ No newline at end of file
+warn_untyped_fields = true
+
+
+[tool.coverage.run]
+source = ['src']
+branch = true
+context = '${CONTEXT}'
+
+[tool.coverage.report]
+precision = 2
+exclude_lines = [
+    'pragma: no cover',
+    'raise NotImplementedError',
+    'if TYPE_CHECKING:',
+    'if typing.TYPE_CHECKING:',
+    '@overload',
+    '@typing.overload',
+    '\(Protocol\):$',
+    'typing.assert_never',
+    'assert_never',
+]
+
+[tool.coverage.paths]
+source = [
+    'src/'
+]
+
+[tool.coverage.html]
+directory = "htmlcov"
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index 683c185..b471f51 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -1,7 +1,7 @@
 from pydantic import BaseModel, Extra
 
 
-class StrictBase(BaseModel, extra=Extra.forbid):
+class StrictBase(BaseModel, extra='forbid'):
     """
     A pydantic basemodel that refuses extra fields.
     """
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
index fbd8459..9e5c8ac 100644
--- a/src/pydantic_ome_ngff/latest/axis.py
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -1,7 +1,8 @@
-from pydantic_ome_ngff.v04 import Axis as AxisV04
+import pydantic_ome_ngff.v04.axis as axisV04
 
+AxisType = axisV04.AxisType
 
-class Axis(AxisV04):
+class Axis(axisV04.Axis):
     """
     Axis metadata.
     See https://ngff.openmicroscopy.org/latest/#axes-md
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index f5e943c..a68de43 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,224 +1,59 @@
 from collections import Counter
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Any, Dict, List, Literal, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic import BaseModel, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import transforms as ctx
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.v04.axis import AxisType
-from pydantic_ome_ngff.latest.axis import Axis
+from pydantic_ome_ngff.latest.axis import AxisType, Axis
+import pydantic_ome_ngff.v04.multiscales as msv04
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
-class MultiscaleDataset(StrictBase):
-    path: str
-    coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
-    )
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_dimensionality(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        ndims = []
-        for tx in transforms:
-            # this repeated conditional logic around transforms is so awful.
-            if type(tx) in (ctx.VectorScaleTransform, ctx.VectorTranslationTransform):
-                ndims.append(ctx.get_transform_ndim(tx))
-        if len(set(ndims)) > 1:
-            raise ValueError(
-                f"""
-            Elements of coordinateTransformations must have the same dimensionality. Got
-            elements with dimensionality = {ndims}.
-            """
-            )
-        return transforms
+class MultiscaleDataset(msv04.MultiscaleDataset):
+    """
+    A single entry in the multiscales.datasets list.
+    See https://ngff.openmicroscopy.org/latest/#multiscale-md
 
-    @field_validator("coordinateTransformations")
-    def check_transforms_types(
-        cls, transforms: List[ctx.CoordinateTransform]
-    ) -> List[ctx.CoordinateTransform]:
-        if (tform := transforms[0].type) != "scale":
-            raise ValueError(
-                f"""
-            The first element of coordinateTransformations must be a scale transform.
-            Got {tform} instead.
-            """
-            )
-        if len(transforms) == 2:
-            if (tform := transforms[1].type) != "translation":
-                raise ValueError(
-                    f"""
-                The second element of coordinateTransformations must be a translation 
-                transform. got {tform} instead.
-                """
-                )
-        return transforms
+    Note that this class is unchanged from the v04 counterpart.
 
+    Attributes:
+    ----------
+    path: str
+        The path to the zarr array that stores the image described by this metadata.
+        This path should be relative to the group that contains this metadata.
+    coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
+        The coordinate transformations for this image.
+    """
+    ...
 
-class Multiscale(StrictVersionedBase):
+class Multiscale(msv04.Multiscale):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
-
-    # we need to put the version here as a private class attribute because the version
-    # is not properly typed by the spec...
     _version = version
-    # SPEC: why is this untyped?
-    version: Any = version
-    # SPEC: why is this nullable instead of reserving the empty string
-    # SPEC: untyped!
-    name: Any = None
-    # SPEC: not clear what this field is for, given the existence of .metadata
-    # SPEC: untyped!
-    type: Any = None
-    # SPEC: should default to empty dict instead of None
-    metadata: Optional[Dict[str, Any]] = None
-    datasets: List[MultiscaleDataset]
-    # SPEC: should not exist at top level and instead
-    # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_length=2, max_length=5)
-    # SPEC: should not live here, and if it is here,
-    # it should default to an empty list instead of being nullable
-    coordinateTransformations: Optional[
-        List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ]
-
-    @field_validator("name")
-    def check_name(cls, name: Optional[str]) -> Optional[str]:
-        if name is None:
-            warnings.warn(
-                f"""
-            The name field was set to None. Version {cls._version} of the OME-NGFF spec 
-            states that the `name` field of a Multiscales object should not be None.
-            """
-            )
-        return name
-
-    @field_validator("axes")
-    def check_axes(cls, axes: List[Axis]) -> List[Axis]:
-        name_dupes = duplicates(a.name for a in axes)
-        if len(name_dupes) > 0:
-            raise ValueError(
-                f"""
-                Axis names must be unique. Axis names {tuple(name_dupes.keys())} are 
-                repeated.
-                """
-            )
-        axis_types = tuple(ax.type for ax in axes)
-        type_census = Counter(axis_types)
-        num_spaces = type_census["space"]
-        if num_spaces < 2 or num_spaces > 3:
-            raise ValueError(
-                f"""
-                Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes 
-                are allowed.
-                """
-            )
+    version: Literal['0.5-dev'] = version
 
-        elif not all(a == "space" for a in axis_types[-num_spaces:]):
-            raise ValueError(
-                f"""
-                Space axes must come last. Got axes with order: {axis_types}
-                """
-            )
-
-        if (num_times := type_census["time"]) > 1:
-            raise ValueError(
-                f"""
-                Invalid number of time axes: {num_times}. Only 1 time axis is allowed.
-                """
-            )
-
-        if (num_channels := type_census["channel"]) > 1:
-            raise ValueError(
-                f"""
-                Invalid number of channel axes: {num_channels}. Only 1 channel axis is 
-                allowed.
-                """
-            )
-
-        custom_axes = set(axis_types) - set(AxisType._member_names_)
-        if len(custom_axes) > 1:
-            raise ValueError(
-                f"""Invalid number of custom axes: {custom_axes}. Only 1 custom axis is
-                allowed.
-                """
-            )
-        return axes
-
-
-class MultiscaleAttrs(BaseModel):
+class MultiscaleAttrs(msv04.MultiscaleAttrs):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
-    multiscales: List[Multiscale]
-
-
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @model_validator(mode="after")
-    def check_arrays_exist(self) -> "MultiscaleGroup":
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if hasattr(v, "shape")
-        }
-        multiscales: List[Multiscale] = attrs.multiscales
-
-        for multiscale in multiscales:
-            for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in array_items:
-                    msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, but no "
-                        "array with that name was found in the items of that group. "
-                        "All arrays in multiscale metadata must be items of the group."
-                    )
-                    raise ValueError(msg)
-        return self
+class MultiscaleGroup(msv04.MultiscaleGroup):
+     """
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
-    @model_validator(mode="after")
-    def check_array_ndim(self) -> "MultiscaleGroup":
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if hasattr(v, "shape")
-        }
-        multiscales: List[Multiscale] = attrs.multiscales
+    Attributes
+    ----------
 
-        ndims = tuple(len(a.shape) for a in array_items.values())
-        if len(set(ndims)) > 1:
-            msg = (
-                "All arrays must have the same dimensionality. "
-                f"Got arrays with dimensionality {ndims}."
-            )
-            raise ValueError(msg)
+    attributes: MultiscaleAttrs
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
+        values are allowed.
+    members Dict[Str, ArraySpec | GroupSpec]:
+        The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
-        # check that each transform has compatible rank
-        for multiscale in multiscales:
-            tforms = []
-            if multiscale.coordinateTransformations is not None:
-                tforms.extend(multiscale.coordinateTransformations)
-            for dataset in multiscale.datasets:
-                tforms.extend(dataset.coordinateTransformations)
-            for tform in tforms:
-                if hasattr(tform, "scale") or hasattr(tform, "translation"):
-                    tform = cast(
-                        Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
-                        tform,
-                    )
-                    if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
-                        msg = (
-                            f"Transform {tform} has dimensionality {tform_dims} "
-                            "which does not match the dimensionality "
-                            f"of the arrays in this group ({ndims}). "
-                            "Transform dimensionality must match array "
-                            "dimensionality."
-                        )
-                        raise ValueError(msg)
-        return self
+    """
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index aa8a86b..99f6f7e 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,61 +1,44 @@
 from typing import Union
-import pydantic_ome_ngff.v04.transforms as ctx
+import pydantic_ome_ngff.v04.transforms as tx
 
-
-class IdentityTransform(ctx.Identity):
+class Identity(tx.Identity):
     """
     An identity transform with no parameters.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathScale(ctx.PathScale):
+class PathScale(tx.PathScale):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathTranslation(ctx.PathTranslation):
+class PathTranslation(tx.PathTranslation):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorTranslationTransform(ctx.VectorTranslation):
+class VectorTranslation(tx.VectorTranslation):
     """
     A translation transform with a `translate` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorScaleTransform(ctx.VectorScale):
+class VectorScale(tx.VectorScale):
     """
     A scale transform with a `scale` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+Scale = Union[VectorScale, PathScale]
+Translation = Union[VectorTranslation, PathTranslation]
+Transform = Union[Scale, Translation, Identity]
 
-def get_transform_ndim(
-    transform: Union[VectorScaleTransform, VectorTranslationTransform],
-) -> int:
-    """
-    Get the dimensionality of a vector transform (scale or translation).
-    """
-    if transform.type == "scale" and hasattr(transform, "scale"):
-        return len(transform.scale)
-    elif transform.type == "translation" and hasattr(transform, "translation"):
-        return len(transform.translation)
-    else:
-        raise ValueError(
-            f"""
-        Transform must be either VectorScaleTransform or VectorTranslationTransform.
-        Got {type(transform)} instead.
-        """
-        )
-
-
-ScaleTransform = Union[VectorScaleTransform, PathScale]
-TranslationTransform = Union[VectorTranslationTransform, PathTranslation]
-CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
+scale_translation = tx.scale_translation
+ensure_dimensionality = tx.ensure_dimensionality
+ndim = tx.ndim
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index e09ce91..3932a35 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,4 +1,7 @@
 from __future__ import annotations
+from typing import Annotated
+
+from pydantic import AfterValidator, model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -67,41 +70,34 @@ class TimeUnit(str, Enum):
     zettasecond = "zettasecond"
 
 
-class Axis(StrictVersionedBase):
+def check_type_unit(model: Axis) -> "Axis":
     """
-    Axis metadata.
-    See https://ngff.openmicroscopy.org/0.4/#axes-md
+    Check that the `unit` attribute of an `Axis` object is valid. This function emits warnings when the units of an `Axis` object
+    are spec-compliant but go against a "SHOULD" statement in the spec.
     """
 
-    _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: str
-    type: str | None
-    unit: str | None
-
-
-def check_unit(model: Axis) -> "Axis":
     typ = model.type
     unit = model.unit
+
     if typ == AxisType.space:
-        if unit not in SpaceUnit.__members__:
+        if unit not in [e.value for e in SpaceUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
     elif typ == AxisType.time:
-        if unit not in TimeUnit.__members__:
+        if unit not in [e.value for e in TimeUnit]:
             msg = (
-                f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                f"with type '{typ}'."
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
         msg = (
-            f"Null axis type. Version {model._version} of the OME-NGFF spec states "
+            f"The `type` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the 'type' field of an axis should be set to a string."
         )
         warnings.warn(msg, UserWarning)
@@ -115,8 +111,26 @@ def check_unit(model: Axis) -> "Axis":
 
     if unit is None:
         msg = (
-            f"Null unit. Version {model._version} of the OME-NGFF spec states "
+            f"The `unit` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the `unit` field of an axis should be set to a string."
         )
         warnings.warn(msg)
     return model
+
+
+
+class Axis(StrictVersionedBase):
+    """
+    Axis metadata.
+    See https://ngff.openmicroscopy.org/0.4/#axes-md
+    """
+
+    _version = version
+    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
+    name: str
+    type: str | None
+    unit: str | None
+
+    @model_validator(mode='after')
+    def check_type_unit(self):
+        return check_type_unit(self)
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index e86412b..454952a 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -1,5 +1,6 @@
+from __future__ import annotations
 import warnings
-from typing import List, Optional, Tuple
+from typing import List, Optional, Tuple, Annotated
 
 from pydantic import BaseModel, Field, field_validator
 from pydantic_ome_ngff.base import VersionedBase
@@ -7,18 +8,23 @@
 
 from pydantic_ome_ngff.v04.base import version
 
+ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
+RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
 
 class Color(BaseModel):
-    label_value: int = Field(..., alias="label-value")
-    rgba: Optional[Tuple[int, int, int, int]]
+    """
+    a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
+    """
+    label_value: int = Field(..., serialization_alias="label-value")
+    rgba: RGBA | None
 
 
 class Source(BaseModel):
-    image: Optional[str] = "../../"
+    image: str | None = "../../"
 
 
 class Properties(BaseModel):
-    label_value: int = Field(..., alias="label-value")
+    label_value: int = Field(..., serialization_alias="label-value")
 
 
 class ImageLabel(VersionedBase):
@@ -27,46 +33,40 @@ class ImageLabel(VersionedBase):
     See https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # field is not required by the spec...
     _version = version
 
-    # SPEC: version is either unset or a string?
     version: Optional[str] = version
-    colors: Optional[List[Color]]
-    properties: Optional[Properties]
-    source: Optional[Source]
-
+    colors: List[Color] | None = None
+    properties: Properties | None = None
+    source: Source | None = None
+    
     @field_validator("version")
-    def check_version(cls, ver: str) -> str:
+    @classmethod
+    def check_version(cls, ver: str | None) -> str:
         if ver is None:
-            warnings.warn(
-                f"""
-            The field "version" is "None". Version {cls._version} of
-            the OME-NGFF spec states that "version" must either be unset or the string
-            "{cls._version}"
-            """
+            msg = (
+                f"The `version` attribute is `None`. Version {cls._version} of "
+                f"the OME-NGFF spec states that `version` must either be unset or the string {cls._version}"
             )
+            warnings.warn(msg, stacklevel=1)
+
         return ver
 
     @field_validator("colors")
+    @classmethod
     def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
-            warnings.warn(
-                f"""
-            The field "colors" is "None". Version {cls._version} of
-            the OME-NGFF spec states that "colors" should be a list of label 
-            descriptors.
-            """
-            )
+            msg = (
+                f"The field `colors` is `None`. Version {cls._version} of"
+                "the OME-NGFF spec states that `colors` should be a list of label descriptors.")
+            warnings.warn(msg, stacklevel=1)
         else:
             dupes = duplicates(x.label_value for x in colors)
-            if len(dupes) > 1:
-                raise ValueError(
-                    f"""
-                    Duplicated label-value: {tuple(dupes.keys())}.
-                    label-values must be unique across elements of `colors`
-                    """
+            if len(dupes) > 0:
+                msg = (
+                    f"Duplicated label-value: {tuple(dupes.keys())}."
+                    "label-values must be unique across elements of `colors`."
                 )
+                raise ValueError(msg)
 
         return colors
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 62505e4..7d666b4 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,32 +1,34 @@
 from collections import Counter
-from typing import Annotated, Any, Dict, List, Optional, Sequence, Union, cast
+from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 
-from pydantic import AfterValidator, BaseModel, conlist, model_validator
+from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
-import pydantic_ome_ngff.v04.transforms as ctx
+import pydantic_ome_ngff.v04.transforms as tx
 
 VALID_NDIM = (2, 3, 4, 5)
 
 
 def ensure_scale_translation(
-    transforms: Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]],
-) -> Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]]:
+    transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
+) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
     Ensure that
         - the first element is a scale transformation
-        - the second element is a translation transform
+        - the second element, if present, is a translation transform
+        - there are only 1 or 2 transforms
     """
-    if len(transforms) == 0:
-        raise ValueError("Invalid transforms: got 0, expected 1 or 2")
+
+    if len(transforms) == 0 or len(transforms) > 2:
+        raise ValueError(f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2")
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
         msg = (
-            "The first element of coordinateTransformations must be a scale "
+            "The first element of `coordinateTransformations` must be a scale "
             f"transform. Got {maybe_scale} instead."
         )
         raise ValueError(msg)
@@ -34,19 +36,17 @@ def ensure_scale_translation(
         maybe_trans = transforms[1]
         if (maybe_trans.type) != "translation":
             msg = (
-                "The second element of coordinateTransformations must be a "
+                "The second element of `coordinateTransformations` must be a "
                 f"translation transform. Got {maybe_trans} instead."
             )
             raise ValueError(msg)
-    else:
-        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
-        raise ValueError(msg)
+
     return transforms
 
 
 def ensure_transforms_length(
-    transforms: Sequence[ctx.VectorScale | ctx.VectorTranslation],
-) -> Sequence[ctx.VectorScale | ctx.VectorTranslation]:
+    transforms: Sequence[tx.VectorScale | tx.VectorTranslation],
+) -> Sequence[tx.VectorScale | tx.VectorTranslation]:
     if (num_tx := len(transforms)) not in (1, 2):
         msg = f"Invalid number of transforms: got {num_tx}, expected 1 or 2"
         raise ValueError(msg)
@@ -63,16 +63,16 @@ class MultiscaleDataset(StrictBase):
     path: str
         The path to the zarr array that stores the image described by this metadata.
         This path should be relative to the group that contains this metadata.
-    coordinateTransformations: Union[ctx.ScaleTransform, ctx.TranslationTransform]
+    coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
     """
 
     path: str
     coordinateTransformations: Annotated[
-        List[ctx.Scale | ctx.Translation],
+        List[tx.Scale | tx.Translation],
         AfterValidator(ensure_transforms_length),
         AfterValidator(ensure_scale_translation),
-        AfterValidator(ctx.ensure_dimensionality),
+        AfterValidator(tx.ensure_dimensionality),
     ]
 
 
@@ -136,15 +136,28 @@ class Multiscale(StrictVersionedBase):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
-    """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    Attributes
+    ----------
+
+    name: Any
+        The name for this multiscale image. Optional. Defaults to `None`.
+    type: Any
+        The type of the multiscale image. Optional. Defaults to `None`.
+    metadata: Dict[str, Any] | None
+        Metadata for this multiscale image. Optional. Defaults to `None`.
+    datasets: List[MultiscaleDataset]
+        A collection of descriptions of arrays that collectively comprise this multiscale image.
+    axes: List[Axis]
+        A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
+    coordinateTransformations: List[tx.Scale, tx.Translation]
+
+    """
     _version = version
     version: Any = version
     name: Any = None
     type: Any = None
-    metadata: Optional[Dict[str, Any]] = None
+    metadata: Dict[str, Any] | None = None
     datasets: List[MultiscaleDataset]
     axes: Annotated[
         List[Axis],
@@ -153,7 +166,7 @@ class Multiscale(StrictVersionedBase):
         AfterValidator(ensure_axis_types),
     ]
 
-    coordinateTransformations: List[ctx.Scale | ctx.Translation] | None = None
+    coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
 class MultiscaleAttrs(BaseModel):
@@ -162,37 +175,57 @@ class MultiscaleAttrs(BaseModel):
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: conlist(Multiscale, min_length=1)
+    multiscales: Annotated[List[Multiscale], Field(..., min_length=1)]
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
+    """
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
+
+    Attributes
+    ----------
+
+    attributes: MultiscaleAttrs
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
+        values are allowed.
+    members Dict[Str, ArraySpec | GroupSpec]:
+        The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
+
+    """
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
+        """
+        Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
+
+        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is 
+        allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
+        """
         attrs = self.attributes
         array_items: dict[str, dict[str, ArraySpec]] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
 
-        multiscales: List[Multiscale] = attrs.multiscales
-
-        for multiscale in multiscales:
+        for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
                     msg = (
                         f"Dataset {dpath} was specified in multiscale metadata, but no "
                         "array with that name was found in the items of that group. "
-                        "All arrays in multiscale metadata must be items of the group."
+                        "All arrays referenced in multiscale metadata must be items of the group."
                     )
                     raise ValueError(msg)
         return self
 
     @model_validator(mode="after")
     def check_array_ndim(self) -> "MultiscaleGroup":
+        """
+        Check that all the arrays referenced by the `multiscales` metadata have the same
+        dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
+        """
         attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
-        multiscales: List[Multiscale] = attrs.multiscales
 
         ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
@@ -203,7 +236,7 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             raise ValueError(msg)
 
         # check that each transform has compatible rank
-        for multiscale in multiscales:
+        for multiscale in attrs.multiscales:
             tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
@@ -212,15 +245,15 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for tform in tforms:
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
-                        Union[ctx.VectorScale, ctx.VectorTranslation],
+                        Union[tx.VectorScale, tx.VectorTranslation],
                         tform,
                     )
-                    if (tform_dims := ctx.ndim(tform)) not in set(ndims):
+                    if (tform_dims := tx.ndim(tform)) not in set(ndims):
                         msg = (
                             f"Transform {tform} has dimensionality {tform_dims} "
-                            "which does notmatch the dimensionality of the arrays "
+                            "which does not match the dimensionality of the arrays "
                             f"in this group ({ndims}). Transform dimensionality "
                             "must match array dimensionality."
                         )
                         raise ValueError(msg)
-        return self
+        return self
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 2b1c07e..483a15b 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from typing import List, Optional
 
 from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 52c23a3..33a79b2 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -61,14 +61,15 @@ def ndim(
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
-    elif hasattr(transform, "translation"):
+    
+    if hasattr(transform, "translation"):
         return len(transform.translation)
-    else:
-        msg = (
-            "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
-            f"Got {type(transform)} instead."
-        )
-        raise ValueError(msg)
+
+    msg = (
+        "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
+        f"Got {type(transform)} instead."
+    )
+    raise ValueError(msg)
 
 
 def scale_translation(
@@ -103,6 +104,9 @@ def scale_translation(
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
+    """
+    Ensure that the elements of `Sequence[VectorTransform]`
+    """
     ndims = tuple(ndim(tx) for tx in transforms)
     ndims_set = set(ndims)
     if len(ndims_set) > 1:
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index bf883d0..bd7cd9e 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from typing import List, Optional, Union
 
 from pydantic import BaseModel, ValidationError, field_validator
diff --git a/tests/latest/__init__.py b/tests/latest/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_latest.py b/tests/latest/test_multiscales.py
similarity index 74%
rename from tests/test_latest.py
rename to tests/latest/test_multiscales.py
index 746c4b8..90bd789 100644
--- a/tests/test_latest.py
+++ b/tests/latest/test_multiscales.py
@@ -1,7 +1,8 @@
-from typing import Tuple, List, Optional
-import jsonschema as jsc
-import pytest
+from __future__ import annotations
+from typing import List, Optional, Tuple
 from pydantic import ValidationError
+import pytest
+import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
@@ -9,13 +10,14 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
+
 from pydantic_ome_ngff.latest.transforms import (
-    CoordinateTransform,
-    VectorScaleTransform,
-    VectorTranslationTransform,
+    Transform,
+    VectorScale,
+    VectorTranslation,
 )
 from pydantic_ome_ngff.latest.axis import Axis
-from .conftest import fetch_schemas
+from tests.conftest import fetch_schemas
 
 
 @pytest.fixture
@@ -32,13 +34,13 @@ def default_multiscale() -> Multiscale:
         MultiscaleDataset(
             path=f"path{idx}",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -54,7 +56,7 @@ def default_multiscale() -> Multiscale:
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(
+            VectorScale(
                 scale=[
                     1,
                 ]
@@ -66,8 +68,8 @@ def default_multiscale() -> Multiscale:
 
 
 def test_multiscale(default_multiscale: Multiscale) -> None:
-    base_schema, strict_schema = fetch_schemas("latest", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
+    _, strict_schema = fetch_schemas("latest", schema_name="image")
+    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -76,12 +78,14 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
 
+    # this should be fine
+
     datasets = [
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -91,7 +95,7 @@ def test_multiscale_unique_axis_names() -> None:
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(scale=[1, 1, 1]),
+            VectorScale(scale=[1, 1, 1]),
         ],
     )
 
@@ -104,8 +108,8 @@ def test_multiscale_unique_axis_names() -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -116,7 +120,7 @@ def test_multiscale_unique_axis_names() -> None:
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
+                VectorScale(scale=[1, 1, 1]),
             ],
         )
 
@@ -126,11 +130,9 @@ def test_multiscale_unique_axis_names() -> None:
     (
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-        (None, "space", "space", None),
-        ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes = [
         Axis(name=str(idx), type=t, unit=units_map.get(t, None))
@@ -141,13 +143,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -157,13 +159,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         )
     ]
     # TODO: make some axis-specifc exceptions
-    with pytest.raises(ValidationError):
+    with pytest.raises(ValidationError, match="Space axes must come last."):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -181,13 +183,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -196,13 +198,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="List should have"):
+    with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -214,12 +216,12 @@ def test_multiscale_axis_length(num_axes: int) -> None:
 
 def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
-        VectorScaleTransform(scale=(1, 1)),
-        VectorTranslationTransform(translation=(1, 1, 1)),
+        VectorScale(scale=(1, 1)),
+        VectorTranslation(translation=(1, 1, 1)),
     ]
     with pytest.raises(
         ValidationError,
-        match="Elements of coordinateTransformations must have the same dimensionality.",  # noqa
+        match="The transforms have inconsistent dimensionality.",  # noqa
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=tforms)
 
@@ -228,24 +230,20 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ]
-        * 3,
+            VectorScale(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+        ],
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-        [
-            VectorScaleTransform(scale=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ],
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform],
+    transforms: List[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="List should have at most 2 items"):
+    with pytest.raises(ValidationError, match="expected 1 or 2"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -253,24 +251,38 @@ def test_coordinate_transforms_invalid_length(
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
-        ]
-        * 2,
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
+        ],
+    ),
+)
+def test_coordinate_transforms_invalid_first_element(
+    transforms: Tuple[Transform, Transform],
+) -> None:
+    with pytest.raises(
+        ValidationError, match="The first element of `coordinateTransformations` must be a"
+    ):
+        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+
+
+@pytest.mark.parametrize(
+    "transforms",
+    (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
-def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform],
+def test_coordinate_transforms_invalid_second_element(
+    transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="element of coordinateTransformations must be a"
+        ValidationError, match="The second element of `coordinateTransformations` must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -306,7 +318,6 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
         )
         for d in default_multiscale.datasets
     }
-
     MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
@@ -330,4 +341,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
diff --git a/tests/v04/__init__.py b/tests/v04/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
new file mode 100644
index 0000000..778d0ba
--- /dev/null
+++ b/tests/v04/test_axis.py
@@ -0,0 +1,17 @@
+import pytest
+
+from pydantic_ome_ngff.v04.axis import Axis
+
+@pytest.mark.parametrize(
+        'axis_type, unit', [
+            ('space', 'second'), 
+            ('time', 'meter'), 
+            ('space', None),
+            (None, None),
+            ('foo', None)
+            ])
+
+def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
+    with pytest.warns(UserWarning):
+        Axis(name='axis', type=axis_type, unit=unit)
+
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
new file mode 100644
index 0000000..31f784d
--- /dev/null
+++ b/tests/v04/test_label.py
@@ -0,0 +1,25 @@
+from typing import List
+import pytest
+from pydantic import ValidationError
+
+
+from pydantic_ome_ngff.v04.label import Color, ImageLabel
+
+@pytest.mark.parametrize('version', ('0.4', None))
+def test_imagelabel_version(version: str | None) -> None:
+    if version is None:
+        with pytest.warns(UserWarning):
+            model = ImageLabel(version=version)
+    else:
+        model = ImageLabel(version=version)
+    assert model.version == version
+
+@pytest.mark.parametrize('colors', (None, 
+                                    [Color(label_value=10, rgba=[0,0,0,0]), Color(label_value=10, rgba=[0,0,0,0])]))
+def test_imagelabel_colors(colors: List[Color] | None):
+    if colors is None:
+        with pytest.warns(UserWarning):
+            model = ImageLabel(colors=colors)
+    else:
+        with pytest.raises(ValidationError, match='Duplicated label-value'):
+            model=ImageLabel(colors=colors)
\ No newline at end of file
diff --git a/tests/test_v04.py b/tests/v04/test_multiscales.py
similarity index 92%
rename from tests/test_v04.py
rename to tests/v04/test_multiscales.py
index 2862117..7115712 100644
--- a/tests/test_v04.py
+++ b/tests/v04/test_multiscales.py
@@ -1,21 +1,23 @@
-from typing import Tuple, List, Optional
-import jsonschema as jsc
-import pytest
+from __future__ import annotations
+from typing import List, Optional, Tuple
 from pydantic import ValidationError
+import pytest
+import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
-from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
     MultiscaleAttrs,
     MultiscaleDataset,
     MultiscaleGroup,
 )
+
 from pydantic_ome_ngff.v04.transforms import (
     Transform,
     VectorScale,
     VectorTranslation,
 )
 from pydantic_ome_ngff.v04.axis import Axis
+from tests.conftest import fetch_schemas
 
 
 @pytest.fixture
@@ -253,20 +255,34 @@ def test_coordinate_transforms_invalid_length(
         ]
         * 2,
         [
+            VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
-        ]
-        * 2,
+        ],
+    ),
+)
+def test_coordinate_transforms_invalid_first_element(
+    transforms: Tuple[Transform, Transform],
+) -> None:
+    with pytest.raises(
+        ValidationError, match="The first element of `coordinateTransformations` must be a"
+    ):
+        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+
+
+@pytest.mark.parametrize(
+    "transforms",
+    (
         [
-            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
-def test_coordinate_transforms_invalid_elements(
+def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="element of coordinateTransformations must be a"
+        ValidationError, match="The second element of `coordinateTransformations` must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -325,4 +341,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file

From 87dad875f4e7d83763bc9cf45cdc5c08db5cd5e3 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 1 Jan 2024 17:57:14 +0100
Subject: [PATCH 07/69] lint

---
 src/pydantic_ome_ngff/base.py               |  4 ++--
 src/pydantic_ome_ngff/latest/axis.py        |  1 +
 src/pydantic_ome_ngff/latest/multiscales.py | 21 +++++++++-----------
 src/pydantic_ome_ngff/latest/transforms.py  |  4 +++-
 src/pydantic_ome_ngff/v04/axis.py           |  6 ++----
 src/pydantic_ome_ngff/v04/label.py          |  7 +++++--
 src/pydantic_ome_ngff/v04/multiscales.py    | 10 +++++++---
 src/pydantic_ome_ngff/v04/transforms.py     |  2 +-
 tests/latest/test_multiscales.py            |  8 +++++---
 tests/v04/test_axis.py                      | 21 ++++++++++----------
 tests/v04/test_label.py                     | 22 +++++++++++++++------
 tests/v04/test_multiscales.py               |  8 +++++---
 12 files changed, 67 insertions(+), 47 deletions(-)

diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index b471f51..2216443 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -1,7 +1,7 @@
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel
 
 
-class StrictBase(BaseModel, extra='forbid'):
+class StrictBase(BaseModel, extra="forbid"):
     """
     A pydantic basemodel that refuses extra fields.
     """
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
index 9e5c8ac..f44723a 100644
--- a/src/pydantic_ome_ngff/latest/axis.py
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -2,6 +2,7 @@
 
 AxisType = axisV04.AxisType
 
+
 class Axis(axisV04.Axis):
     """
     Axis metadata.
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index a68de43..f7e24bd 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,15 +1,7 @@
-from collections import Counter
-from typing import Any, Dict, List, Literal, Optional, Union, cast
-import warnings
+from typing import Literal
 
-from pydantic import BaseModel, model_validator, field_validator
-from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.latest import transforms as ctx
-from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.latest.axis import AxisType, Axis
 import pydantic_ome_ngff.v04.multiscales as msv04
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(msv04.MultiscaleDataset):
@@ -27,15 +19,19 @@ class MultiscaleDataset(msv04.MultiscaleDataset):
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
     """
+
     ...
 
+
 class Multiscale(msv04.Multiscale):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
+
     _version = version
-    version: Literal['0.5-dev'] = version
+    version: Literal["0.5-dev"] = version
+
 
 class MultiscaleAttrs(msv04.MultiscaleAttrs):
     """
@@ -43,8 +39,9 @@ class MultiscaleAttrs(msv04.MultiscaleAttrs):
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
+
 class MultiscaleGroup(msv04.MultiscaleGroup):
-     """
+    """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
     Attributes
@@ -56,4 +53,4 @@ class MultiscaleGroup(msv04.MultiscaleGroup):
     members Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
-    """
\ No newline at end of file
+    """
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index 99f6f7e..7198077 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,6 +1,7 @@
 from typing import Union
 import pydantic_ome_ngff.v04.transforms as tx
 
+
 class Identity(tx.Identity):
     """
     An identity transform with no parameters.
@@ -35,10 +36,11 @@ class VectorScale(tx.VectorScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+
 Scale = Union[VectorScale, PathScale]
 Translation = Union[VectorTranslation, PathTranslation]
 Transform = Union[Scale, Translation, Identity]
 
 scale_translation = tx.scale_translation
 ensure_dimensionality = tx.ensure_dimensionality
-ndim = tx.ndim
\ No newline at end of file
+ndim = tx.ndim
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 3932a35..d780f2a 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
-from typing import Annotated
 
-from pydantic import AfterValidator, model_validator
+from pydantic import model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -118,7 +117,6 @@ def check_type_unit(model: Axis) -> "Axis":
     return model
 
 
-
 class Axis(StrictVersionedBase):
     """
     Axis metadata.
@@ -131,6 +129,6 @@ class Axis(StrictVersionedBase):
     type: str | None
     unit: str | None
 
-    @model_validator(mode='after')
+    @model_validator(mode="after")
     def check_type_unit(self):
         return check_type_unit(self)
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 454952a..602d857 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -11,10 +11,12 @@
 ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
 RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
 
+
 class Color(BaseModel):
     """
     a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
     """
+
     label_value: int = Field(..., serialization_alias="label-value")
     rgba: RGBA | None
 
@@ -39,7 +41,7 @@ class ImageLabel(VersionedBase):
     colors: List[Color] | None = None
     properties: Properties | None = None
     source: Source | None = None
-    
+
     @field_validator("version")
     @classmethod
     def check_version(cls, ver: str | None) -> str:
@@ -58,7 +60,8 @@ def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
             msg = (
                 f"The field `colors` is `None`. Version {cls._version} of"
-                "the OME-NGFF spec states that `colors` should be a list of label descriptors.")
+                "the OME-NGFF spec states that `colors` should be a list of label descriptors."
+            )
             warnings.warn(msg, stacklevel=1)
         else:
             dupes = duplicates(x.label_value for x in colors)
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 7d666b4..453ce3d 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -23,7 +23,9 @@ def ensure_scale_translation(
     """
 
     if len(transforms) == 0 or len(transforms) > 2:
-        raise ValueError(f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2")
+        raise ValueError(
+            f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        )
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
@@ -153,6 +155,7 @@ class Multiscale(StrictVersionedBase):
     coordinateTransformations: List[tx.Scale, tx.Translation]
 
     """
+
     _version = version
     version: Any = version
     name: Any = None
@@ -192,12 +195,13 @@ class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
         """
         Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
 
-        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is 
+        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is
         allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
         """
         attrs = self.attributes
@@ -256,4 +260,4 @@ def check_array_ndim(self) -> "MultiscaleGroup":
                             "must match array dimensionality."
                         )
                         raise ValueError(msg)
-        return self
\ No newline at end of file
+        return self
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 33a79b2..729b5f3 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -61,7 +61,7 @@ def ndim(
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
-    
+
     if hasattr(transform, "translation"):
         return len(transform.translation)
 
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 90bd789..8ad245a 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -264,7 +264,8 @@ def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The first element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The first element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -282,7 +283,8 @@ def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The second element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The second element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -341,4 +343,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
index 778d0ba..968c507 100644
--- a/tests/v04/test_axis.py
+++ b/tests/v04/test_axis.py
@@ -2,16 +2,17 @@
 
 from pydantic_ome_ngff.v04.axis import Axis
 
-@pytest.mark.parametrize(
-        'axis_type, unit', [
-            ('space', 'second'), 
-            ('time', 'meter'), 
-            ('space', None),
-            (None, None),
-            ('foo', None)
-            ])
 
+@pytest.mark.parametrize(
+    "axis_type, unit",
+    [
+        ("space", "second"),
+        ("time", "meter"),
+        ("space", None),
+        (None, None),
+        ("foo", None),
+    ],
+)
 def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
     with pytest.warns(UserWarning):
-        Axis(name='axis', type=axis_type, unit=unit)
-
+        Axis(name="axis", type=axis_type, unit=unit)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index 31f784d..7636620 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -5,7 +5,8 @@
 
 from pydantic_ome_ngff.v04.label import Color, ImageLabel
 
-@pytest.mark.parametrize('version', ('0.4', None))
+
+@pytest.mark.parametrize("version", ("0.4", None))
 def test_imagelabel_version(version: str | None) -> None:
     if version is None:
         with pytest.warns(UserWarning):
@@ -14,12 +15,21 @@ def test_imagelabel_version(version: str | None) -> None:
         model = ImageLabel(version=version)
     assert model.version == version
 
-@pytest.mark.parametrize('colors', (None, 
-                                    [Color(label_value=10, rgba=[0,0,0,0]), Color(label_value=10, rgba=[0,0,0,0])]))
+
+@pytest.mark.parametrize(
+    "colors",
+    (
+        None,
+        [
+            Color(label_value=10, rgba=[0, 0, 0, 0]),
+            Color(label_value=10, rgba=[0, 0, 0, 0]),
+        ],
+    ),
+)
 def test_imagelabel_colors(colors: List[Color] | None):
     if colors is None:
         with pytest.warns(UserWarning):
-            model = ImageLabel(colors=colors)
+            ImageLabel(colors=colors)
     else:
-        with pytest.raises(ValidationError, match='Duplicated label-value'):
-            model=ImageLabel(colors=colors)
\ No newline at end of file
+        with pytest.raises(ValidationError, match="Duplicated label-value"):
+            ImageLabel(colors=colors)
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 7115712..16cad6d 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -264,7 +264,8 @@ def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The first element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The first element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -282,7 +283,8 @@ def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The second element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The second element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -341,4 +343,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)

From ec6649fc37cdfb15467e1fa7453676d33b5afb66 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 9 Jan 2024 15:49:32 +0100
Subject: [PATCH 08/69] feat: use a tighter module-local name convention for
 specialized GroupSpec instances, and expand ImageLabel metadata

---
 src/pydantic_ome_ngff/latest/__init__.py    |   2 +-
 src/pydantic_ome_ngff/latest/label.py       |   3 +-
 src/pydantic_ome_ngff/latest/multiscales.py |   8 +-
 src/pydantic_ome_ngff/latest/plate.py       |   4 +-
 src/pydantic_ome_ngff/latest/well.py        |   2 +-
 src/pydantic_ome_ngff/v04/__init__.py       |  24 ++--
 src/pydantic_ome_ngff/v04/axis.py           |  32 +++--
 src/pydantic_ome_ngff/v04/label.py          | 127 ++++++++++++++------
 src/pydantic_ome_ngff/v04/multiscales.py    |  21 ++--
 src/pydantic_ome_ngff/v04/plate.py          |  24 ++--
 src/pydantic_ome_ngff/v04/well.py           |  21 ++--
 tests/latest/test_multiscales.py            |  60 ++++-----
 tests/v04/test_label.py                     |  35 +++++-
 tests/v04/test_multiscales.py               |  60 ++++-----
 14 files changed, 249 insertions(+), 174 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index fb9e90e..1bccf6f 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,5 +1,5 @@
 from pydantic_ome_ngff.latest.axis import Axis  # noqa
-from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
+from pydantic_ome_ngff.latest.multiscales import MultiscaleMetadata  # noqa
 from pydantic_ome_ngff.latest.label import ImageLabel  # noqa
 from pydantic_ome_ngff.latest.well import WellMeta  # noqa
 from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
diff --git a/src/pydantic_ome_ngff/latest/label.py b/src/pydantic_ome_ngff/latest/label.py
index e48d93f..18e6697 100644
--- a/src/pydantic_ome_ngff/latest/label.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -1,6 +1,5 @@
 from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
 from pydantic_ome_ngff.latest.base import version
-from typing import Optional
 
 
 class ImageLabel(ImageLabelV04):
@@ -12,4 +11,4 @@ class ImageLabel(ImageLabelV04):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index f7e24bd..1064f47 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -4,7 +4,7 @@
 import pydantic_ome_ngff.v04.multiscales as msv04
 
 
-class MultiscaleDataset(msv04.MultiscaleDataset):
+class Dataset(msv04.Dataset):
     """
     A single entry in the multiscales.datasets list.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -23,7 +23,7 @@ class MultiscaleDataset(msv04.MultiscaleDataset):
     ...
 
 
-class Multiscale(msv04.Multiscale):
+class MultiscaleMetadata(msv04.MultiscaleMetadata):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -33,14 +33,14 @@ class Multiscale(msv04.Multiscale):
     version: Literal["0.5-dev"] = version
 
 
-class MultiscaleAttrs(msv04.MultiscaleAttrs):
+class GroupAttrs(msv04.GroupAttrs):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
 
-class MultiscaleGroup(msv04.MultiscaleGroup):
+class Group(msv04.Group):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index 6a04eeb..69ba478 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -2,7 +2,7 @@
 
 
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.plate import PlateMeta as PlateMetaV04
+from pydantic_ome_ngff.v04.plate import PlateMetadata as PlateMetaV04
 
 
 class PlateMeta(PlateMetaV04):
@@ -11,7 +11,5 @@ class PlateMeta(PlateMetaV04):
     See https://ngff.openmicroscopy.org/latest/#plate-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
     _version = version
     version: Optional[str] = version
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index 16fd610..1004d07 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,6 +1,6 @@
 from typing import Optional
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.well import WellMeta as WellMetaV04
+from pydantic_ome_ngff.v04.well import WellMetadata as WellMetaV04
 
 
 class WellMeta(WellMetaV04):
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index ffd00cb..f63d655 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -1,7 +1,17 @@
-from pydantic_ome_ngff.v04.axis import Axis  # noqa
-from pydantic_ome_ngff.v04.transforms import Transform  # noqa
-from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.v04.label import ImageLabel  # noqa
-from pydantic_ome_ngff.v04.well import WellMeta  # noqa
-from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
-from pydantic_ome_ngff.v04.base import version  # noqa
+from pydantic_ome_ngff.v04.axis import Axis
+from pydantic_ome_ngff.v04.transforms import Transform
+from pydantic_ome_ngff.v04.multiscales import MultiscaleMetadata
+from pydantic_ome_ngff.v04.label import ImageLabel
+from pydantic_ome_ngff.v04.well import WellMetadata
+from pydantic_ome_ngff.v04.plate import PlateMetadata
+from pydantic_ome_ngff.v04.base import version
+
+__all__ = [
+    "Axis",
+    "Transform",
+    "MultiscaleMetadata",
+    "ImageLabel",
+    "WellMetadata",
+    "PlateMetadata",
+    "version",
+]
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index d780f2a..21e0731 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -69,29 +69,28 @@ class TimeUnit(str, Enum):
     zettasecond = "zettasecond"
 
 
-def check_type_unit(model: Axis) -> "Axis":
+def check_type_unit(model: Axis) -> Axis:
     """
-    Check that the `unit` attribute of an `Axis` object is valid. This function emits warnings when the units of an `Axis` object
+    Check that the `unit` attribute of an `Axis` object is valid.
+    This function emits warnings when the units of an `Axis` object
     are spec-compliant but go against a "SHOULD" statement in the spec.
     """
 
     typ = model.type
     unit = model.unit
 
-    if typ == AxisType.space:
-        if unit not in [e.value for e in SpaceUnit]:
-            msg = (
-                f"Unit '{unit}' is not recognized as a standard unit "
-                f"for an axis with type '{typ}'."
-            )
-            warnings.warn(msg)
-    elif typ == AxisType.time:
-        if unit not in [e.value for e in TimeUnit]:
-            msg = (
-                f"Unit '{unit}' is not recognized as a standard unit "
-                f"for an axis with type '{typ}'."
-            )
-            warnings.warn(msg)
+    if typ == AxisType.space and unit not in [e.value for e in SpaceUnit]:
+        msg = (
+            f"Unit '{unit}' is not recognized as a standard unit "
+            f"for an axis with type '{typ}'."
+        )
+        warnings.warn(msg)
+    elif typ == AxisType.time and unit not in [e.value for e in TimeUnit]:
+        msg = (
+            f"Unit '{unit}' is not recognized as a standard unit "
+            f"for an axis with type '{typ}'."
+        )
+        warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -124,7 +123,6 @@ class Axis(StrictVersionedBase):
     """
 
     _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
     name: str
     type: str | None
     unit: str | None
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 602d857..436d3c8 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -1,12 +1,13 @@
 from __future__ import annotations
 import warnings
-from typing import List, Optional, Tuple, Annotated
+from typing import List, Literal, Optional, Tuple, Annotated
 
-from pydantic import BaseModel, Field, field_validator
+from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.utils import duplicates
+from pydantic_ome_ngff.v04.base import version as NGFF_VERSION
 
-from pydantic_ome_ngff.v04.base import version
+import pydantic_ome_ngff.v04.multiscales as multiscales
 
 ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
 RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
@@ -18,58 +19,104 @@ class Color(BaseModel):
     """
 
     label_value: int = Field(..., serialization_alias="label-value")
-    rgba: RGBA | None
+    rgba: Optional[RGBA]
 
 
 class Source(BaseModel):
-    image: str | None = "../../"
+    # todo: add validation that this path resolves to something
+    image: Optional[str] = "../../"
 
 
-class Properties(BaseModel):
+class Property(BaseModel):
     label_value: int = Field(..., serialization_alias="label-value")
 
 
+def parse_colors(colors: List[Color] | None) -> List[Color] | None:
+    if colors is None:
+        msg = (
+            f"The field `colors` is `None`. Version {NGFF_VERSION} of"
+            "the OME-NGFF spec states that `colors` should be a list of label descriptors."
+        )
+        warnings.warn(msg, stacklevel=1)
+    else:
+        dupes = duplicates(x.label_value for x in colors)
+        if len(dupes) > 0:
+            msg = (
+                f"Duplicated label-value: {tuple(dupes.keys())}."
+                "label-values must be unique across elements of `colors`."
+            )
+            raise ValueError(msg)
+
+    return colors
+
+
+def parse_version(version: Literal["0.4"] | None) -> Literal["0.4"] | None:
+    if version is None:
+        msg = (
+            f"The `version` attribute is `None`. Version {NGFF_VERSION} of "
+            f"the OME-NGFF spec states that `version` must either be unset or the string {NGFF_VERSION}"
+        )
+        warnings.warn(msg, stacklevel=1)
+    return version
+
+
+def parse_imagelabel(model: ImageLabel):
+    """
+    check that label_values are consistent across properties and colors
+    """
+    if model.colors is not None and model.properties is not None:
+        prop_label_value = [prop.label_value for prop in model.properties]
+        color_label_value = [color.label_value for color in model.colors]
+
+        prop_label_value_set = set(prop_label_value)
+        color_label_value_set = set(color_label_value)
+        if color_label_value_set != prop_label_value_set:
+            msg = (
+                "Inconsistent `label_value` attributes in `colors` and `properties`."
+                f"The `properties` attributes have `label_values` {prop_label_value}, "
+                f"The `colors` attributes have `label_values` {color_label_value}, "
+            )
+            raise ValueError(msg)
+    return model
+
+
 class ImageLabel(VersionedBase):
     """
     image-label metadata.
     See https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
-    _version = version
+    _version: Literal["0.4"] = NGFF_VERSION
 
-    version: Optional[str] = version
-    colors: List[Color] | None = None
-    properties: Properties | None = None
-    source: Source | None = None
+    version: Annotated[
+        Literal["0.4"] | None, AfterValidator(parse_version)
+    ] = NGFF_VERSION
+    colors: Annotated[Optional[List[Color]], AfterValidator(parse_colors)] = None
+    properties: Optional[List[Property]] = None
+    source: Optional[Source] = None
 
-    @field_validator("version")
-    @classmethod
-    def check_version(cls, ver: str | None) -> str:
-        if ver is None:
-            msg = (
-                f"The `version` attribute is `None`. Version {cls._version} of "
-                f"the OME-NGFF spec states that `version` must either be unset or the string {cls._version}"
-            )
-            warnings.warn(msg, stacklevel=1)
+    @model_validator(mode="after")
+    def parse_model(self):
+        return parse_imagelabel(self)
 
-        return ver
 
-    @field_validator("colors")
-    @classmethod
-    def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
-        if colors is None:
-            msg = (
-                f"The field `colors` is `None`. Version {cls._version} of"
-                "the OME-NGFF spec states that `colors` should be a list of label descriptors."
-            )
-            warnings.warn(msg, stacklevel=1)
-        else:
-            dupes = duplicates(x.label_value for x in colors)
-            if len(dupes) > 0:
-                msg = (
-                    f"Duplicated label-value: {tuple(dupes.keys())}."
-                    "label-values must be unique across elements of `colors`."
-                )
-                raise ValueError(msg)
-
-        return colors
+class GroupAttrs(multiscales.GroupAttrs):
+    """
+    Attributes for a Zarr group that contains `image-label` metadata.
+    Inherits from `v04.multiscales.MultiscaleAttrs`.
+
+    See https://ngff.openmicroscopy.org/0.4/#label-md
+
+    Attributes
+    ----------
+    image_label: `ImageLabel`
+        Image label metadata.
+    multiscales: List[v04.multiscales.Multiscales]
+        Multiscale image metadata.
+    """
+
+    image_label: Annotated[ImageLabel, Field(..., serialization_alias="image-label")]
+
+
+class Group(multiscales.Group):
+    attributes: GroupAttrs
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 453ce3d..5313d9e 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -55,7 +55,7 @@ def ensure_transforms_length(
     return transforms
 
 
-class MultiscaleDataset(StrictBase):
+class Dataset(StrictBase):
     """
     A single entry in the multiscales.datasets list.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -134,7 +134,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     return axes
 
 
-class Multiscale(StrictVersionedBase):
+class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -161,7 +161,7 @@ class Multiscale(StrictVersionedBase):
     name: Any = None
     type: Any = None
     metadata: Dict[str, Any] | None = None
-    datasets: List[MultiscaleDataset]
+    datasets: Annotated[List[Dataset], Field(..., min_length=1)]
     axes: Annotated[
         List[Axis],
         AfterValidator(ensure_axis_length),
@@ -172,16 +172,16 @@ class Multiscale(StrictVersionedBase):
     coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
-class MultiscaleAttrs(BaseModel):
+class GroupAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: Annotated[List[Multiscale], Field(..., min_length=1)]
+    multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
+class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
 
@@ -189,20 +189,19 @@ class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
     ----------
 
     attributes: MultiscaleAttrs
-        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
-        values are allowed.
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`.
     members Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
 
     @model_validator(mode="after")
-    def check_arrays_exist(self) -> "MultiscaleGroup":
+    def check_arrays_exist(self) -> "Group":
         """
         Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
 
         Note that this is currently too strict, since it will not check for arrays in subgroups, but this is
-        allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
+        allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
         array_items: dict[str, dict[str, ArraySpec]] = {
@@ -221,7 +220,7 @@ def check_arrays_exist(self) -> "MultiscaleGroup":
         return self
 
     @model_validator(mode="after")
-    def check_array_ndim(self) -> "MultiscaleGroup":
+    def check_array_ndim(self) -> "Group":
         """
         Check that all the arrays referenced by the `multiscales` metadata have the same
         dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 483a15b..3a03b9a 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -7,7 +7,7 @@
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
-from pydantic_ome_ngff.v04.well import WellGroup
+import pydantic_ome_ngff.v04.well as well
 
 
 class Acquisition(BaseModel):
@@ -20,14 +20,14 @@ class Entry(BaseModel):
     name: str
 
 
-class WellMeta(BaseModel):
+class WellMetadata(BaseModel):
     # must be {rowName}/{columnName}
     path: str
     rowIndex: PositiveInt
     columnIndex: PositiveInt
 
 
-class PlateMeta(VersionedBase):
+class PlateMetadata(VersionedBase):
     """
     Plate metadata
     see https://ngff.openmicroscopy.org/0.4/#plate-md
@@ -35,28 +35,28 @@ class PlateMeta(VersionedBase):
 
     # the version here as a private class attribute because the version is not required by the spec
     _version = version
-    version: Optional[str] = version
-    name: Optional[str] = None
+    version: str | None = version
+    name: str | None = None
     acquisitions: List[Acquisition]
     columns: List[Entry]
     rows: List[Entry]
     field_count: PositiveInt
-    wells: List[WellMeta]
+    wells: List[WellMetadata]
 
 
-class PlateAttributes(BaseModel):
-    plate: PlateMeta
+class GroupAttrs(BaseModel):
+    plate: PlateMetadata
 
 
-class PlateGroup(GroupSpec[PlateAttributes, Union[WellGroup, GroupSpec, ArraySpec]]):
+class Group(GroupSpec[GroupAttrs, Union[well.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
     def contains_well(
-        cls, members: Union[WellGroup, GroupSpec, ArraySpec]
-    ) -> Union[WellGroup, GroupSpec, ArraySpec]:
+        cls, members: Union[Group, GroupSpec, ArraySpec]
+    ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a WellGroup
         """
-        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+        if not any(map(lambda v: isinstance(v, Group), members.values())):
             raise ValidationError
         return members
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index bd7cd9e..170c3db 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -5,7 +5,7 @@
 from pydantic_ome_ngff.base import VersionedBase
 
 from pydantic_ome_ngff.v04.base import version
-from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+import pydantic_ome_ngff.v04.multiscales as multiscales
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
@@ -14,33 +14,30 @@ class Image(BaseModel):
     acquisition: Optional[int]
 
 
-class WellMeta(VersionedBase):
+class WellMetadata(VersionedBase):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/0.4/#well-md
     """
 
-    # the version here as a private class attribute because the version is not required by the spec
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
     images: List[Image]
 
 
-class WellAttributes(BaseModel):
-    well: WellMeta
+class GroupAttrs(BaseModel):
+    well: WellMetadata
 
 
-class WellGroup(
-    GroupSpec[WellAttributes, Union[MultiscaleGroup, GroupSpec, ArraySpec]]
-):
+class Group(GroupSpec[GroupAttrs, Union[multiscales.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
     def contains_well(
-        cls, members: Union[MultiscaleGroup, GroupSpec, ArraySpec]
-    ) -> Union[MultiscaleGroup, GroupSpec, ArraySpec]:
+        cls, members: Union[Group, GroupSpec, ArraySpec]
+    ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a MultiscaleGroup
         """
-        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+        if not any(map(lambda v: isinstance(v, Group), members.values())):
             raise ValidationError
         return members
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 8ad245a..f895721 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -5,10 +5,10 @@
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
-    Multiscale,
-    MultiscaleAttrs,
-    MultiscaleDataset,
-    MultiscaleGroup,
+    MultiscaleMetadata,
+    GroupAttrs,
+    Dataset,
+    Group,
 )
 
 from pydantic_ome_ngff.latest.transforms import (
@@ -21,7 +21,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> Multiscale:
+def default_multiscale() -> MultiscaleMetadata:
     axes = [
         Axis(name="c", type="channel", unit=None),
         Axis(name="z", type="space", unit="meter"),
@@ -31,7 +31,7 @@ def default_multiscale() -> Multiscale:
     rank = len(axes)
     num_datasets = 3
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path=f"path{idx}",
             coordinateTransformations=[
                 VectorScale(
@@ -51,7 +51,7 @@ def default_multiscale() -> Multiscale:
         for idx in range(num_datasets)
     ]
 
-    multi = Multiscale(
+    multi = MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -67,7 +67,7 @@ def default_multiscale() -> Multiscale:
     return multi
 
 
-def test_multiscale(default_multiscale: Multiscale) -> None:
+def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     _, strict_schema = fetch_schemas("latest", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
@@ -81,7 +81,7 @@ def test_multiscale_unique_axis_names() -> None:
     # this should be fine
 
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -90,7 +90,7 @@ def test_multiscale_unique_axis_names() -> None:
         )
     ]
 
-    Multiscale(
+    MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -105,7 +105,7 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -115,7 +115,7 @@ def test_multiscale_unique_axis_names() -> None:
     ]
 
     with pytest.raises(ValidationError, match="Axis names must be unique."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -140,7 +140,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     rank = len(axes)
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -160,7 +160,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     # TODO: make some axis-specifc exceptions
     with pytest.raises(ValidationError, match="Space axes must come last."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -180,7 +180,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -199,7 +199,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -223,7 +223,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
         ValidationError,
         match="The transforms have inconsistent dimensionality.",  # noqa
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=tforms)
+        Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
@@ -244,7 +244,7 @@ def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -267,7 +267,7 @@ def test_coordinate_transforms_invalid_first_element(
         ValidationError,
         match="The first element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -286,18 +286,20 @@ def test_coordinate_transforms_invalid_second_element(
         ValidationError,
         match="The second element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_exist(
+    default_multiscale: MultiscaleMetadata,
+) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -309,18 +311,18 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -335,7 +337,7 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
@@ -343,4 +345,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index 7636620..e2c4523 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -1,19 +1,42 @@
-from typing import List
+from typing import List, Literal
 import pytest
 from pydantic import ValidationError
+from pydantic_ome_ngff.v04 import version as NGFF_VERSION
 
+from pydantic_ome_ngff.v04.label import Color, ImageLabel, Property
 
-from pydantic_ome_ngff.v04.label import Color, ImageLabel
 
+@pytest.mark.parametrize("version", (None, "0.4"))
+def test_imagelabel(version: Literal["0.4"] | None):
+    color = Color(label_value=1, rgba=[0, 0, 0, 0])
+    model = ImageLabel(colors=[color], version=version)
+    dumped = model.model_dump()
 
-@pytest.mark.parametrize("version", ("0.4", None))
+    assert dumped["colors"] == [color.model_dump()]
+    # check that if the version is None, then we didn't write it out
+    if version == "0.4":
+        assert dumped["version"] == NGFF_VERSION
+
+
+def test_properties_colors_match():
+    color = Color(label_value=0, rgba=(0, 0, 0, 0))
+    prop = Property(label_value=1)
+
+    with pytest.raises(
+        ValidationError,
+        match="Inconsistent `label_value` attributes in `colors` and `properties`.",
+    ):
+        ImageLabel(colors=[color], properties=[prop])
+
+
+@pytest.mark.parametrize("version", ("0.5", None))
 def test_imagelabel_version(version: str | None) -> None:
     if version is None:
         with pytest.warns(UserWarning):
-            model = ImageLabel(version=version)
+            _ = ImageLabel(version=version)
     else:
-        model = ImageLabel(version=version)
-    assert model.version == version
+        with pytest.raises(ValidationError, match="Input should be '0.4'"):
+            _ = ImageLabel(version=version)
 
 
 @pytest.mark.parametrize(
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 16cad6d..b4ca419 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -5,10 +5,10 @@
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.v04.multiscales import (
-    Multiscale,
-    MultiscaleAttrs,
-    MultiscaleDataset,
-    MultiscaleGroup,
+    MultiscaleMetadata,
+    GroupAttrs,
+    Dataset,
+    Group,
 )
 
 from pydantic_ome_ngff.v04.transforms import (
@@ -21,7 +21,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> Multiscale:
+def default_multiscale() -> MultiscaleMetadata:
     axes = [
         Axis(name="c", type="channel", unit=None),
         Axis(name="z", type="space", unit="meter"),
@@ -31,7 +31,7 @@ def default_multiscale() -> Multiscale:
     rank = len(axes)
     num_datasets = 3
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path=f"path{idx}",
             coordinateTransformations=[
                 VectorScale(
@@ -51,7 +51,7 @@ def default_multiscale() -> Multiscale:
         for idx in range(num_datasets)
     ]
 
-    multi = Multiscale(
+    multi = MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -67,7 +67,7 @@ def default_multiscale() -> Multiscale:
     return multi
 
 
-def test_multiscale(default_multiscale: Multiscale) -> None:
+def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
@@ -81,7 +81,7 @@ def test_multiscale_unique_axis_names() -> None:
     # this should be fine
 
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -90,7 +90,7 @@ def test_multiscale_unique_axis_names() -> None:
         )
     ]
 
-    Multiscale(
+    MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -105,7 +105,7 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -115,7 +115,7 @@ def test_multiscale_unique_axis_names() -> None:
     ]
 
     with pytest.raises(ValidationError, match="Axis names must be unique."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -140,7 +140,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     rank = len(axes)
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -160,7 +160,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     # TODO: make some axis-specifc exceptions
     with pytest.raises(ValidationError, match="Space axes must come last."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -180,7 +180,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -199,7 +199,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -223,7 +223,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
         ValidationError,
         match="The transforms have inconsistent dimensionality.",  # noqa
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=tforms)
+        Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
@@ -244,7 +244,7 @@ def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -267,7 +267,7 @@ def test_coordinate_transforms_invalid_first_element(
         ValidationError,
         match="The first element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -286,18 +286,20 @@ def test_coordinate_transforms_invalid_second_element(
         ValidationError,
         match="The second element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_exist(
+    default_multiscale: MultiscaleMetadata,
+) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -309,18 +311,18 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -335,7 +337,7 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
@@ -343,4 +345,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)

From 4044348c9f854c22991a5aa3394474bc26eef743 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Sun, 4 Feb 2024 17:16:57 +0100
Subject: [PATCH 09/69] begin adding docs and convenience function for
 multiscale creation

---
 docs/api/v04/axis.md                        |  1 +
 docs/api/v04/label.md                       |  1 +
 docs/api/v04/multiscales.md                 |  1 +
 docs/api/v04/plate.md                       |  1 +
 docs/api/v04/transforms.md                  |  1 +
 docs/index.md                               | 17 ++++
 src/pydantic_ome_ngff/latest/multiscales.py |  2 +-
 src/pydantic_ome_ngff/v04/axis.py           | 46 +++++++----
 src/pydantic_ome_ngff/v04/label.py          |  2 +-
 src/pydantic_ome_ngff/v04/multiscales.py    | 87 ++++++++++++++-------
 src/pydantic_ome_ngff/v04/plate.py          |  4 +-
 src/pydantic_ome_ngff/v04/transforms.py     | 74 ++++++++++++++----
 src/pydantic_ome_ngff/v04/well.py           |  4 +-
 13 files changed, 176 insertions(+), 65 deletions(-)
 create mode 100644 docs/api/v04/axis.md
 create mode 100644 docs/api/v04/label.md
 create mode 100644 docs/api/v04/multiscales.md
 create mode 100644 docs/api/v04/plate.md
 create mode 100644 docs/api/v04/transforms.md
 create mode 100644 docs/index.md

diff --git a/docs/api/v04/axis.md b/docs/api/v04/axis.md
new file mode 100644
index 0000000..5f1cec1
--- /dev/null
+++ b/docs/api/v04/axis.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.axis
\ No newline at end of file
diff --git a/docs/api/v04/label.md b/docs/api/v04/label.md
new file mode 100644
index 0000000..fa0d46d
--- /dev/null
+++ b/docs/api/v04/label.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.label
\ No newline at end of file
diff --git a/docs/api/v04/multiscales.md b/docs/api/v04/multiscales.md
new file mode 100644
index 0000000..f520758
--- /dev/null
+++ b/docs/api/v04/multiscales.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.multiscales
\ No newline at end of file
diff --git a/docs/api/v04/plate.md b/docs/api/v04/plate.md
new file mode 100644
index 0000000..add6722
--- /dev/null
+++ b/docs/api/v04/plate.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.plate
\ No newline at end of file
diff --git a/docs/api/v04/transforms.md b/docs/api/v04/transforms.md
new file mode 100644
index 0000000..8a9a01f
--- /dev/null
+++ b/docs/api/v04/transforms.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.transforms
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..000ea34
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,17 @@
+# Welcome to MkDocs
+
+For full documentation visit [mkdocs.org](https://www.mkdocs.org).
+
+## Commands
+
+* `mkdocs new [dir-name]` - Create a new project.
+* `mkdocs serve` - Start the live-reloading docs server.
+* `mkdocs build` - Build the documentation site.
+* `mkdocs -h` - Print help message and exit.
+
+## Project layout
+
+    mkdocs.yml    # The configuration file.
+    docs/
+        index.md  # The documentation homepage.
+        ...       # Other markdown pages, images and other files.
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 1064f47..8f43d4d 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -14,7 +14,7 @@ class Dataset(msv04.Dataset):
     Attributes:
     ----------
     path: str
-        The path to the zarr array that stores the image described by this metadata.
+        The path to the Zarr array that stores the image described by this metadata.
         This path should be relative to the group that contains this metadata.
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 21e0731..8e6a511 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -9,6 +9,9 @@
 
 
 class AxisType(str, Enum):
+    """
+    String enum representing the three axis types (`space`, `time`, `channel`) defined in the specification.
+    """
     space = "space"
     time = "time"
     channel = "channel"
@@ -72,25 +75,27 @@ class TimeUnit(str, Enum):
 def check_type_unit(model: Axis) -> Axis:
     """
     Check that the `unit` attribute of an `Axis` object is valid.
-    This function emits warnings when the units of an `Axis` object
-    are spec-compliant but go against a "SHOULD" statement in the spec.
+    This function emits warnings when the `unit` attribute of of an `Axis` object
+    is spec-compliant but contravenes a "SHOULD" statement in the spec.
     """
 
     typ = model.type
     unit = model.unit
 
-    if typ == AxisType.space and unit not in [e.value for e in SpaceUnit]:
-        msg = (
-            f"Unit '{unit}' is not recognized as a standard unit "
-            f"for an axis with type '{typ}'."
-        )
-        warnings.warn(msg)
-    elif typ == AxisType.time and unit not in [e.value for e in TimeUnit]:
-        msg = (
-            f"Unit '{unit}' is not recognized as a standard unit "
-            f"for an axis with type '{typ}'."
-        )
-        warnings.warn(msg)
+    if typ == AxisType.space:
+         if unit not in [e.value for e in SpaceUnit]:
+            msg = (
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
+            )
+            warnings.warn(msg)
+    elif typ == AxisType.time:
+        if unit not in [e.value for e in TimeUnit]:
+            msg = (
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
+            )
+            warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -119,7 +124,18 @@ def check_type_unit(model: Axis) -> Axis:
 class Axis(StrictVersionedBase):
     """
     Axis metadata.
-    See https://ngff.openmicroscopy.org/0.4/#axes-md
+
+    See [https://ngff.openmicroscopy.org/0.4/#axes-md](https://ngff.openmicroscopy.org/0.4/#axes-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+
+    name: str
+        The name for this axis.
+    type: str | None
+        The type for this axis, e.g. `space`.
+    unit: str | None
+        The unit of measure associated with the interval defined by this axis.
     """
 
     _version = version
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 436d3c8..95ef442 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -15,7 +15,7 @@
 
 class Color(BaseModel):
     """
-    a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
+    A label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
     label_value: int = Field(..., serialization_alias="label-value")
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 5313d9e..99d0778 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -8,24 +8,21 @@
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
+import numpy.typing as npt
 
 VALID_NDIM = (2, 3, 4, 5)
 
-
 def ensure_scale_translation(
     transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
 ) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
-    Ensure that
-        - the first element is a scale transformation
-        - the second element, if present, is a translation transform
-        - there are only 1 or 2 transforms
+    Ensures that the first element is a scale transformation, the second element, 
+    if present, is a translation transform, and that there are only 1 or 2 transforms.
     """
 
     if len(transforms) == 0 or len(transforms) > 2:
-        raise ValueError(
-            f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
-        )
+        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        raise ValueError(msg)
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
@@ -57,16 +54,17 @@ def ensure_transforms_length(
 
 class Dataset(StrictBase):
     """
-    A single entry in the multiscales.datasets list.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    A single entry in the `multiscales.datasets` list.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
-    Attributes:
+    Attributes
     ----------
     path: str
-        The path to the zarr array that stores the image described by this metadata.
-        This path should be relative to the group that contains this metadata.
+        The path to the Zarr array that stores the image described by this metadata. This path should be relative to the group that contains this metadata.
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
+
     """
 
     path: str
@@ -80,7 +78,7 @@ class Dataset(StrictBase):
 
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that there are between 2 and 5 axes (inclusive)
+    Ensures that there are between 2 and 5 axes (inclusive)
     """
     if (len_axes := len(axes)) not in VALID_NDIM:
         msg = f"Incorrect number of axes provided ({len_axes}). Only 2, 3, 4, or 5 axes are allowed."
@@ -90,7 +88,7 @@ def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that the names of the axes are unique
+    Ensures that the names of the axes are unique.
     """
     name_dupes = duplicates(a.name for a in axes)
     if len(name_dupes) > 0:
@@ -101,12 +99,13 @@ def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that the following conditions hold:
-        - there are only 2 or 3 axes with type "space"
-        - the axes with type "space" are last in the list of axes
-        - there is only 1 axis with type "time"
-        - there is only 1 axis with type "channel"
-        - there is only 1 axis with a custom type
+        Ensures that the following conditions are true:
+
+        - there are only 2 or 3 axes with type `space`
+        - the axes with type `space` are last in the list of axes
+        - there is only 1 axis with type `time`
+        - there is only 1 axis with type `channel`
+        - there is only 1 axis with a type that is not `space`, `time`, or `channel`
     """
     axis_types = [ax.type for ax in axes]
     type_census = Counter(axis_types)
@@ -137,7 +136,8 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
 class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
     ----------
@@ -153,7 +153,8 @@ class MultiscaleMetadata(StrictVersionedBase):
     axes: List[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
     coordinateTransformations: List[tx.Scale, tx.Translation]
-
+        Coordinate transformations that express a scaling and translation shared by all elements of 
+        `datasets`.
     """
 
     _version = version
@@ -168,14 +169,19 @@ class MultiscaleMetadata(StrictVersionedBase):
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
     ]
-
     coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
 class GroupAttrs(BaseModel):
     """
-    Attributes of a multiscale group.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    A model of the required attributes of a Zarr group that implements OME-NGFF Multiscales metadata.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.    
+    
+    Attributes
+    ----------
+    multiscales: List[MultiscaleMetadata]
+        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image. 
     """
 
     multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
@@ -183,7 +189,9 @@ class GroupAttrs(BaseModel):
 
 class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
-    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
     ----------
@@ -194,6 +202,31 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+    @classmethod
+    def from_arrays(
+        cls, 
+        arrays: npt.NDArray[Any],
+        paths: Sequence[str],
+        transforms: Sequence[Sequence[tx.Transform]],
+        axes: Sequence[Axis],
+        *, 
+        name: str | None = None, 
+        type: str | None = None, 
+        metadata: Dict[str, Any] | None = None,
+        top_level_transforms: List[tx.Transform] | None = None, 
+        **kwargs):
+            """
+            Create a `Group` from a sequence of arrays + spatial metadata.
+            """
+            members = {key: ArraySpec.from_array(arr, **kwargs) for key, arr in zip(paths, arrays, strict=True)}
+            multimeta = MultiscaleMetadata(
+                name=name, 
+                type=type,
+                metadata=metadata,
+                axes=axes,
+                datasets=[Dataset(path=path, coordinateTransformations=txs) for path, txs in zip(paths, transforms, strict=True)],
+                coordinateTransformations=top_level_transforms)
+            return cls(members=members, attributes=multimeta)
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 3a03b9a..b5c3e41 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -51,12 +51,12 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, Union[well.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
-    def contains_well(
+    def contains_well_group(
         cls, members: Union[Group, GroupSpec, ArraySpec]
     ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a WellGroup
         """
-        if not any(map(lambda v: isinstance(v, Group), members.values())):
+        if not any(map(lambda v: isinstance(v, well.Group), members.values())):
             raise ValidationError
         return members
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 729b5f3..adf5af1 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -6,17 +6,34 @@
 
 class Identity(StrictBase):
     """
-    An identity transform. It has no parameters, and no valid use according to the spec.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    An identity transform. It has no parameters other than `type`, and no valid use according to the spec.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+
+    type: Literal["identity"]
+        The string "identity".
+
     """
 
-    type: str = "identity"
+    type: Literal["identity"] = "identity"
 
 
 class PathTranslation(StrictBase):
     """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A translation transformation with a `path` field. The spec states that `path` should resolve to "binary data".
+
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+    
+    Attributes
+    ----------
+
+    type: Literal["translation"]
+        The string "translation".
+    path: str
+        A string reference to something that can be interpreted as defining a translation transformation.
     """
 
     type: Literal["translation"] = "translation"
@@ -25,8 +42,16 @@ class PathTranslation(StrictBase):
 
 class PathScale(StrictBase):
     """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A scaling transformation with a `path` field. The spec states that `path` should resolve to "binary data".
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["scale"]
+        The string "scale".
+    path: str
+        A string reference to something that can be interpreted as defining a scaling transformation.
     """
 
     type: Literal["scale"] = "scale"
@@ -35,8 +60,16 @@ class PathScale(StrictBase):
 
 class VectorTranslation(StrictBase):
     """
-    A translation transform with a `translate` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A translation transformation defined by a sequence of numbers.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["translation"]
+        The string "translation".
+    translation: Sequence[float | int]
+        A sequence of numbers that define an N-dimensional translation transformation.
     """
 
     type: Literal["translation"] = "translation"
@@ -45,8 +78,16 @@ class VectorTranslation(StrictBase):
 
 class VectorScale(StrictBase):
     """
-    A scale transform with a `scale` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A scaling transformation defined by a sequence of numbers.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["scale"]
+        The string "scale".
+    scale: Sequence[float | int]
+        A sequence of numbers that define an  N-dimensional scaling transformation.
     """
 
     type: Literal["scale"] = "scale"
@@ -57,7 +98,7 @@ def ndim(
     transform: Union[VectorScale, VectorTranslation],
 ) -> int:
     """
-    Get the dimensionality of a vector transform (scale or translation).
+    Get the dimensionality of a `VectorScale` or `VectorTranslation`.
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
@@ -76,15 +117,15 @@ def scale_translation(
     scale: Sequence[float], translation: Sequence[float]
 ) -> Tuple[Scale, Translation]:
     """
-    Create a scale and transformation transformation from a scale and a translation parameter
+    Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
     """
     len_scale = len(scale)
     len_translation = len(translation)
     if len_scale < 1:
-        msg = f"Not enough values in scale. Got {len_scale}"
+        msg = f"Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation < 1:
-        msg = f"Not enough values in `tranlsation`. Got {len_translation}"
+        msg = f"Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation != len_scale:
         msg = (
@@ -100,12 +141,11 @@ def scale_translation(
 Translation = VectorTranslation | PathTranslation
 Transform = Scale | Translation
 
-
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
     """
-    Ensure that the elements of `Sequence[VectorTransform]`
+    Ensures that the elements in the input sequence define transformations with identical dimensionality.
     """
     ndims = tuple(ndim(tx) for tx in transforms)
     ndims_set = set(ndims)
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 170c3db..c9c6780 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -32,12 +32,12 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, Union[multiscales.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
-    def contains_well(
+    def contains_multiscale_group(
         cls, members: Union[Group, GroupSpec, ArraySpec]
     ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a MultiscaleGroup
         """
-        if not any(map(lambda v: isinstance(v, Group), members.values())):
+        if not any(map(lambda v: isinstance(v, multiscales.Group), members.values())):
             raise ValidationError
         return members

From 845bf4ecba8038475119636c1b15944335448c5b Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 12 Feb 2024 12:05:05 +0100
Subject: [PATCH 10/69] docs: add mkdocs.yml

---
 mkdocs.yml     |  63 ++++
 poetry.lock    | 896 ++++++++++++++++++++++++++++++++++++++++---------
 pyproject.toml |   7 +
 3 files changed, 808 insertions(+), 158 deletions(-)
 create mode 100644 mkdocs.yml

diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..a358917
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,63 @@
+site_name: pydantic-ome-ngff
+site_url: https://janeliascicomp.github.io/pydantic-ome-ngff/
+site_author: Davis Bennett
+site_description: >-
+  Pydantic models for the OME-NGFF file format.
+
+# Repository
+repo_name: janeliascicomp/pydantic-ome-ngff
+repo_url: https://github.com/janeliascicomp/pydantic-zarr
+
+# Copyright
+copyright: Copyright &copy; 2016 - 2023 HHMI / Janelia
+
+theme:
+  features:
+    - navigation.expand
+  name: material
+  palette: 
+  # Palette toggle for light mode
+  - scheme: default
+    toggle:
+      icon: material/brightness-7 
+      name: Switch to dark mode
+
+  # Palette toggle for dark mode
+  - scheme: slate
+    toggle:
+      icon: material/brightness-4
+      name: Switch to light mode
+
+nav:
+    - About: index.md
+    - API:
+      - v04:
+        - api/v04/multiscales.md
+        - api/v04/axis.md
+        - api/v04/transforms.md
+
+plugins:
+- mkdocstrings:
+    handlers:
+        python:
+          options:
+            docstring_style: numpy
+            members_order: source
+            separate_signature: true
+            filters: ["!^_"]
+            docstring_options:
+              ignore_init_summary: true
+            merge_init_into_class: true
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - toc:
+      baselevel: 2
+      toc_depth: 4
+      permalink: "#"
diff --git a/poetry.lock b/poetry.lock
index eeb582f..7f86b0e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,24 +2,24 @@
 
 [[package]]
 name = "aiobotocore"
-version = "2.9.0"
+version = "2.11.1"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.9.0-py3-none-any.whl", hash = "sha256:acf5e49644e6e434b9ecc26284ae7e05d557effbdcdd8185e2eb08925f011853"},
-    {file = "aiobotocore-2.9.0.tar.gz", hash = "sha256:4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e"},
+    {file = "aiobotocore-2.11.1-py3-none-any.whl", hash = "sha256:904a7ad7cc8671d662cfd596906dafe839118ea2a66332c37908e3dcfdee1e45"},
+    {file = "aiobotocore-2.11.1.tar.gz", hash = "sha256:0b095af50da2d6f94e93ca959e2a4876f0f0d84d534b61b21d8e050832d04ab6"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.33.2,<1.33.14"
+botocore = ">=1.33.2,<1.34.28"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.31.2,<1.31.14)"]
-boto3 = ["boto3 (>=1.33.2,<1.33.14)"]
+awscli = ["awscli (>=1.31.2,<1.32.28)"]
+boto3 = ["boto3 (>=1.33.2,<1.34.28)"]
 
 [[package]]
 name = "aiohttp"
@@ -193,15 +193,75 @@ tests = ["attrs[tests-no-zope]", "zope-interface"]
 tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
 tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "black"
+version = "24.1.0"
+description = "The uncompromising code formatter."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "black-24.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:94d5280d020dadfafc75d7cae899609ed38653d3f5e82e7ce58f75e76387ed3d"},
+    {file = "black-24.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:aaf9aa85aaaa466bf969e7dd259547f4481b712fe7ee14befeecc152c403ee05"},
+    {file = "black-24.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ec489cae76eac3f7573629955573c3a0e913641cafb9e3bfc87d8ce155ebdb29"},
+    {file = "black-24.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:a5a0100b4bdb3744dd68412c3789f472d822dc058bb3857743342f8d7f93a5a7"},
+    {file = "black-24.1.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6cc5a6ba3e671cfea95a40030b16a98ee7dc2e22b6427a6f3389567ecf1b5262"},
+    {file = "black-24.1.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:e0e367759062dcabcd9a426d12450c6d61faf1704a352a49055a04c9f9ce8f5a"},
+    {file = "black-24.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:be305563ff4a2dea813f699daaffac60b977935f3264f66922b1936a5e492ee4"},
+    {file = "black-24.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:6a8977774929b5db90442729f131221e58cc5d8208023c6af9110f26f75b6b20"},
+    {file = "black-24.1.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:d74d4d0da276fbe3b95aa1f404182562c28a04402e4ece60cf373d0b902f33a0"},
+    {file = "black-24.1.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:39addf23f7070dbc0b5518cdb2018468ac249d7412a669b50ccca18427dba1f3"},
+    {file = "black-24.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:827a7c0da520dd2f8e6d7d3595f4591aa62ccccce95b16c0e94bb4066374c4c2"},
+    {file = "black-24.1.0-cp312-cp312-win_amd64.whl", hash = "sha256:0cd59d01bf3306ff7e3076dd7f4435fcd2fafe5506a6111cae1138fc7de52382"},
+    {file = "black-24.1.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:bf8dd261ee82df1abfb591f97e174345ab7375a55019cc93ad38993b9ff5c6ad"},
+    {file = "black-24.1.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:82d9452aeabd51d1c8f0d52d4d18e82b9f010ecb30fd55867b5ff95904f427ff"},
+    {file = "black-24.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9aede09f72b2a466e673ee9fca96e4bccc36f463cac28a35ce741f0fd13aea8b"},
+    {file = "black-24.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:780f13d03066a7daf1707ec723fdb36bd698ffa29d95a2e7ef33a8dd8fe43b5c"},
+    {file = "black-24.1.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a15670c650668399c4b5eae32e222728185961d6ef6b568f62c1681d57b381ba"},
+    {file = "black-24.1.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:1e0fa70b8464055069864a4733901b31cbdbe1273f63a24d2fa9d726723d45ac"},
+    {file = "black-24.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7fa8d9aaa22d846f8c0f7f07391148e5e346562e9b215794f9101a8339d8b6d8"},
+    {file = "black-24.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:f0dfbfbacfbf9cd1fac7a5ddd3e72510ffa93e841a69fcf4a6358feab1685382"},
+    {file = "black-24.1.0-py3-none-any.whl", hash = "sha256:5134a6f6b683aa0a5592e3fd61dd3519d8acd953d93e2b8b76f9981245b65594"},
+    {file = "black-24.1.0.tar.gz", hash = "sha256:30fbf768cd4f4576598b1db0202413fafea9a227ef808d1a12230c643cefe9fc"},
+]
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
 [[package]]
 name = "botocore"
-version = "1.33.13"
+version = "1.34.27"
 description = "Low-level, data-driven core of boto 3."
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
-    {file = "botocore-1.33.13-py3-none-any.whl", hash = "sha256:aeadccf4b7c674c7d47e713ef34671b834bc3e89723ef96d994409c9f54666e6"},
-    {file = "botocore-1.33.13.tar.gz", hash = "sha256:fb577f4cb175605527458b04571451db1bd1a2036976b626206036acd4496617"},
+    {file = "botocore-1.34.27-py3-none-any.whl", hash = "sha256:1c10f247136ad17b6ef1588c1e043e294dbaebdebe9ce84dc56713029f515c53"},
+    {file = "botocore-1.34.27.tar.gz", hash = "sha256:a0e68ba264275b358b8c1cca604161f4d9465cf7847d73e929543a9f30ff22d1"},
 ]
 
 [package.dependencies]
@@ -210,7 +270,7 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.19.17)"]
+crt = ["awscrt (==0.19.19)"]
 
 [[package]]
 name = "certifi"
@@ -333,6 +393,20 @@ files = [
     {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"},
 ]
 
+[[package]]
+name = "click"
+version = "8.1.7"
+description = "Composable command line interface toolkit"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -584,6 +658,37 @@ smb = ["smbprotocol"]
 ssh = ["paramiko"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "ghp-import"
+version = "2.1.0"
+description = "Copy your docs directly to the gh-pages branch."
+optional = false
+python-versions = "*"
+files = [
+    {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"},
+    {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.8.1"
+
+[package.extras]
+dev = ["flake8", "markdown", "twine", "wheel"]
+
+[[package]]
+name = "griffe"
+version = "0.39.1"
+description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "griffe-0.39.1-py3-none-any.whl", hash = "sha256:6ce4ecffcf0d2f96362c5974b3f7df812da8f8d4cfcc5ebc8202ef72656fc087"},
+    {file = "griffe-0.39.1.tar.gz", hash = "sha256:ead8dfede6e6531cce6bf69090a4f3c6d36fdf923c43f8e85aa530552cef0c09"},
+]
+
+[package.dependencies]
+colorama = ">=0.4"
+
 [[package]]
 name = "identify"
 version = "2.5.33"
@@ -634,6 +739,23 @@ files = [
 [package.extras]
 colors = ["colorama (>=0.4.6)"]
 
+[[package]]
+name = "jinja2"
+version = "3.1.3"
+description = "A very fast and expressive template engine."
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
 [[package]]
 name = "jmespath"
 version = "1.0.1"
@@ -647,13 +769,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.20.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
 ]
 
 [package.dependencies]
@@ -680,6 +802,21 @@ files = [
 [package.dependencies]
 referencing = ">=0.31.0"
 
+[[package]]
+name = "markdown"
+version = "3.5.2"
+description = "Python implementation of John Gruber's Markdown."
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.extras]
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+testing = ["coverage", "pyyaml"]
+
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -704,6 +841,75 @@ profiling = ["gprof2dot"]
 rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
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+version = "2.1.4"
+description = "Safely add untrusted strings to HTML/XML markup."
+optional = false
+python-versions = ">=3.7"
+files = [
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+
 [[package]]
 name = "mdurl"
 version = "0.1.2"
@@ -715,6 +921,144 @@ files = [
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 ]
 
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+optional = false
+python-versions = ">=3.6"
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+description = "Project documentation with Markdown."
+optional = false
+python-versions = ">=3.7"
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 ]
 
 [package.extras]
@@ -1181,6 +1546,24 @@ files = [
 plugins = ["importlib-metadata"]
 windows-terminal = ["colorama (>=0.4.6)"]
 
+[[package]]
+name = "pymdown-extensions"
+version = "10.7"
+description = "Extension pack for Python Markdown."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pymdown_extensions-10.7-py3-none-any.whl", hash = "sha256:6ca215bc57bc12bf32b414887a68b810637d039124ed9b2e5bd3325cbb2c050c"},
+    {file = "pymdown_extensions-10.7.tar.gz", hash = "sha256:c0d64d5cf62566f59e6b2b690a4095c931107c250a8c8e1351c1de5f6b036deb"},
+]
+
+[package.dependencies]
+markdown = ">=3.5"
+pyyaml = "*"
+
+[package.extras]
+extra = ["pygments (>=2.12)"]
+
 [[package]]
 name = "pytest"
 version = "7.4.4"
@@ -1221,6 +1604,22 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
+[[package]]
+name = "pytest-examples"
+version = "0.0.9"
+description = "Pytest plugin for testing examples in docstrings and markdown files."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest_examples-0.0.9-py3-none-any.whl", hash = "sha256:a37c798289580bd8fce47582a67cf821e6dda0d45b63fa8e9cbbd4713ed2bf08"},
+    {file = "pytest_examples-0.0.9.tar.gz", hash = "sha256:d5f9d670d4ae16f55f3e4ef79949e1133ee5e52856cc482fb9e305f2cdf4016a"},
+]
+
+[package.dependencies]
+black = ">=23"
+pytest = ">=7"
+ruff = ">=0.0.258"
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.2"
@@ -1294,21 +1693,137 @@ files = [
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
+[[package]]
+name = "pyyaml-env-tag"
+version = "0.1"
+description = "A custom YAML tag for referencing environment variables in YAML files. "
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pyyaml_env_tag-0.1-py3-none-any.whl", hash = "sha256:af31106dec8a4d68c60207c1886031cbf839b68aa7abccdb19868200532c2069"},
+    {file = "pyyaml_env_tag-0.1.tar.gz", hash = "sha256:70092675bda14fdec33b31ba77e7543de9ddc88f2e5b99160396572d11525bdb"},
+]
+
+[package.dependencies]
+pyyaml = "*"
+
 [[package]]
 name = "referencing"
-version = "0.32.0"
+version = "0.32.1"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "referencing-0.32.0-py3-none-any.whl", hash = "sha256:bdcd3efb936f82ff86f993093f6da7435c7de69a3b3a5a06678a6050184bee99"},
-    {file = "referencing-0.32.0.tar.gz", hash = "sha256:689e64fe121843dcfd57b71933318ef1f91188ffb45367332700a86ac8fd6161"},
+    {file = "referencing-0.32.1-py3-none-any.whl", hash = "sha256:7e4dc12271d8e15612bfe35792f5ea1c40970dadf8624602e33db2758f7ee554"},
+    {file = "referencing-0.32.1.tar.gz", hash = "sha256:3c57da0513e9563eb7e203ebe9bb3a1b509b042016433bd1e45a2853466c3dd3"},
 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
 rpds-py = ">=0.7.0"
 
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-content-hash = "ee46872069c5871528c57be240af3e1e784f1130e07bf77eff4c00621f71004e"
+content-hash = "f5afbf936caecbd37768b0fbdbbd193014831dfdf71897f94aaad8e20798b31a"
diff --git a/pyproject.toml b/pyproject.toml
index 1f2df7c..68d523e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,7 @@ pydantic-zarr = "0.5.2"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
 rich = "^13.6.0"
+mkdocs-material = "^9.5.5"
 
 
 [tool.poetry.group.dev.dependencies]
@@ -24,6 +25,12 @@ mypy = "^1.0.1"
 requests = "^2.28.2"
 pytest-cov = "^4.0.0"
 
+
+[tool.poetry.group.docs.dependencies]
+mkdocs-material = "^9.5.5"
+mkdocstrings = {extras = ["python"], version = "^0.24.0"}
+pytest-examples = "^0.0.9"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

From 62ab448d06b25402e9bf6f8090d110ee2ed2759f Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 14:04:20 +0100
Subject: [PATCH 11/69] merge branch "use_pydantic_zarr" from origin

---
 src/pydantic_ome_ngff/__about__.py          |  4 +
 src/pydantic_ome_ngff/base.py               |  4 -
 src/pydantic_ome_ngff/latest/base.py        |  8 +-
 src/pydantic_ome_ngff/latest/label.py       |  4 +-
 src/pydantic_ome_ngff/latest/multiscales.py |  2 +-
 src/pydantic_ome_ngff/latest/plate.py       |  5 +-
 src/pydantic_ome_ngff/latest/transforms.py  |  2 +
 src/pydantic_ome_ngff/latest/well.py        |  5 +-
 src/pydantic_ome_ngff/utils.py              |  4 +-
 src/pydantic_ome_ngff/v04/axis.py           | 17 +++--
 src/pydantic_ome_ngff/v04/multiscales.py    | 85 ++++++++++++---------
 src/pydantic_ome_ngff/v04/plate.py          |  7 +-
 src/pydantic_ome_ngff/v04/transforms.py     | 25 +++---
 src/pydantic_ome_ngff/v04/well.py           |  8 +-
 tests/conftest.py                           |  5 +-
 tests/latest/test_multiscales.py            | 17 +++--
 tests/v04/test_multiscales.py               | 45 ++++++++---
 17 files changed, 151 insertions(+), 96 deletions(-)
 create mode 100644 src/pydantic_ome_ngff/__about__.py

diff --git a/src/pydantic_ome_ngff/__about__.py b/src/pydantic_ome_ngff/__about__.py
new file mode 100644
index 0000000..9068a16
--- /dev/null
+++ b/src/pydantic_ome_ngff/__about__.py
@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2023-present Davis Vann Bennett <davis.v.bennett@gmail.com>
+#
+# SPDX-License-Identifier: MIT
+__version__ = "0.3.0"
diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index 2216443..acb4010 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -6,8 +6,6 @@ class StrictBase(BaseModel, extra="forbid"):
     A pydantic basemodel that refuses extra fields.
     """
 
-    ...
-
 
 class VersionedBase(BaseModel):
     """
@@ -21,5 +19,3 @@ class StrictVersionedBase(VersionedBase, StrictBase):
     """
     An internally versioned pydantic basemodel that refuses extra fields.
     """
-
-    ...
diff --git a/src/pydantic_ome_ngff/latest/base.py b/src/pydantic_ome_ngff/latest/base.py
index 17d27e7..7998d64 100644
--- a/src/pydantic_ome_ngff/latest/base.py
+++ b/src/pydantic_ome_ngff/latest/base.py
@@ -1 +1,7 @@
-version = "0.5-dev"
+from __future__ import annotations
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Literal
+
+version: Literal["0.5-dev"] = "0.5-dev"
diff --git a/src/pydantic_ome_ngff/latest/label.py b/src/pydantic_ome_ngff/latest/label.py
index 18e6697..0f8212f 100644
--- a/src/pydantic_ome_ngff/latest/label.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -1,5 +1,7 @@
-from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
+from __future__ import annotations
+
 from pydantic_ome_ngff.latest.base import version
+from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
 
 
 class ImageLabel(ImageLabelV04):
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 8f43d4d..733dfaf 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,5 +1,5 @@
+from __future__ import annotations
 from typing import Literal
-
 from pydantic_ome_ngff.latest.base import version
 import pydantic_ome_ngff.v04.multiscales as msv04
 
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index 69ba478..d6d85f5 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -1,5 +1,4 @@
-from typing import Optional
-
+from __future__ import annotations
 
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.v04.plate import PlateMetadata as PlateMetaV04
@@ -12,4 +11,4 @@ class PlateMeta(PlateMetaV04):
     """
 
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index 7198077..d2ab7c5 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Union
 import pydantic_ome_ngff.v04.transforms as tx
 
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index 1004d07..b3dbad3 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,4 +1,5 @@
-from typing import Optional
+from __future__ import annotations
+
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.v04.well import WellMetadata as WellMetaV04
 
@@ -12,4 +13,4 @@ class WellMeta(WellMetaV04):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index b1b71bc..88b80de 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -1,8 +1,8 @@
 from collections import Counter
-from typing import Dict, Iterable, Hashable
+from collections.abc import Hashable, Iterable
 
 
-def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
+def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
     elements of the input that occurred at least once, and the values are the
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 8e6a511..e0fb97a 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,17 +1,18 @@
 from __future__ import annotations
+from enum import Enum
+import warnings
 
 from pydantic import model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
-import warnings
-from enum import Enum
 
 
 class AxisType(str, Enum):
     """
     String enum representing the three axis types (`space`, `time`, `channel`) defined in the specification.
     """
+
     space = "space"
     time = "time"
     channel = "channel"
@@ -83,19 +84,19 @@ def check_type_unit(model: Axis) -> Axis:
     unit = model.unit
 
     if typ == AxisType.space:
-         if unit not in [e.value for e in SpaceUnit]:
+        if unit not in [e.value for e in SpaceUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
-            warnings.warn(msg)
+            warnings.warn(msg, stacklevel=1)
     elif typ == AxisType.time:
         if unit not in [e.value for e in TimeUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
-            warnings.warn(msg)
+            warnings.warn(msg, stacklevel=1)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -103,21 +104,21 @@ def check_type_unit(model: Axis) -> Axis:
             f"The `type` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the 'type' field of an axis should be set to a string."
         )
-        warnings.warn(msg, UserWarning)
+        warnings.warn(msg, stacklevel=1)
     else:
         msg = (
             f"Unknown axis type '{typ}'. Version {model._version} of the OME-NGFF "
             " spec states that the 'type' field of an axis should be one of "
             f"{AxisType._member_names_}."
         )
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=1)
 
     if unit is None:
         msg = (
             f"The `unit` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the `unit` field of an axis should be set to a string."
         )
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=1)
     return model
 
 
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 99d0778..1361cbd 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from collections import Counter
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 
@@ -11,12 +13,14 @@
 import numpy.typing as npt
 
 VALID_NDIM = (2, 3, 4, 5)
+NUM_TX_MAX = 2
+
 
 def ensure_scale_translation(
     transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
 ) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
-    Ensures that the first element is a scale transformation, the second element, 
+    Ensures that the first element is a scale transformation, the second element,
     if present, is a translation transform, and that there are only 1 or 2 transforms.
     """
 
@@ -31,7 +35,7 @@ def ensure_scale_translation(
             f"transform. Got {maybe_scale} instead."
         )
         raise ValueError(msg)
-    if len(transforms) == 2:
+    if len(transforms) == NUM_TX_MAX:
         maybe_trans = transforms[1]
         if (maybe_trans.type) != "translation":
             msg = (
@@ -55,7 +59,7 @@ def ensure_transforms_length(
 class Dataset(StrictBase):
     """
     A single entry in the `multiscales.datasets` list.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -99,13 +103,13 @@ def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-        Ensures that the following conditions are true:
+    Ensures that the following conditions are true:
 
-        - there are only 2 or 3 axes with type `space`
-        - the axes with type `space` are last in the list of axes
-        - there is only 1 axis with type `time`
-        - there is only 1 axis with type `channel`
-        - there is only 1 axis with a type that is not `space`, `time`, or `channel`
+    - there are only 2 or 3 axes with type `space`
+    - the axes with type `space` are last in the list of axes
+    - there is only 1 axis with type `time`
+    - there is only 1 axis with type `channel`
+    - there is only 1 axis with a type that is not `space`, `time`, or `channel`
     """
     axis_types = [ax.type for ax in axes]
     type_census = Counter(axis_types)
@@ -114,7 +118,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
         msg = f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes are allowed."
         raise ValueError(msg)
 
-    elif not all(a == "space" for a in axis_types[-num_spaces:]):
+    if not all(a == "space" for a in axis_types[-num_spaces:]):
         msg = f"Space axes must come last. Got axes with order: {axis_types}."
         raise ValueError(msg)
 
@@ -136,7 +140,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
 class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -153,7 +157,7 @@ class MultiscaleMetadata(StrictVersionedBase):
     axes: List[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
     coordinateTransformations: List[tx.Scale, tx.Translation]
-        Coordinate transformations that express a scaling and translation shared by all elements of 
+        Coordinate transformations that express a scaling and translation shared by all elements of
         `datasets`.
     """
 
@@ -164,7 +168,7 @@ class MultiscaleMetadata(StrictVersionedBase):
     metadata: Dict[str, Any] | None = None
     datasets: Annotated[List[Dataset], Field(..., min_length=1)]
     axes: Annotated[
-        List[Axis],
+        list[Axis],
         AfterValidator(ensure_axis_length),
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
@@ -175,13 +179,13 @@ class MultiscaleMetadata(StrictVersionedBase):
 class GroupAttrs(BaseModel):
     """
     A model of the required attributes of a Zarr group that implements OME-NGFF Multiscales metadata.
-    
-    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.    
-    
+
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
+
     Attributes
     ----------
     multiscales: List[MultiscaleMetadata]
-        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image. 
+        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image.
     """
 
     multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
@@ -190,7 +194,7 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -202,31 +206,40 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+
     @classmethod
     def from_arrays(
-        cls, 
+        cls,
         arrays: npt.NDArray[Any],
         paths: Sequence[str],
         transforms: Sequence[Sequence[tx.Transform]],
         axes: Sequence[Axis],
-        *, 
-        name: str | None = None, 
-        type: str | None = None, 
+        *,
+        name: str | None = None,
+        type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        top_level_transforms: List[tx.Transform] | None = None, 
-        **kwargs):
-            """
-            Create a `Group` from a sequence of arrays + spatial metadata.
-            """
-            members = {key: ArraySpec.from_array(arr, **kwargs) for key, arr in zip(paths, arrays, strict=True)}
-            multimeta = MultiscaleMetadata(
-                name=name, 
-                type=type,
-                metadata=metadata,
-                axes=axes,
-                datasets=[Dataset(path=path, coordinateTransformations=txs) for path, txs in zip(paths, transforms, strict=True)],
-                coordinateTransformations=top_level_transforms)
-            return cls(members=members, attributes=multimeta)
+        top_level_transforms: List[tx.Transform] | None = None,
+        **kwargs,
+    ):
+        """
+        Create a `Group` from a sequence of arrays + spatial metadata.
+        """
+        members = {
+            key: ArraySpec.from_array(arr, **kwargs)
+            for key, arr in zip(paths, arrays, strict=True)
+        }
+        multimeta = MultiscaleMetadata(
+            name=name,
+            type=type,
+            metadata=metadata,
+            axes=axes,
+            datasets=[
+                Dataset(path=path, coordinateTransformations=txs)
+                for path, txs in zip(paths, transforms, strict=True)
+            ],
+            coordinateTransformations=top_level_transforms,
+        )
+        return cls(members=members, attributes=multimeta)
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index b5c3e41..575aea9 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,10 +1,11 @@
 from __future__ import annotations
-from typing import List, Optional
+from typing import List
 
 from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
+
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
 import pydantic_ome_ngff.v04.well as well
@@ -12,7 +13,7 @@
 
 class Acquisition(BaseModel):
     id: PositiveInt
-    name: Optional[str] = None
+    name: str | None = None
     maximumfieldcount: PositiveInt
 
 
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index adf5af1..3d192fc 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -1,13 +1,17 @@
 from __future__ import annotations
 
-from typing import Literal, Sequence, Tuple, Union
+from typing import TYPE_CHECKING, Literal
+
 from pydantic_ome_ngff.base import StrictBase
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 
 class Identity(StrictBase):
     """
     An identity transform. It has no parameters other than `type`, and no valid use according to the spec.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -26,7 +30,7 @@ class PathTranslation(StrictBase):
     A translation transformation with a `path` field. The spec states that `path` should resolve to "binary data".
 
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
-    
+
     Attributes
     ----------
 
@@ -43,7 +47,7 @@ class PathTranslation(StrictBase):
 class PathScale(StrictBase):
     """
     A scaling transformation with a `path` field. The spec states that `path` should resolve to "binary data".
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -61,7 +65,7 @@ class PathScale(StrictBase):
 class VectorTranslation(StrictBase):
     """
     A translation transformation defined by a sequence of numbers.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -79,7 +83,7 @@ class VectorTranslation(StrictBase):
 class VectorScale(StrictBase):
     """
     A scaling transformation defined by a sequence of numbers.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -95,7 +99,7 @@ class VectorScale(StrictBase):
 
 
 def ndim(
-    transform: Union[VectorScale, VectorTranslation],
+    transform: VectorScale | VectorTranslation,
 ) -> int:
     """
     Get the dimensionality of a `VectorScale` or `VectorTranslation`.
@@ -115,17 +119,17 @@ def ndim(
 
 def scale_translation(
     scale: Sequence[float], translation: Sequence[float]
-) -> Tuple[Scale, Translation]:
+) -> tuple[Scale, Translation]:
     """
     Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
     """
     len_scale = len(scale)
     len_translation = len(translation)
     if len_scale < 1:
-        msg = f"Not enough values in scale. Got 0, expected at least 1."
+        msg = "Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation < 1:
-        msg = f"Not enough values in `translation`. Got 0, expected at least 1."
+        msg = "Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation != len_scale:
         msg = (
@@ -141,6 +145,7 @@ def scale_translation(
 Translation = VectorTranslation | PathTranslation
 Transform = Scale | Translation
 
+
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index c9c6780..c900962 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,17 +1,17 @@
 from __future__ import annotations
-from typing import List, Optional, Union
+from typing import List, Union
 
 from pydantic import BaseModel, ValidationError, field_validator
-from pydantic_ome_ngff.base import VersionedBase
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
 
+from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
 import pydantic_ome_ngff.v04.multiscales as multiscales
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class Image(BaseModel):
     path: str
-    acquisition: Optional[int]
+    acquisition: int | None
 
 
 class WellMetadata(VersionedBase):
diff --git a/tests/conftest.py b/tests/conftest.py
index 47b5ae7..c5e2e12 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,8 +1,9 @@
-from typing import Tuple, Any
+from typing import Any
+
 import requests
 
 
-def fetch_schemas(version: str, schema_name: str) -> Tuple[Any, Any]:
+def fetch_schemas(version: str, schema_name: str) -> tuple[Any, Any]:
     """
     Get the relaxed and strict schemas for a given version of the spec.
     """
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index f895721..daad28d 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -4,6 +4,8 @@
 import pytest
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
+
+from pydantic_ome_ngff.latest.axis import Axis
 from pydantic_ome_ngff.latest.multiscales import (
     MultiscaleMetadata,
     GroupAttrs,
@@ -16,7 +18,6 @@
     VectorScale,
     VectorTranslation,
 )
-from pydantic_ome_ngff.latest.axis import Axis
 from tests.conftest import fetch_schemas
 
 
@@ -127,10 +128,10 @@ def test_multiscale_unique_axis_names() -> None:
 
 @pytest.mark.parametrize(
     "axis_types",
-    (
+    [
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-    ),
+    ],
 )
 def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
@@ -175,7 +176,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
         )
 
 
-@pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
+@pytest.mark.parametrize("num_axes", [0, 1, 6, 7])
 def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
@@ -228,7 +229,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorScale(scale=(1, 1, 1)),
             VectorTranslation(translation=(1, 1, 1)),
@@ -238,7 +239,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
             VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
@@ -249,7 +250,7 @@ def test_coordinate_transforms_invalid_length(
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorTranslation(translation=(1, 1, 1)),
         ]
@@ -258,7 +259,7 @@ def test_coordinate_transforms_invalid_length(
             VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index b4ca419..c0caf54 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import List, Optional, Tuple
+from typing import Tuple
 from pydantic import ValidationError
 import pytest
 import jsonschema as jsc
@@ -127,12 +127,12 @@ def test_multiscale_unique_axis_names() -> None:
 
 @pytest.mark.parametrize(
     "axis_types",
-    (
+    [
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-    ),
+    ],
 )
-def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes = [
         Axis(name=str(idx), type=t, unit=units_map.get(t, None))
@@ -175,7 +175,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
         )
 
 
-@pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
+@pytest.mark.parametrize("num_axes", [0, 1, 6, 7])
 def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
@@ -221,14 +221,14 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     ]
     with pytest.raises(
         ValidationError,
-        match="The transforms have inconsistent dimensionality.",  # noqa
+        match="The transforms have inconsistent dimensionality.",
     ):
         Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorScale(scale=(1, 1, 1)),
             VectorTranslation(translation=(1, 1, 1)),
@@ -238,10 +238,10 @@ def test_coordinate_transforms_invalid_ndims() -> None:
             VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: List[Transform],
+    transforms: list[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
         Dataset(path="foo", coordinateTransformations=transforms)
@@ -249,7 +249,7 @@ def test_coordinate_transforms_invalid_length(
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorTranslation(translation=(1, 1, 1)),
         ]
@@ -258,7 +258,7 @@ def test_coordinate_transforms_invalid_length(
             VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
@@ -301,6 +301,13 @@ def test_multiscale_group_datasets_exist(
     }
     Group(attributes=group_attrs, members=good_items)
 
+    bad_items = {
+        d.path + "x": ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
+        for d in default_multiscale.datasets
+    }
+
     with pytest.raises(
         ValidationError,
         match="array with that name was found in the items of that group.",
@@ -324,6 +331,17 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
     }
     Group(attributes=group_attrs, members=good_items)
 
+    # arrays with varying rank
+    bad_items = {
+        d.path: ArraySpec(
+            shape=(1,) * (idx + 1),
+            dtype="uint8",
+            chunks=(1,) * (idx + 1),
+            attributes={},
+        )
+        for idx, d in enumerate(default_multiscale.datasets)
+    }
+
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
@@ -339,6 +357,11 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
         }
         Group(attributes=group_attrs, members=bad_items)
 
+    # arrays with rank that doesn't match the transform
+    bad_items = {
+        d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
+        for d in default_multiscale.datasets
+    }
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {

From 192d6e0b108346d60c37ba2c0bec82399193123d Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 13:50:56 +0100
Subject: [PATCH 12/69] tighten some names and type annotations

---
 src/pydantic_ome_ngff/latest/transforms.py | 10 ++++++++++
 src/pydantic_ome_ngff/v04/transforms.py    |  5 +----
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index d2ab7c5..583e143 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -10,6 +10,8 @@ class Identity(tx.Identity):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class PathScale(tx.PathScale):
     """ "
@@ -17,6 +19,8 @@ class PathScale(tx.PathScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class PathTranslation(tx.PathTranslation):
     """ "
@@ -24,6 +28,8 @@ class PathTranslation(tx.PathTranslation):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class VectorTranslation(tx.VectorTranslation):
     """
@@ -31,6 +37,8 @@ class VectorTranslation(tx.VectorTranslation):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class VectorScale(tx.VectorScale):
     """
@@ -38,6 +46,8 @@ class VectorScale(tx.VectorScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 Scale = Union[VectorScale, PathScale]
 Translation = Union[VectorTranslation, PathTranslation]
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 3d192fc..df1a9f5 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -1,12 +1,9 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Literal
+from typing import Literal, Sequence
 
 from pydantic_ome_ngff.base import StrictBase
 
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-
 
 class Identity(StrictBase):
     """

From 7d28336e8b0bec2a513e0c25f0cc09f5fa9fc734 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 19:41:43 +0100
Subject: [PATCH 13/69] start handling deeper arrays

---
 docs/index.md                            | 26 ++++---
 example.py                               |  5 ++
 src/pydantic_ome_ngff/utils.py           | 57 +++++++++++++-
 src/pydantic_ome_ngff/v04/axis.py        | 11 +--
 src/pydantic_ome_ngff/v04/label.py       |  7 +-
 src/pydantic_ome_ngff/v04/multiscales.py | 98 +++++++++++++++++++-----
 tests/latest/test_multiscales.py         |  2 +-
 tests/test_utils.py                      | 33 ++++++++
 tests/v04/test_axis.py                   | 18 -----
 tests/v04/test_label.py                  | 12 +--
 tests/v04/test_multiscales.py            | 60 ++++++++++++++-
 11 files changed, 256 insertions(+), 73 deletions(-)
 create mode 100644 example.py
 create mode 100644 tests/test_utils.py
 delete mode 100644 tests/v04/test_axis.py

diff --git a/docs/index.md b/docs/index.md
index 000ea34..ad01c67 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,17 +1,19 @@
-# Welcome to MkDocs
+# pydantic-ome-ngff
 
-For full documentation visit [mkdocs.org](https://www.mkdocs.org).
+[Pydantic](https://docs.pydantic.dev/latest/) models for [OME-NGFF](https://ngff.openmicroscopy.org/)
 
-## Commands
+# About
 
-* `mkdocs new [dir-name]` - Create a new project.
-* `mkdocs serve` - Start the live-reloading docs server.
-* `mkdocs build` - Build the documentation site.
-* `mkdocs -h` - Print help message and exit.
+This library aims to provide models for the the metadata objects and Zarr hierarchies described in the [OME-NGFF](https://ngff.openmicroscopy.org/) specifications.
 
-## Project layout
+# Reading Multiscale metadata
 
-    mkdocs.yml    # The configuration file.
-    docs/
-        index.md  # The documentation homepage.
-        ...       # Other markdown pages, images and other files.
+```python
+# example data on S3-compatible cloud storage
+from pydantic_ome_ngff.v04.multiscales import Group
+import zarr
+url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+zgroup = zarr.open(url)
+group = Group.from_zarr(zgroup)
+
+```
diff --git a/example.py b/example.py
new file mode 100644
index 0000000..ee18a04
--- /dev/null
+++ b/example.py
@@ -0,0 +1,5 @@
+from pydantic_ome_ngff.v04.multiscales import Group
+import zarr
+url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+zgroup = zarr.open(url)
+group = Group.from_zarr(zgroup)
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index 88b80de..7dd675c 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -1,8 +1,16 @@
+from __future__ import annotations
+from typing import TYPE_CHECKING, runtime_checkable
 from collections import Counter
-from collections.abc import Hashable, Iterable
+from typing import Protocol
+import numpy as np
 
+if TYPE_CHECKING:
+    from typing import Dict, Iterable, Hashable, Tuple
 
-def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
+import os
+
+def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
     elements of the input that occurred at least once, and the values are the
@@ -10,3 +18,48 @@ def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
     """
     counts = Counter(values)
     return {k: v for k, v in counts.items() if v > 1}
+
+
+def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, ArraySpec | GroupSpec]:
+    """
+    Flatten a `GroupSpec` or `ArraySpec`.
+    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are 
+    `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
+    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute 
+    under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
+    to the name of each member.
+
+    Paramters
+    ---------
+    node: `GroupSpec` | `ArraySpec`
+        The node to flatten.
+    path: `str`, default is '/'
+        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be 
+        made relative to `path` when used as keys in the result dictionary.
+
+    Returns
+    -------
+    `Dict[str, GroupSpec | ArraySpec]`
+
+    """
+    result = {}
+    if isinstance(node, ArraySpec):
+        model_copy = node.model_copy(deep=True)
+
+    else:
+        model_copy = node.model_copy(update={"members": {}})
+        for name, value in node.members.items():
+            result.update(flatten_node(value, os.path.join(path, name)))
+
+    result[path] = model_copy
+        
+    return result
+
+@runtime_checkable
+class ArrayLike(Protocol):
+    shape: Tuple[int, ...]
+    dtype: np.dtype
+
+@runtime_checkable
+class ChunkedArrayLike(ArrayLike, Protocol):
+    chunks: Tuple[int, ...]
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index e0fb97a..043c7b4 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 from enum import Enum
+from typing import Optional
 import warnings
 
 from pydantic import model_validator
@@ -134,16 +135,12 @@ class Axis(StrictVersionedBase):
     name: str
         The name for this axis.
     type: str | None
-        The type for this axis, e.g. `space`.
+        The type for this axis, e.g. "space".
     unit: str | None
         The unit of measure associated with the interval defined by this axis.
     """
 
     _version = version
     name: str
-    type: str | None
-    unit: str | None
-
-    @model_validator(mode="after")
-    def check_type_unit(self):
-        return check_type_unit(self)
+    type: Optional[str] = None
+    unit: Optional[str] = None
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 95ef442..7ccc5ce 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -52,11 +52,12 @@ def parse_colors(colors: List[Color] | None) -> List[Color] | None:
 
 def parse_version(version: Literal["0.4"] | None) -> Literal["0.4"] | None:
     if version is None:
-        msg = (
+        _ = (
             f"The `version` attribute is `None`. Version {NGFF_VERSION} of "
-            f"the OME-NGFF spec states that `version` must either be unset or the string {NGFF_VERSION}"
+            f"the OME-NGFF spec states that `version` should either be unset or the string {NGFF_VERSION}"
         )
-        warnings.warn(msg, stacklevel=1)
+        # This goes against a recommendation from the spec, but emitting a warning is annoying. 
+        # leaving this here as a placeholder.
     return version
 
 
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 1361cbd..a82d1e3 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -2,16 +2,15 @@
 
 from collections import Counter
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
-
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-from pydantic_ome_ngff.utils import duplicates
+from pydantic_ome_ngff.utils import ArrayLike, ChunkedArrayLike, duplicates, flatten_node
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
-import numpy.typing as npt
-
+import zarr
+from zarr.errors import ArrayNotFoundError, ContainsGroupError
 VALID_NDIM = (2, 3, 4, 5)
 NUM_TX_MAX = 2
 
@@ -80,6 +79,18 @@ class Dataset(StrictBase):
     ]
 
 
+def create_dataset(
+        path: str, 
+        scale: Sequence[int | float], 
+        translation: Sequence[int | float]) -> Dataset:
+    """
+    Create a `Dataset` from a path, a scale, and a translation.
+    """
+    return Dataset(
+        path=path,
+        coordinateTransformations=[tx.VectorScale(scale=scale), tx.VectorTranslation(translation=translation)])
+
+
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
     Ensures that there are between 2 and 5 axes (inclusive)
@@ -207,23 +218,67 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
 
     """
 
+    @classmethod
+    def from_zarr(cls, node: zarr.Group) -> Group:
+        guess = GroupSpec.from_zarr(node)
+        
+        try:
+            multi_meta_maybe = guess.attributes['multiscales']
+        except KeyError as e:
+            msg = (f"Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
+                  f"{node.store.path}/{node.path}")
+            raise ValueError(msg) from e
+        
+        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
+
+        for multiscale in multi_meta.multiscales:
+            for dataset in multiscale.datasets:
+                array_path = '/'.join([node.path, dataset.path])
+                try:
+                    array = zarr.open_array(
+                        store=node.store, 
+                        path=array_path,
+                        mode='r')
+                    array_spec = ArraySpec.from_zarr(array)
+                except ArrayNotFoundError as e:
+                    raise ValueError(f"Expected to find an array at {array_path}, but no array was found there.")
+                except ContainsGroupError as e:
+
+
+        return guess
+
     @classmethod
     def from_arrays(
         cls,
-        arrays: npt.NDArray[Any],
         paths: Sequence[str],
-        transforms: Sequence[Sequence[tx.Transform]],
         axes: Sequence[Axis],
+        arrays: Sequence[ArrayLike | ChunkedArrayLike],
+        scales: Sequence[int | float],
+        translations: Sequence[int | float],
         *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        top_level_transforms: List[tx.Transform] | None = None,
+        group_scale: tx.Scale | None = None,
+        group_translation: tx.Translation | None = None,
         **kwargs,
     ):
         """
-        Create a `Group` from a sequence of arrays + spatial metadata.
+        Create a `Group` from a sequence of arrays and spatial metadata.
+
+        Parameters
+        ----------
+        paths: Sequence[str]
+            The paths to the arrays.
         """
+        
+        group_transforms = list(filter(lambda v: v is not None, [group_scale, group_translation]))
+        for idx, value in enumerate(group_transforms):
+            if idx == 0:
+                group_transforms[idx] = tx.VectorScale(scale=value)
+            if idx == 1:
+                group_transforms[idx] = tx.VectorTranslation(translation=value) 
+
         members = {
             key: ArraySpec.from_array(arr, **kwargs)
             for key, arr in zip(paths, arrays, strict=True)
@@ -234,12 +289,12 @@ def from_arrays(
             metadata=metadata,
             axes=axes,
             datasets=[
-                Dataset(path=path, coordinateTransformations=txs)
-                for path, txs in zip(paths, transforms, strict=True)
+                create_dataset(path=path, scale=scale, translation=translation)
+                for path, scale, translation in zip(paths, scales, translations, strict=True)
             ],
-            coordinateTransformations=top_level_transforms,
+            coordinateTransformations=group_transforms,
         )
-        return cls(members=members, attributes=multimeta)
+        return cls(members=members, attributes=GroupAttrs(multiscales=[multimeta]))
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
@@ -250,17 +305,20 @@ def check_arrays_exist(self) -> "Group":
         allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
-        array_items: dict[str, dict[str, ArraySpec]] = {
-            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
-        }
-
+        flattened = flatten_node(self)
+        
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in array_items:
+                dpath = '/' + dataset.path
+                if dpath in flattened:
+                    if not isinstance(flattened[dpath], ArraySpec):
+                        msg = f'The node at {dpath} should be an array, found {type(flattened[dpath])} instead'
+                        raise ValueError(msg)
+                else:
                     msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, but no "
-                        "array with that name was found in the items of that group. "
-                        "All arrays referenced in multiscale metadata must be items of the group."
+                        f"Dataset {dataset.path} was specified in multiscale metadata, but no "
+                        "array with that name was found in the hierarchy. "
+                        "All arrays referenced in multiscale metadata must be contained in the group."
                     )
                     raise ValueError(msg)
         return self
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index daad28d..45ca771 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -304,7 +304,7 @@ def test_multiscale_group_datasets_exist(
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the items of that group.",
+        match="array with that name was found in the hierarchy.",
     ):
         bad_items = {
             d.path + "x": ArraySpec(
diff --git a/tests/test_utils.py b/tests/test_utils.py
new file mode 100644
index 0000000..df62bb7
--- /dev/null
+++ b/tests/test_utils.py
@@ -0,0 +1,33 @@
+from __future__ import annotations
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from typing import Any, List
+
+from pydantic_ome_ngff.utils import duplicates, flatten_node
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
+import numpy as np
+import pytest
+
+def test_flatten_node() -> None:
+    a = ArraySpec.from_array(np.arange(10))
+    flattened = flatten_node(a)
+    assert flattened == {'/': a}
+
+    b = GroupSpec(attributes={'foo': 10}, members={'name': a})
+    flattened_b = flatten_node(b)
+    assert flattened_b['/'] == b.model_copy(update={"members": {}})
+    assert flattened_b['/name'] == a
+
+    c = GroupSpec(attributes={}, members={'b': b, 'a': a})
+    flattened_c = flatten_node(c, path='c')
+    assert flattened_c['c'] == c.model_copy(update={"members": {}})
+    assert flattened_c["c/b"] == b.model_copy(update={"members": {}})
+    assert flattened_c["c/a"] == a
+    assert flattened_c["c/b/name"] == a
+
+@pytest.mark.parametrize('data', [[0], [0,1,1,1,2], ['a','a','b','b','c','c','d']])
+def test_duplicates(data: List[Any]) -> None:
+    dupes = duplicates(data)
+    for key, value in dupes.items():
+        assert data.count(key) == value
+        assert value > 1
\ No newline at end of file
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
deleted file mode 100644
index 968c507..0000000
--- a/tests/v04/test_axis.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import pytest
-
-from pydantic_ome_ngff.v04.axis import Axis
-
-
-@pytest.mark.parametrize(
-    "axis_type, unit",
-    [
-        ("space", "second"),
-        ("time", "meter"),
-        ("space", None),
-        (None, None),
-        ("foo", None),
-    ],
-)
-def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
-    with pytest.warns(UserWarning):
-        Axis(name="axis", type=axis_type, unit=unit)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index e2c4523..f94365d 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -29,14 +29,10 @@ def test_properties_colors_match():
         ImageLabel(colors=[color], properties=[prop])
 
 
-@pytest.mark.parametrize("version", ("0.5", None))
-def test_imagelabel_version(version: str | None) -> None:
-    if version is None:
-        with pytest.warns(UserWarning):
-            _ = ImageLabel(version=version)
-    else:
-        with pytest.raises(ValidationError, match="Input should be '0.4'"):
-            _ = ImageLabel(version=version)
+@pytest.mark.parametrize("version", ("0.5", "0.3"))
+def test_imagelabel_version(version: str) -> None:
+    with pytest.raises(ValidationError, match="Input should be '0.4'"):
+        _ = ImageLabel(version=version)
 
 
 @pytest.mark.parametrize(
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index c0caf54..e8a7680 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import Tuple
+from typing import Dict, Tuple
 from pydantic import ValidationError
 import pytest
 import jsonschema as jsc
@@ -310,7 +310,7 @@ def test_multiscale_group_datasets_exist(
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the items of that group.",
+        match="array with that name was found in the hierarchy",
     ):
         bad_items = {
             d.path + "x": ArraySpec(
@@ -369,3 +369,59 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
             for d in default_multiscale.datasets
         }
         Group(attributes=group_attrs, members=bad_items)
+
+
+import numpy as np
+from itertools import accumulate
+import operator
+@pytest.mark.parametrize('name', [None, "foo"])
+@pytest.mark.parametrize('type', [None, "foo"])
+@pytest.mark.parametrize('path_pattern', ['{0}', 's{0}'])
+@pytest.mark.parametrize('metadata', [None, {'foo': 10}])
+@pytest.mark.parametrize('ndim', [2,3,4,5])
+def test_from_arrays(
+    name: str | None, 
+    type: str | None, 
+    path_pattern: str,
+    metadata: Dict[str, int] | str | None, 
+    ndim: int):
+    arrays = [np.arange(x ** ndim).reshape((x,) * ndim) for  x in [3,2,1]]
+    paths = [path_pattern.format(idx) for idx in range(len(arrays))]
+    scales = [(2 ** idx, ) * ndim for idx in range(len(arrays))]
+    translations = [(t,) * ndim for t in accumulate([(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add)]
+    
+    group_scale = (1,) * ndim
+    group_translation = (0,) * ndim
+
+
+    all_axes = [Axis(name="x", type="space",), Axis(name="y", type="space"), Axis(name="z", type="space"), Axis(name="t", type="time"), Axis(name="c", type="barf")]
+    # spatial axes have to come last
+    if ndim in (2, 3):
+        axes = all_axes[:ndim]
+    else:
+        axes = [*all_axes[4:], *all_axes[:3]]
+    
+    group = Group.from_arrays(
+        paths=paths,
+        axes=axes,
+        arrays=arrays,
+        scales=scales,
+        translations=translations,
+        name=name,
+        type=type,
+        metadata=metadata, 
+        group_scale=group_scale,
+        group_translation=group_translation
+    )
+
+    assert group.attributes.multiscales[0].name == name
+    assert group.attributes.multiscales[0].type == type
+    assert group.attributes.multiscales[0].metadata == metadata
+    assert group.attributes.multiscales[0].coordinateTransformations == [VectorScale(scale=group_scale), VectorTranslation(translation=group_translation)]
+    assert group.attributes.multiscales[0].axes == axes
+    for idx, array in enumerate(arrays):
+        assert array.shape == group.members[paths[idx]].shape
+        assert array.dtype == group.members[paths[idx]].dtype
+        assert group.attributes.multiscales[0].datasets[idx].coordinateTransformations == [VectorScale(scale=scales[idx]), VectorTranslation(translation=translations[idx])]
+
+

From 601972b73e5956be6f18f96fe7cb7bf2028dbf09 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 20 Feb 2024 13:18:20 +0100
Subject: [PATCH 14/69] flattening and unflattening routines for GroupSpec

---
 src/pydantic_ome_ngff/utils.py           | 56 ++++++++++++++---
 src/pydantic_ome_ngff/v04/multiscales.py | 79 +++++++++++++++++-------
 2 files changed, 102 insertions(+), 33 deletions(-)

diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index 7dd675c..f9e4b4a 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -5,11 +5,12 @@
 import numpy as np
 
 if TYPE_CHECKING:
-    from typing import Dict, Iterable, Hashable, Tuple
+    from typing import Dict, Iterable, Hashable, Tuple, Any
 
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 import os
 
+
 def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
@@ -20,12 +21,14 @@ def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     return {k: v for k, v in counts.items() if v > 1}
 
 
-def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, ArraySpec | GroupSpec]:
+def flatten_node(
+    node: ArraySpec | GroupSpec, path: str = "/"
+) -> Dict[str, ArraySpec | GroupSpec]:
     """
     Flatten a `GroupSpec` or `ArraySpec`.
-    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are 
+    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are
     `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
-    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute 
+    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute
     under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
     to the name of each member.
 
@@ -33,8 +36,8 @@ def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, Arra
     ---------
     node: `GroupSpec` | `ArraySpec`
         The node to flatten.
-    path: `str`, default is '/'
-        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be 
+    path: `str`, default is 'root'
+        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be
         made relative to `path` when used as keys in the result dictionary.
 
     Returns
@@ -52,14 +55,49 @@ def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, Arra
             result.update(flatten_node(value, os.path.join(path, name)))
 
     result[path] = model_copy
-        
+
     return result
 
+
+ArraySpec.model_dump
+
+
+def unflatten_node(
+    tree: Dict[str, ArraySpec | GroupSpec], attributes: Dict[str, Any] = {}
+) -> ArraySpec | GroupSpec:
+    member_lobby = {}
+    tree_mut: Dict[str, Dict[str, ArraySpec | GroupSpec]] = {}
+    for key, value in tree.items():
+        key_parts = key.split("/")
+        if key_parts[0] != "":
+            raise ValueError(f'Invalid path: {key} does not start with "/".')
+        if len(key_parts) == 2:
+            member_lobby[key_parts[1]] = value
+        else:
+            subparent = key_parts[1]
+            if subparent not in tree_mut:
+                tree_mut[subparent] = {}
+            tree_mut[subparent]["/".join(["", *key_parts[2:]])] = value
+    for subparent, subchildren in tree_mut.items():
+        if subparent in member_lobby:
+            if isinstance(member_lobby[subparent], ArraySpec):
+                msg = f"Invalid tree: the node named {subparent} is declared both as ArraySpec and GroupSpec"
+                raise ValueError(msg)
+            else:
+                member_lobby[subparent] = unflatten_node(
+                    subchildren, attributes=member_lobby[subparent].attributes
+                )
+        else:
+            member_lobby[subparent] = unflatten_node(subchildren)
+    return GroupSpec(members=member_lobby, attributes=attributes)
+
+
 @runtime_checkable
 class ArrayLike(Protocol):
     shape: Tuple[int, ...]
-    dtype: np.dtype
+    dtype: np.dtype[Any]
+
 
 @runtime_checkable
 class ChunkedArrayLike(ArrayLike, Protocol):
-    chunks: Tuple[int, ...]
\ No newline at end of file
+    chunks: Tuple[int, ...]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index a82d1e3..31bfa27 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -4,13 +4,20 @@
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-from pydantic_ome_ngff.utils import ArrayLike, ChunkedArrayLike, duplicates, flatten_node
+from pydantic_ome_ngff.utils import (
+    ArrayLike,
+    ChunkedArrayLike,
+    duplicates,
+    flatten_node,
+    resolve_groups,
+)
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
 import zarr
 from zarr.errors import ArrayNotFoundError, ContainsGroupError
+
 VALID_NDIM = (2, 3, 4, 5)
 NUM_TX_MAX = 2
 
@@ -80,15 +87,18 @@ class Dataset(StrictBase):
 
 
 def create_dataset(
-        path: str, 
-        scale: Sequence[int | float], 
-        translation: Sequence[int | float]) -> Dataset:
+    path: str, scale: Sequence[int | float], translation: Sequence[int | float]
+) -> Dataset:
     """
     Create a `Dataset` from a path, a scale, and a translation.
     """
     return Dataset(
         path=path,
-        coordinateTransformations=[tx.VectorScale(scale=scale), tx.VectorTranslation(translation=translation)])
+        coordinateTransformations=[
+            tx.VectorScale(scale=scale),
+            tx.VectorTranslation(translation=translation),
+        ],
+    )
 
 
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
@@ -221,29 +231,46 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     @classmethod
     def from_zarr(cls, node: zarr.Group) -> Group:
         guess = GroupSpec.from_zarr(node)
-        
+
         try:
-            multi_meta_maybe = guess.attributes['multiscales']
+            multi_meta_maybe = guess.attributes["multiscales"]
         except KeyError as e:
-            msg = (f"Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
-                  f"{node.store.path}/{node.path}")
+            msg = (
+                "Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
+                f"{node.store.path}/{node.path}",
+            )
             raise ValueError(msg) from e
-        
-        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
 
+        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
         for multiscale in multi_meta.multiscales:
+            members = {}
             for dataset in multiscale.datasets:
-                array_path = '/'.join([node.path, dataset.path])
+                array_path = "/".join([node.path, dataset.path])
                 try:
-                    array = zarr.open_array(
-                        store=node.store, 
-                        path=array_path,
-                        mode='r')
+                    array = zarr.open_array(store=node.store, path=array_path, mode="r")
                     array_spec = ArraySpec.from_zarr(array)
                 except ArrayNotFoundError as e:
-                    raise ValueError(f"Expected to find an array at {array_path}, but no array was found there.")
+                    msg = (
+                        f"Expected to find an array at {array_path}, ",
+                        "but no array was found there.",
+                    )
+                    raise ArrayNotFoundError(msg) from e
                 except ContainsGroupError as e:
+                    msg = (
+                        f"Expected to find an array at {array_path}, ",
+                        "but a group was found there instead.",
+                    )
+                    raise ContainsGroupError(msg) from e
+                dataset_path_parts = dataset.path.split("/")
+                if len(dataset_path_parts) == 1:
+                    members[dataset.path] = array_spec
+                else:
+                    # this will not be correct for multiple arrays in the same deep group
+                    members[dataset.path] = resolve_groups(
+                        "/".join(dataset_path_parts[1:]), array_spec
+                    )
 
+            guess = guess.model_copy(update={**guess.members, **members})
 
         return guess
 
@@ -271,13 +298,15 @@ def from_arrays(
         paths: Sequence[str]
             The paths to the arrays.
         """
-        
-        group_transforms = list(filter(lambda v: v is not None, [group_scale, group_translation]))
+
+        group_transforms = list(
+            filter(lambda v: v is not None, [group_scale, group_translation])
+        )
         for idx, value in enumerate(group_transforms):
             if idx == 0:
                 group_transforms[idx] = tx.VectorScale(scale=value)
             if idx == 1:
-                group_transforms[idx] = tx.VectorTranslation(translation=value) 
+                group_transforms[idx] = tx.VectorTranslation(translation=value)
 
         members = {
             key: ArraySpec.from_array(arr, **kwargs)
@@ -290,7 +319,9 @@ def from_arrays(
             axes=axes,
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
-                for path, scale, translation in zip(paths, scales, translations, strict=True)
+                for path, scale, translation in zip(
+                    paths, scales, translations, strict=True
+                )
             ],
             coordinateTransformations=group_transforms,
         )
@@ -306,13 +337,13 @@ def check_arrays_exist(self) -> "Group":
         """
         attrs = self.attributes
         flattened = flatten_node(self)
-        
+
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                dpath = '/' + dataset.path
+                dpath = "/" + dataset.path
                 if dpath in flattened:
                     if not isinstance(flattened[dpath], ArraySpec):
-                        msg = f'The node at {dpath} should be an array, found {type(flattened[dpath])} instead'
+                        msg = f"The node at {dpath} should be an array, found {type(flattened[dpath])} instead"
                         raise ValueError(msg)
                 else:
                     msg = (

From ba81fa026d6b79b698e18184a77b6a266295cf63 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:09:24 +0100
Subject: [PATCH 15/69] fix: use tuple instead of list for transforms; defer to
 pydantic-zarr for flattening / unflattening; handle arrays in subgroups when
 validating multiscale metadata

---
 poetry.lock                              | 1299 +++++++++++-----------
 pyproject.toml                           |    2 +-
 src/pydantic_ome_ngff/utils.py           |   74 --
 src/pydantic_ome_ngff/v04/multiscales.py |  125 ++-
 src/pydantic_ome_ngff/v04/transforms.py  |   20 +-
 tests/latest/test_multiscales.py         |   52 +-
 tests/test_utils.py                      |   27 +-
 tests/v04/test_multiscales.py            |  130 ++-
 8 files changed, 844 insertions(+), 885 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7f86b0e..7663d52 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,109 +1,109 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.11.1"
+version = "2.12.0"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.11.1-py3-none-any.whl", hash = "sha256:904a7ad7cc8671d662cfd596906dafe839118ea2a66332c37908e3dcfdee1e45"},
-    {file = "aiobotocore-2.11.1.tar.gz", hash = "sha256:0b095af50da2d6f94e93ca959e2a4876f0f0d84d534b61b21d8e050832d04ab6"},
+    {file = "aiobotocore-2.12.0-py3-none-any.whl", hash = "sha256:e121503dca049cf361dea19730e335aff2e7508f7f8b24db2e6a43a6fb70299e"},
+    {file = "aiobotocore-2.12.0.tar.gz", hash = "sha256:bc841cef234afcb781f2d600680c9e49d01b9a2e8169790a32579bb0df51777f"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.33.2,<1.34.28"
+botocore = ">=1.34.41,<1.34.52"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.31.2,<1.32.28)"]
-boto3 = ["boto3 (>=1.33.2,<1.34.28)"]
+awscli = ["awscli (>=1.32.41,<1.32.52)"]
+boto3 = ["boto3 (>=1.34.41,<1.34.52)"]
 
 [[package]]
 name = "aiohttp"
-version = "3.9.1"
+version = "3.9.3"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e1f80197f8b0b846a8d5cf7b7ec6084493950d0882cc5537fb7b96a69e3c8590"},
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c72444d17777865734aa1a4d167794c34b63e5883abb90356a0364a28904e6c0"},
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9b05d5cbe9dafcdc733262c3a99ccf63d2f7ce02543620d2bd8db4d4f7a22f83"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5c4fa235d534b3547184831c624c0b7c1e262cd1de847d95085ec94c16fddcd5"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:289ba9ae8e88d0ba16062ecf02dd730b34186ea3b1e7489046fc338bdc3361c4"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:bff7e2811814fa2271be95ab6e84c9436d027a0e59665de60edf44e529a42c1f"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81b77f868814346662c96ab36b875d7814ebf82340d3284a31681085c051320f"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3b9c7426923bb7bd66d409da46c41e3fb40f5caf679da624439b9eba92043fa6"},
-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:8d44e7bf06b0c0a70a20f9100af9fcfd7f6d9d3913e37754c12d424179b4e48f"},
-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:22698f01ff5653fe66d16ffb7658f582a0ac084d7da1323e39fd9eab326a1f26"},
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 [package.dependencies]
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 [[package]]
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 ]
 
 [package.dependencies]
@@ -255,13 +255,13 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.27"
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 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.8"
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 [package.dependencies]
@@ -274,13 +274,13 @@ crt = ["awscrt (==0.19.19)"]
 
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+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
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 [package.dependencies]
@@ -677,13 +677,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.39.1"
+version = "0.41.2"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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 [[package]]
 name = "identify"
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+version = "2.5.35"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
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 [[package]]
@@ -964,28 +964,29 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-autorefs"
-version = "0.5.0"
+version = "1.0.1"
 description = "Automatically link across pages in MkDocs."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 Markdown = ">=3.3"
+markupsafe = ">=2.0.1"
 mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.5"
+version = "9.5.12"
 description = "Documentation that simply works"
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1002,7 +1003,7 @@ regex = ">=2022.4"
 requests = ">=2.26,<3.0"
 
 [package.extras]
-git = ["mkdocs-git-committers-plugin-2 (>=1.1,<2.0)", "mkdocs-git-revision-date-localized-plugin (>=1.2,<2.0)"]
+git = ["mkdocs-git-committers-plugin-2 (>=1.1,<2.0)", "mkdocs-git-revision-date-localized-plugin (>=1.2.4,<2.0)"]
 imaging = ["cairosvg (>=2.6,<3.0)", "pillow (>=10.2,<11.0)"]
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@@ -1019,13 +1020,13 @@ files = [
 
 [[package]]
 name = "mkdocstrings"
-version = "0.24.0"
+version = "0.24.1"
 description = "Automatic documentation from sources, for MkDocs."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1061,85 +1062,101 @@ mkdocstrings = ">=0.20"
 
 [[package]]
 name = "multidict"
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+version = "6.0.5"
 description = "multidict implementation"
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 python-versions = ">=3.7"
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 [[package]]
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 [[package]]
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 [[package]]
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@@ -2057,13 +2048,13 @@ files = [
 
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 [[package]]
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 [[package]]
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 [package.dependencies]
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 [[package]]
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-    {file = "watchdog-3.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:c9d8c8ec7efb887333cf71e328e39cffbf771d8f8f95d308ea4125bf5f90ba64"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:0e06ab8858a76e1219e68c7573dfeba9dd1c0219476c5a44d5333b01d7e1743a"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:d00e6be486affb5781468457b21a6cbe848c33ef43f9ea4a73b4882e5f188a44"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:c07253088265c363d1ddf4b3cdb808d59a0468ecd017770ed716991620b8f77a"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:5113334cf8cf0ac8cd45e1f8309a603291b614191c9add34d33075727a967709"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:51f90f73b4697bac9c9a78394c3acbbd331ccd3655c11be1a15ae6fe289a8c83"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:ba07e92756c97e3aca0912b5cbc4e5ad802f4557212788e72a72a47ff376950d"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:d429c2430c93b7903914e4db9a966c7f2b068dd2ebdd2fa9b9ce094c7d459f33"},
-    {file = "watchdog-3.0.0-py3-none-win32.whl", hash = "sha256:3ed7c71a9dccfe838c2f0b6314ed0d9b22e77d268c67e015450a29036a81f60f"},
-    {file = "watchdog-3.0.0-py3-none-win_amd64.whl", hash = "sha256:4c9956d27be0bb08fc5f30d9d0179a855436e655f046d288e2bcc11adfae893c"},
-    {file = "watchdog-3.0.0-py3-none-win_ia64.whl", hash = "sha256:5d9f3a10e02d7371cd929b5d8f11e87d4bad890212ed3901f9b4d68767bee759"},
-    {file = "watchdog-3.0.0.tar.gz", hash = "sha256:4d98a320595da7a7c5a18fc48cb633c2e73cda78f93cac2ef42d42bf609a33f9"},
+    {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:39cb34b1f1afbf23e9562501673e7146777efe95da24fab5707b88f7fb11649b"},
+    {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c522392acc5e962bcac3b22b9592493ffd06d1fc5d755954e6be9f4990de932b"},
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+    {file = "watchdog-4.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:8350d4055505412a426b6ad8c521bc7d367d1637a762c70fdd93a3a0d595990b"},
+    {file = "watchdog-4.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:c17d98799f32e3f55f181f19dd2021d762eb38fdd381b4a748b9f5a36738e935"},
+    {file = "watchdog-4.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4986db5e8880b0e6b7cd52ba36255d4793bf5cdc95bd6264806c233173b1ec0b"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:11e12fafb13372e18ca1bbf12d50f593e7280646687463dd47730fd4f4d5d257"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:5369136a6474678e02426bd984466343924d1df8e2fd94a9b443cb7e3aa20d19"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:76ad8484379695f3fe46228962017a7e1337e9acadafed67eb20aabb175df98b"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:45cc09cc4c3b43fb10b59ef4d07318d9a3ecdbff03abd2e36e77b6dd9f9a5c85"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:eed82cdf79cd7f0232e2fdc1ad05b06a5e102a43e331f7d041e5f0e0a34a51c4"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:ba30a896166f0fee83183cec913298151b73164160d965af2e93a20bbd2ab605"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:d18d7f18a47de6863cd480734613502904611730f8def45fc52a5d97503e5101"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:2895bf0518361a9728773083908801a376743bcc37dfa252b801af8fd281b1ca"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:87e9df830022488e235dd601478c15ad73a0389628588ba0b028cb74eb72fed8"},
+    {file = "watchdog-4.0.0-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6e949a8a94186bced05b6508faa61b7adacc911115664ccb1923b9ad1f1ccf7b"},
+    {file = "watchdog-4.0.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6a4db54edea37d1058b08947c789a2354ee02972ed5d1e0dca9b0b820f4c7f92"},
+    {file = "watchdog-4.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:d31481ccf4694a8416b681544c23bd271f5a123162ab603c7d7d2dd7dd901a07"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:8fec441f5adcf81dd240a5fe78e3d83767999771630b5ddfc5867827a34fa3d3"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:6a9c71a0b02985b4b0b6d14b875a6c86ddea2fdbebd0c9a720a806a8bbffc69f"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:557ba04c816d23ce98a06e70af6abaa0485f6d94994ec78a42b05d1c03dcbd50"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:d0f9bd1fd919134d459d8abf954f63886745f4660ef66480b9d753a7c9d40927"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:f9b2fdca47dc855516b2d66eef3c39f2672cbf7e7a42e7e67ad2cbfcd6ba107d"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:73c7a935e62033bd5e8f0da33a4dcb763da2361921a69a5a95aaf6c93aa03a87"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:6a80d5cae8c265842c7419c560b9961561556c4361b297b4c431903f8c33b269"},
+    {file = "watchdog-4.0.0-py3-none-win32.whl", hash = "sha256:8f9a542c979df62098ae9c58b19e03ad3df1c9d8c6895d96c0d51da17b243b1c"},
+    {file = "watchdog-4.0.0-py3-none-win_amd64.whl", hash = "sha256:f970663fa4f7e80401a7b0cbeec00fa801bf0287d93d48368fc3e6fa32716245"},
+    {file = "watchdog-4.0.0-py3-none-win_ia64.whl", hash = "sha256:9a03e16e55465177d416699331b0f3564138f1807ecc5f2de9d55d8f188d08c7"},
+    {file = "watchdog-4.0.0.tar.gz", hash = "sha256:e3e7065cbdabe6183ab82199d7a4f6b3ba0a438c5a512a68559846ccb76a78ec"},
 ]
 
 [package.extras]
@@ -2326,26 +2319,26 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zarr"
-version = "2.16.1"
+version = "2.17.0"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
-    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
+    {file = "zarr-2.17.0-py3-none-any.whl", hash = "sha256:d287cb61019c4a0a0f386f76eeaa7f0b1160b1cb90cf96173a4b6cbc135df6e1"},
+    {file = "zarr-2.17.0.tar.gz", hash = "sha256:6390a2b8af31babaab4c963efc45bf1da7f9500c9aafac193f84cf019a7c66b0"},
 ]
 
 [package.dependencies]
 asciitree = "*"
-fasteners = "*"
+fasteners = {version = "*", markers = "sys_platform != \"emscripten\""}
 numcodecs = ">=0.10.0"
-numpy = ">=1.20,<1.21.0 || >1.21.0"
+numpy = ">=1.21.1"
 
 [package.extras]
-docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "f5afbf936caecbd37768b0fbdbbd193014831dfdf71897f94aaad8e20798b31a"
+content-hash = "9fcbaf31547db3838421ab6496d8081ee87f365ddadc7790d16c605d5e258444"
diff --git a/pyproject.toml b/pyproject.toml
index 68d523e..c228f99 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-pydantic-zarr = "0.5.2"
+pydantic-zarr = "0.6.1"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
 rich = "^13.6.0"
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index f9e4b4a..a1cf0c4 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -7,9 +7,6 @@
 if TYPE_CHECKING:
     from typing import Dict, Iterable, Hashable, Tuple, Any
 
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
-import os
-
 
 def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
@@ -21,77 +18,6 @@ def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     return {k: v for k, v in counts.items() if v > 1}
 
 
-def flatten_node(
-    node: ArraySpec | GroupSpec, path: str = "/"
-) -> Dict[str, ArraySpec | GroupSpec]:
-    """
-    Flatten a `GroupSpec` or `ArraySpec`.
-    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are
-    `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
-    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute
-    under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
-    to the name of each member.
-
-    Paramters
-    ---------
-    node: `GroupSpec` | `ArraySpec`
-        The node to flatten.
-    path: `str`, default is 'root'
-        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be
-        made relative to `path` when used as keys in the result dictionary.
-
-    Returns
-    -------
-    `Dict[str, GroupSpec | ArraySpec]`
-
-    """
-    result = {}
-    if isinstance(node, ArraySpec):
-        model_copy = node.model_copy(deep=True)
-
-    else:
-        model_copy = node.model_copy(update={"members": {}})
-        for name, value in node.members.items():
-            result.update(flatten_node(value, os.path.join(path, name)))
-
-    result[path] = model_copy
-
-    return result
-
-
-ArraySpec.model_dump
-
-
-def unflatten_node(
-    tree: Dict[str, ArraySpec | GroupSpec], attributes: Dict[str, Any] = {}
-) -> ArraySpec | GroupSpec:
-    member_lobby = {}
-    tree_mut: Dict[str, Dict[str, ArraySpec | GroupSpec]] = {}
-    for key, value in tree.items():
-        key_parts = key.split("/")
-        if key_parts[0] != "":
-            raise ValueError(f'Invalid path: {key} does not start with "/".')
-        if len(key_parts) == 2:
-            member_lobby[key_parts[1]] = value
-        else:
-            subparent = key_parts[1]
-            if subparent not in tree_mut:
-                tree_mut[subparent] = {}
-            tree_mut[subparent]["/".join(["", *key_parts[2:]])] = value
-    for subparent, subchildren in tree_mut.items():
-        if subparent in member_lobby:
-            if isinstance(member_lobby[subparent], ArraySpec):
-                msg = f"Invalid tree: the node named {subparent} is declared both as ArraySpec and GroupSpec"
-                raise ValueError(msg)
-            else:
-                member_lobby[subparent] = unflatten_node(
-                    subchildren, attributes=member_lobby[subparent].attributes
-                )
-        else:
-            member_lobby[subparent] = unflatten_node(subchildren)
-    return GroupSpec(members=member_lobby, attributes=attributes)
-
-
 @runtime_checkable
 class ArrayLike(Protocol):
     shape: Tuple[int, ...]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 31bfa27..97ab4b7 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,15 +1,13 @@
 from __future__ import annotations
 
 from collections import Counter
-from typing import Annotated, Any, Dict, List, Sequence, Union, cast
+from typing import Annotated, Any, Dict, List, Self, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import (
     ArrayLike,
     ChunkedArrayLike,
     duplicates,
-    flatten_node,
-    resolve_groups,
 )
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -79,8 +77,7 @@ class Dataset(StrictBase):
 
     path: str
     coordinateTransformations: Annotated[
-        List[tx.Scale | tx.Translation],
-        AfterValidator(ensure_transforms_length),
+        tuple[tx.Scale] | tuple[tx.Scale, tx.Translation],
         AfterValidator(ensure_scale_translation),
         AfterValidator(tx.ensure_dimensionality),
     ]
@@ -194,7 +191,9 @@ class MultiscaleMetadata(StrictVersionedBase):
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
     ]
-    coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
+    coordinateTransformations: tuple[tx.Scale] | tuple[
+        tx.Scale, tx.Translation
+    ] | None = None
 
 
 class GroupAttrs(BaseModel):
@@ -230,6 +229,22 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
 
     @classmethod
     def from_zarr(cls, node: zarr.Group) -> Group:
+        """
+        Create an instance of `Group` from a `node`, a `zarr.Group`. This method infers the
+        discovers Zarr arrays in the hierarchy rooted at `node` by inspecting the OME-NGFF
+        multiscales metadata.
+
+        Paramters
+        ---------
+        node: zarr.Group
+            A Zarr group that has valid OME-NGFF multiscale metadata.
+
+        Returns
+        -------
+        Group
+            A model of the zarr Group.
+        """
+        # on unlistable storage backends, the members of this group will be {}
         guess = GroupSpec.from_zarr(node)
 
         try:
@@ -242,37 +257,32 @@ def from_zarr(cls, node: zarr.Group) -> Group:
             raise ValueError(msg) from e
 
         multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
+        members_tree_flat = {}
         for multiscale in multi_meta.multiscales:
-            members = {}
             for dataset in multiscale.datasets:
                 array_path = "/".join([node.path, dataset.path])
                 try:
                     array = zarr.open_array(store=node.store, path=array_path, mode="r")
                     array_spec = ArraySpec.from_zarr(array)
-                except ArrayNotFoundError as e:
+                except ArrayNotFoundError:
                     msg = (
                         f"Expected to find an array at {array_path}, ",
                         "but no array was found there.",
                     )
-                    raise ArrayNotFoundError(msg) from e
-                except ContainsGroupError as e:
+                    raise ArrayNotFoundError(msg)
+                except ContainsGroupError:
                     msg = (
                         f"Expected to find an array at {array_path}, ",
                         "but a group was found there instead.",
                     )
-                    raise ContainsGroupError(msg) from e
-                dataset_path_parts = dataset.path.split("/")
-                if len(dataset_path_parts) == 1:
-                    members[dataset.path] = array_spec
-                else:
-                    # this will not be correct for multiple arrays in the same deep group
-                    members[dataset.path] = resolve_groups(
-                        "/".join(dataset_path_parts[1:]), array_spec
-                    )
-
-            guess = guess.model_copy(update={**guess.members, **members})
+                    raise ContainsGroupError(msg)
+                members_tree_flat["/" + dataset.path] = array_spec
+        members_normalized = GroupSpec.from_flat(members_tree_flat)
 
-        return guess
+        guess_inferred_members = guess.model_copy(
+            update={"members": {**guess.members, **members_normalized.members}}
+        )
+        return guess_inferred_members
 
     @classmethod
     def from_arrays(
@@ -280,16 +290,16 @@ def from_arrays(
         paths: Sequence[str],
         axes: Sequence[Axis],
         arrays: Sequence[ArrayLike | ChunkedArrayLike],
-        scales: Sequence[int | float],
-        translations: Sequence[int | float],
+        scales: Sequence[Sequence[int | float]],
+        translations: Sequence[Sequence[int | float]],
         *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        group_scale: tx.Scale | None = None,
-        group_translation: tx.Translation | None = None,
-        **kwargs,
-    ):
+        group_scale: Sequence[int | float] | None = None,
+        group_translation: Sequence[int | float] | None = None,
+        **kwargs: Any,
+    ) -> Self:
         """
         Create a `Group` from a sequence of arrays and spatial metadata.
 
@@ -298,25 +308,20 @@ def from_arrays(
         paths: Sequence[str]
             The paths to the arrays.
         """
+        group_transforms = None
+        if group_scale is not None:
+            group_transforms = tx.scale_translation(group_scale, group_translation)
 
-        group_transforms = list(
-            filter(lambda v: v is not None, [group_scale, group_translation])
-        )
-        for idx, value in enumerate(group_transforms):
-            if idx == 0:
-                group_transforms[idx] = tx.VectorScale(scale=value)
-            if idx == 1:
-                group_transforms[idx] = tx.VectorTranslation(translation=value)
-
-        members = {
-            key: ArraySpec.from_array(arr, **kwargs)
+        members_flat = {
+            "/" + key.lstrip("/"): ArraySpec.from_array(arr, **kwargs)
             for key, arr in zip(paths, arrays, strict=True)
         }
+
         multimeta = MultiscaleMetadata(
             name=name,
             type=type,
             metadata=metadata,
-            axes=axes,
+            axes=list(axes),
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
                 for path, scale, translation in zip(
@@ -325,7 +330,10 @@ def from_arrays(
             ],
             coordinateTransformations=group_transforms,
         )
-        return cls(members=members, attributes=GroupAttrs(multiscales=[multimeta]))
+        return cls(
+            members=GroupSpec.from_flat(members_flat).members,
+            attributes=GroupAttrs(multiscales=[multimeta]),
+        )
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
@@ -336,14 +344,17 @@ def check_arrays_exist(self) -> "Group":
         allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
-        flattened = flatten_node(self)
+        flattened = self.to_flat()
 
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                dpath = "/" + dataset.path
+                dpath = "/" + dataset.path.lstrip("/")
                 if dpath in flattened:
                     if not isinstance(flattened[dpath], ArraySpec):
-                        msg = f"The node at {dpath} should be an array, found {type(flattened[dpath])} instead"
+                        msg = (
+                            f"The node at {dpath} should be an array, "
+                            f"found {type(flattened[dpath])} instead"
+                        )
                         raise ValueError(msg)
                 else:
                     msg = (
@@ -358,14 +369,26 @@ def check_arrays_exist(self) -> "Group":
     def check_array_ndim(self) -> "Group":
         """
         Check that all the arrays referenced by the `multiscales` metadata have the same
-        dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
+        dimensionality, and that this dimensionality is consistent with the
+        `coordinateTransformations` metadata.
         """
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
-        }
+        multimeta = self.attributes.multiscales
+
+        flat_self = self.to_flat()
+        ndims = []
+        # get shapes from all the arrays referenced in `multiscales`
+        for multiscale in multimeta:
+            for dataset in multiscale.datasets:
+                node = flat_self["/" + dataset.path.lstrip("/")]
+                if isinstance(node, ArraySpec):
+                    ndims.append(len(flat_self["/" + dataset.path.lstrip("/")].shape))
+                else:
+                    msg = (
+                        f"Expected an instance of ArraySpec at {dataset.path}, "
+                        f"got {type(node)} instead"
+                    )
+                    raise TypeError(msg)
 
-        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             msg = (
                 "All arrays must have the same dimensionality. "
@@ -374,7 +397,7 @@ def check_array_ndim(self) -> "Group":
             raise ValueError(msg)
 
         # check that each transform has compatible rank
-        for multiscale in attrs.multiscales:
+        for multiscale in multimeta:
             tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index df1a9f5..67dc998 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -115,16 +115,24 @@ def ndim(
 
 
 def scale_translation(
-    scale: Sequence[float], translation: Sequence[float]
-) -> tuple[Scale, Translation]:
+    scale: Sequence[float], translation: Sequence[float] | None
+) -> tuple[Scale] | tuple[Scale, Translation]:
     """
-    Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
+    Create a `VectorScale` and, optionally, a `VectorTranslation` from a scale and a translation
+    parameter.
     """
     len_scale = len(scale)
-    len_translation = len(translation)
+
     if len_scale < 1:
         msg = "Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
+
+    vec_scale = VectorScale(scale=scale)
+
+    if translation is None:
+        return (vec_scale,)
+
+    len_translation = len(translation)
     if len_translation < 1:
         msg = "Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
@@ -135,7 +143,9 @@ def scale_translation(
         )
         raise ValueError(msg)
 
-    return (VectorScale(scale=scale), VectorTranslation(translation=translation))
+    vec_trans = VectorTranslation(translation=translation)
+
+    return (vec_scale, vec_trans)
 
 
 Scale = VectorScale | PathScale
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 45ca771..c14d2ca 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -34,7 +34,7 @@ def default_multiscale() -> MultiscaleMetadata:
     datasets = [
         Dataset(
             path=f"path{idx}",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -47,7 +47,7 @@ def default_multiscale() -> MultiscaleMetadata:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
         for idx in range(num_datasets)
     ]
@@ -56,21 +56,23 @@ def default_multiscale() -> MultiscaleMetadata:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
+        coordinateTransformations=(
             VectorScale(
                 scale=[
                     1,
                 ]
                 * rank
             ),
-        ],
+        ),
     )
     return multi
 
 
 def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     _, strict_schema = fetch_schemas("latest", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
+    jsc.validate(
+        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
+    )
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -84,10 +86,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -95,9 +97,7 @@ def test_multiscale_unique_axis_names() -> None:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
-            VectorScale(scale=[1, 1, 1]),
-        ],
+        coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
     )
 
     # make axis names collide
@@ -108,10 +108,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -120,9 +120,7 @@ def test_multiscale_unique_axis_names() -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
-                VectorScale(scale=[1, 1, 1]),
-            ],
+            coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
         )
 
 
@@ -143,7 +141,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -156,7 +154,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     # TODO: make some axis-specifc exceptions
@@ -165,14 +163,14 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -183,7 +181,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -196,7 +194,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
@@ -204,14 +202,14 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -244,7 +242,9 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="expected 1 or 2"):
+    with pytest.raises(
+        ValidationError, match=f"after validation, not {len(transforms)}"
+    ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -266,7 +266,7 @@ def test_coordinate_transforms_invalid_first_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The first element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorScale",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -285,7 +285,7 @@ def test_coordinate_transforms_invalid_second_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The second element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorTranslation",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index df62bb7..4672071 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,33 +1,18 @@
 from __future__ import annotations
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     from typing import Any, List
 
-from pydantic_ome_ngff.utils import duplicates, flatten_node
-from pydantic_zarr.v2 import ArraySpec, GroupSpec
-import numpy as np
+from pydantic_ome_ngff.utils import duplicates
 import pytest
 
-def test_flatten_node() -> None:
-    a = ArraySpec.from_array(np.arange(10))
-    flattened = flatten_node(a)
-    assert flattened == {'/': a}
-
-    b = GroupSpec(attributes={'foo': 10}, members={'name': a})
-    flattened_b = flatten_node(b)
-    assert flattened_b['/'] == b.model_copy(update={"members": {}})
-    assert flattened_b['/name'] == a
-
-    c = GroupSpec(attributes={}, members={'b': b, 'a': a})
-    flattened_c = flatten_node(c, path='c')
-    assert flattened_c['c'] == c.model_copy(update={"members": {}})
-    assert flattened_c["c/b"] == b.model_copy(update={"members": {}})
-    assert flattened_c["c/a"] == a
-    assert flattened_c["c/b/name"] == a
 
-@pytest.mark.parametrize('data', [[0], [0,1,1,1,2], ['a','a','b','b','c','c','d']])
+@pytest.mark.parametrize(
+    "data", [[0], [0, 1, 1, 1, 2], ["a", "a", "b", "b", "c", "c", "d"]]
+)
 def test_duplicates(data: List[Any]) -> None:
     dupes = duplicates(data)
     for key, value in dupes.items():
         assert data.count(key) == value
-        assert value > 1
\ No newline at end of file
+        assert value > 1
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index e8a7680..ad3a2ed 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -18,6 +18,9 @@
 )
 from pydantic_ome_ngff.v04.axis import Axis
 from tests.conftest import fetch_schemas
+import numpy as np
+from itertools import accumulate
+import operator
 
 
 @pytest.fixture
@@ -33,7 +36,7 @@ def default_multiscale() -> MultiscaleMetadata:
     datasets = [
         Dataset(
             path=f"path{idx}",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -46,7 +49,7 @@ def default_multiscale() -> MultiscaleMetadata:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
         for idx in range(num_datasets)
     ]
@@ -55,21 +58,23 @@ def default_multiscale() -> MultiscaleMetadata:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
+        coordinateTransformations=(
             VectorScale(
                 scale=[
                     1,
                 ]
                 * rank
             ),
-        ],
+        ),
     )
     return multi
 
 
 def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
+    jsc.validate(
+        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
+    )
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -83,10 +88,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -94,9 +99,7 @@ def test_multiscale_unique_axis_names() -> None:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
-            VectorScale(scale=[1, 1, 1]),
-        ],
+        coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
     )
 
     # make axis names collide
@@ -107,10 +110,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -119,9 +122,7 @@ def test_multiscale_unique_axis_names() -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
-                VectorScale(scale=[1, 1, 1]),
-            ],
+            coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
         )
 
 
@@ -142,7 +143,7 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -155,7 +156,7 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     # TODO: make some axis-specifc exceptions
@@ -164,14 +165,14 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -182,7 +183,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -195,7 +196,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
@@ -203,14 +204,14 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -243,7 +244,9 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 def test_coordinate_transforms_invalid_length(
     transforms: list[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="expected 1 or 2"):
+    with pytest.raises(
+        ValidationError, match=f"after validation, not {len(transforms)}"
+    ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -265,7 +268,7 @@ def test_coordinate_transforms_invalid_first_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The first element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorScale",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -280,11 +283,11 @@ def test_coordinate_transforms_invalid_first_element(
     ),
 )
 def test_coordinate_transforms_invalid_second_element(
-    transforms: Tuple[Transform, Transform],
+    transforms: Tuple[VectorScale, VectorScale],
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The second element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorTranslation",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -371,36 +374,47 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
         Group(attributes=group_attrs, members=bad_items)
 
 
-import numpy as np
-from itertools import accumulate
-import operator
-@pytest.mark.parametrize('name', [None, "foo"])
-@pytest.mark.parametrize('type', [None, "foo"])
-@pytest.mark.parametrize('path_pattern', ['{0}', 's{0}'])
-@pytest.mark.parametrize('metadata', [None, {'foo': 10}])
-@pytest.mark.parametrize('ndim', [2,3,4,5])
+@pytest.mark.parametrize("name", [None, "foo"])
+@pytest.mark.parametrize("type", [None, "foo"])
+@pytest.mark.parametrize("path_pattern", ["{0}", "s{0}", "foo/{0}"])
+@pytest.mark.parametrize("metadata", [None, {"foo": 10}])
+@pytest.mark.parametrize("ndim", [2, 3, 4, 5])
 def test_from_arrays(
-    name: str | None, 
-    type: str | None, 
+    name: str | None,
+    type: str | None,
     path_pattern: str,
-    metadata: Dict[str, int] | str | None, 
-    ndim: int):
-    arrays = [np.arange(x ** ndim).reshape((x,) * ndim) for  x in [3,2,1]]
+    metadata: Dict[str, int] | None,
+    ndim: int,
+) -> None:
+    arrays = [np.arange(x**ndim).reshape((x,) * ndim) for x in [3, 2, 1]]
     paths = [path_pattern.format(idx) for idx in range(len(arrays))]
-    scales = [(2 ** idx, ) * ndim for idx in range(len(arrays))]
-    translations = [(t,) * ndim for t in accumulate([(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add)]
-    
+    scales = [(2**idx,) * ndim for idx in range(len(arrays))]
+    translations = [
+        (t,) * ndim
+        for t in accumulate(
+            [(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add
+        )
+    ]
+
     group_scale = (1,) * ndim
     group_translation = (0,) * ndim
 
-
-    all_axes = [Axis(name="x", type="space",), Axis(name="y", type="space"), Axis(name="z", type="space"), Axis(name="t", type="time"), Axis(name="c", type="barf")]
+    all_axes = [
+        Axis(
+            name="x",
+            type="space",
+        ),
+        Axis(name="y", type="space"),
+        Axis(name="z", type="space"),
+        Axis(name="t", type="time"),
+        Axis(name="c", type="barf"),
+    ]
     # spatial axes have to come last
     if ndim in (2, 3):
         axes = all_axes[:ndim]
     else:
         axes = [*all_axes[4:], *all_axes[:3]]
-    
+
     group = Group.from_arrays(
         paths=paths,
         axes=axes,
@@ -409,19 +423,27 @@ def test_from_arrays(
         translations=translations,
         name=name,
         type=type,
-        metadata=metadata, 
+        metadata=metadata,
         group_scale=group_scale,
-        group_translation=group_translation
+        group_translation=group_translation,
     )
 
+    group_flat = group.to_flat()
+
     assert group.attributes.multiscales[0].name == name
     assert group.attributes.multiscales[0].type == type
     assert group.attributes.multiscales[0].metadata == metadata
-    assert group.attributes.multiscales[0].coordinateTransformations == [VectorScale(scale=group_scale), VectorTranslation(translation=group_translation)]
+    assert group.attributes.multiscales[0].coordinateTransformations == (
+        VectorScale(scale=group_scale),
+        VectorTranslation(translation=group_translation),
+    )
     assert group.attributes.multiscales[0].axes == axes
     for idx, array in enumerate(arrays):
-        assert array.shape == group.members[paths[idx]].shape
-        assert array.dtype == group.members[paths[idx]].dtype
-        assert group.attributes.multiscales[0].datasets[idx].coordinateTransformations == [VectorScale(scale=scales[idx]), VectorTranslation(translation=translations[idx])]
-
-
+        assert array.shape == group_flat["/" + paths[idx]].shape
+        assert array.dtype == group_flat["/" + paths[idx]].dtype
+        assert group.attributes.multiscales[0].datasets[
+            idx
+        ].coordinateTransformations == (
+            VectorScale(scale=scales[idx]),
+            VectorTranslation(translation=translations[idx]),
+        )

From f50108b1999486bbbbebedac59081e49837b9b27 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:10:33 +0100
Subject: [PATCH 16/69] chore: add gha

---
 .github/workflows/test.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..04d4084
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,24 @@
+name: Linux Testing
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install dependencies
+      shell: "bash -l {0}"
+      run: |
+        pip install poetry
+        poetry install
+    - name: Test
+      run: |
+        poetry run pytest
\ No newline at end of file

From ae5fb4a05f4028a0b0b25566d121a28549340c19 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 6 Jun 2023 12:00:01 -0400
Subject: [PATCH 17/69] feat: use pydantic-zarr for representing multiscale
 groups

---
 poetry.lock                                 | 129 +++++++++++++++++++-
 pyproject.toml                              |   1 +
 src/pydantic_ome_ngff/latest/multiscales.py |  59 ++++-----
 src/pydantic_ome_ngff/tree.py               |  79 ------------
 src/pydantic_ome_ngff/v04/multiscales.py    |  56 ++++-----
 tests/test_latest.py                        |  96 +++++----------
 tests/test_v04.py                           |  70 +++++------
 7 files changed, 241 insertions(+), 249 deletions(-)
 delete mode 100644 src/pydantic_ome_ngff/tree.py

diff --git a/poetry.lock b/poetry.lock
index b11fe59..40e11bb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,16 @@
 # This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
 
+[[package]]
+name = "asciitree"
+version = "0.3.3"
+description = "Draws ASCII trees."
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "asciitree-0.3.3.tar.gz", hash = "sha256:4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e"},
+]
+
 [[package]]
 name = "attrs"
 version = "23.1.0"
@@ -228,6 +239,18 @@ files = [
     {file = "distlib-0.3.7.tar.gz", hash = "sha256:9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8"},
 ]
 
+[[package]]
+name = "entrypoints"
+version = "0.4"
+description = "Discover and load entry points from installed packages."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "entrypoints-0.4-py3-none-any.whl", hash = "sha256:f174b5ff827504fd3cd97cc3f8649f3693f51538c7e4bdf3ef002c8429d42f9f"},
+    {file = "entrypoints-0.4.tar.gz", hash = "sha256:b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4"},
+]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.1.2"
@@ -243,6 +266,18 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "fasteners"
+version = "0.18"
+description = "A python package that provides useful locks"
+category = "main"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "fasteners-0.18-py3-none-any.whl", hash = "sha256:1d4caf5f8db57b0e4107d94fd5a1d02510a450dced6ca77d1839064c1bacf20c"},
+    {file = "fasteners-0.18.tar.gz", hash = "sha256:cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953"},
+]
+
 [[package]]
 name = "filelock"
 version = "3.12.2"
@@ -427,6 +462,77 @@ files = [
 [package.dependencies]
 setuptools = "*"
 
+[[package]]
+name = "numcodecs"
+version = "0.11.0"
+description = "A Python package providing buffer compression and transformation codecs for use"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "numcodecs-0.11.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c0bc116752be45b4f9dca4315e5a2b4185e3b46f68c997dbb84aef334ceb5a1d"},
+    {file = "numcodecs-0.11.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c27dfca402f69fbfa01c46fb572086e77f38121192160cc8ed1177dc30702c52"},
+    {file = "numcodecs-0.11.0-cp310-cp310-win_amd64.whl", hash = "sha256:0fabc7dfdf64a9555bf8a34911e05b415793c67a1377207dc79cd96342291fa1"},
+    {file = "numcodecs-0.11.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:7dae3f5678f247336c84e7315a0c59a4fec7c33eb7db72d78ff5c776479a812e"},
+    {file = "numcodecs-0.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:32697785b786bb0039d3feeaabdc10f25eda6c149700cde954653aaa47637832"},
+    {file = "numcodecs-0.11.0-cp311-cp311-win_amd64.whl", hash = "sha256:8c2f36b21162c6ebccc05d3fe896f86b91dcf8709946809f730cc23a37f8234d"},
+    {file = "numcodecs-0.11.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:0c240858bf29e0ff254b1db60430e8b2658b8c8328b684f80033289d94807a7c"},
+    {file = "numcodecs-0.11.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ee5bda16e9d26a7a39fc20b6c1cec23b4debc314df5cfae3ed505149c2eeafc4"},
+    {file = "numcodecs-0.11.0-cp38-cp38-win_amd64.whl", hash = "sha256:bd05cdb853c7bcfde2efc809a9df2c5e205b96f70405b810e5788b45d0d81f73"},
+    {file = "numcodecs-0.11.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:694dc2e80b1f169b7deb14bdd0a04b20e5f17ef32cb0f81b71ab690406ec6bd9"},
+    {file = "numcodecs-0.11.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bf3925eeb37aed0e6c04d7fb9614133a3c8426dc77f8bda54c99c601a44b3bd3"},
+    {file = "numcodecs-0.11.0-cp39-cp39-win_amd64.whl", hash = "sha256:11596b71267417425ea8afb407477a67d684f434c8b07b1dd59c25a97d5c3ccb"},
+    {file = "numcodecs-0.11.0.tar.gz", hash = "sha256:6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb"},
+]
+
+[package.dependencies]
+entrypoints = "*"
+numpy = ">=1.7"
+
+[package.extras]
+docs = ["mock", "numpydoc", "sphinx", "sphinx-issues"]
+msgpack = ["msgpack"]
+test = ["coverage", "flake8", "pytest", "pytest-cov"]
+zfpy = ["zfpy (>=1.0.0)"]
+
+[[package]]
+name = "numpy"
+version = "1.24.3"
+description = "Fundamental package for array computing in Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "numpy-1.24.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:3c1104d3c036fb81ab923f507536daedc718d0ad5a8707c6061cdfd6d184e570"},
+    {file = "numpy-1.24.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:202de8f38fc4a45a3eea4b63e2f376e5f2dc64ef0fa692838e31a808520efaf7"},
+    {file = "numpy-1.24.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:8535303847b89aa6b0f00aa1dc62867b5a32923e4d1681a35b5eef2d9591a463"},
+    {file = "numpy-1.24.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2d926b52ba1367f9acb76b0df6ed21f0b16a1ad87c6720a1121674e5cf63e2b6"},
+    {file = "numpy-1.24.3-cp310-cp310-win32.whl", hash = "sha256:f21c442fdd2805e91799fbe044a7b999b8571bb0ab0f7850d0cb9641a687092b"},
+    {file = "numpy-1.24.3-cp310-cp310-win_amd64.whl", hash = "sha256:ab5f23af8c16022663a652d3b25dcdc272ac3f83c3af4c02eb8b824e6b3ab9d7"},
+    {file = "numpy-1.24.3-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:9a7721ec204d3a237225db3e194c25268faf92e19338a35f3a224469cb6039a3"},
+    {file = "numpy-1.24.3-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:d6cc757de514c00b24ae8cf5c876af2a7c3df189028d68c0cb4eaa9cd5afc2bf"},
+    {file = "numpy-1.24.3-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:76e3f4e85fc5d4fd311f6e9b794d0c00e7002ec122be271f2019d63376f1d385"},
+    {file = "numpy-1.24.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a1d3c026f57ceaad42f8231305d4653d5f05dc6332a730ae5c0bea3513de0950"},
+    {file = "numpy-1.24.3-cp311-cp311-win32.whl", hash = "sha256:c91c4afd8abc3908e00a44b2672718905b8611503f7ff87390cc0ac3423fb096"},
+    {file = "numpy-1.24.3-cp311-cp311-win_amd64.whl", hash = "sha256:5342cf6aad47943286afa6f1609cad9b4266a05e7f2ec408e2cf7aea7ff69d80"},
+    {file = "numpy-1.24.3-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:7776ea65423ca6a15255ba1872d82d207bd1e09f6d0894ee4a64678dd2204078"},
+    {file = "numpy-1.24.3-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:ae8d0be48d1b6ed82588934aaaa179875e7dc4f3d84da18d7eae6eb3f06c242c"},
+    {file = "numpy-1.24.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ecde0f8adef7dfdec993fd54b0f78183051b6580f606111a6d789cd14c61ea0c"},
+    {file = "numpy-1.24.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:4749e053a29364d3452c034827102ee100986903263e89884922ef01a0a6fd2f"},
+    {file = "numpy-1.24.3-cp38-cp38-win32.whl", hash = "sha256:d933fabd8f6a319e8530d0de4fcc2e6a61917e0b0c271fded460032db42a0fe4"},
+    {file = "numpy-1.24.3-cp38-cp38-win_amd64.whl", hash = "sha256:56e48aec79ae238f6e4395886b5eaed058abb7231fb3361ddd7bfdf4eed54289"},
+    {file = "numpy-1.24.3-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:4719d5aefb5189f50887773699eaf94e7d1e02bf36c1a9d353d9f46703758ca4"},
+    {file = "numpy-1.24.3-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:0ec87a7084caa559c36e0a2309e4ecb1baa03b687201d0a847c8b0ed476a7187"},
+    {file = "numpy-1.24.3-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:ea8282b9bcfe2b5e7d491d0bf7f3e2da29700cec05b49e64d6246923329f2b02"},
+    {file = "numpy-1.24.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:210461d87fb02a84ef243cac5e814aad2b7f4be953b32cb53327bb49fd77fbb4"},
+    {file = "numpy-1.24.3-cp39-cp39-win32.whl", hash = "sha256:784c6da1a07818491b0ffd63c6bbe5a33deaa0e25a20e1b3ea20cf0e43f8046c"},
+    {file = "numpy-1.24.3-cp39-cp39-win_amd64.whl", hash = "sha256:d5036197ecae68d7f491fcdb4df90082b0d4960ca6599ba2659957aafced7c17"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:352ee00c7f8387b44d19f4cada524586f07379c0d49270f87233983bc5087ca0"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1a7d6acc2e7524c9955e5c903160aa4ea083736fde7e91276b0e5d98e6332812"},
+    {file = "numpy-1.24.3-pp38-pypy38_pp73-win_amd64.whl", hash = "sha256:35400e6a8d102fd07c71ed7dcadd9eb62ee9a6e84ec159bd48c28235bbb0f8e4"},
+    {file = "numpy-1.24.3.tar.gz", hash = "sha256:ab344f1bf21f140adab8e47fdbc7c35a477dc01408791f8ba00d018dd0bc5155"},
+]
+
 [[package]]
 name = "packaging"
 version = "23.1"
@@ -860,7 +966,28 @@ platformdirs = ">=3.9.1,<4"
 docs = ["furo (>=2023.5.20)", "proselint (>=0.13)", "sphinx (>=7.0.1)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"]
 test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"]
 
+[[package]]
+name = "zarr"
+version = "2.14.2"
+description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
+    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+]
+
+[package.dependencies]
+asciitree = "*"
+fasteners = "*"
+numcodecs = ">=0.10.0"
+numpy = ">=1.20"
+
+[package.extras]
+jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
+
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "8f9c860337789e81ded8ae4a32435c60b9be73f28993b839a0c8bf304b4af637"
+content-hash = "4d1e5c2217e358fbade28531c262f70bf716a876f8d6222c3c8643ef34a9efef"
diff --git a/pyproject.toml b/pyproject.toml
index fa9b46b..f008f5c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 [tool.poetry.dependencies]
 python = "^3.9"
 pydantic = "^1.10.4"
+pydantic-zarr = "^0.1.3"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index d287218..4b320e4 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,17 +1,16 @@
 from __future__ import annotations
 from collections import Counter
-import textwrap
-from typing import Any, Dict, List, Optional, Tuple, Union, cast
+from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, root_validator, validator
-from pydantic_ome_ngff.base import VersionedBase
+from pydantic import BaseModel, conlist, root_validator, validator, Field
+from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
-from pydantic_ome_ngff.tree import Array, Attrs, Group
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.axes import AxisType
 from pydantic_ome_ngff.latest.axes import Axis
+from pydantic_zarr import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(BaseModel):
@@ -147,7 +146,7 @@ def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         return axes
 
 
-class MultiscaleAttrs(Attrs):
+class MultiscaleAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -156,42 +155,37 @@ class MultiscaleAttrs(Attrs):
     multiscales: List[Multiscale]
 
 
-class MultiscaleGroup(Group):
-    attrs: MultiscaleAttrs
-
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
     @root_validator
     def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        children: List[Union[Array, Group]] = values["children"]
-        child_arrays = []
-        child_groups = []
-
-        for child in children:
-            if isinstance(child, Group):
-                child_groups.append(child)
-            else:
-                child_arrays.append(child)
-        child_array_names = [a.name for a in child_arrays]
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
+
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in child_array_names:
-                    msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, "
-                        "but no array with that name was found in the children of "
-                        "that group. All arrays in multiscale metadata must be "
-                        "children of the group."
+                if (dpath := dataset.path) not in array_items:
+                    raise ValueError(
+                        f"""
+                    Dataset {dpath} was specified in multiscale metadata, but no 
+                    array with that name was found in the items of that group. All 
+                    arrays in multiscale metadata must be items of the group.
+                    """
                     )
                     raise ValueError(textwrap.fill(msg))
         return values
 
     @root_validator
     def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        array_children: Tuple[Array, ...] = tuple(
-            filter(lambda v: hasattr(v, "shape"), values["children"])
-        )
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
 
-        ndims = [len(a.shape) for a in array_children]
+        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             msg = (
                 "All arrays must have the same dimensionality. "
@@ -201,12 +195,13 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
-            tforms: List[ctx.CoordinateTransform] = []
+            tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
             for dataset in multiscale.datasets:
                 tforms.extend(dataset.coordinateTransformations)
             for tform in tforms:
+
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
                         Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
diff --git a/src/pydantic_ome_ngff/tree.py b/src/pydantic_ome_ngff/tree.py
deleted file mode 100644
index b14b93f..0000000
--- a/src/pydantic_ome_ngff/tree.py
+++ /dev/null
@@ -1,79 +0,0 @@
-from __future__ import annotations
-from typing import (
-    Protocol,
-    Tuple,
-    Dict,
-    Any,
-    Iterable,
-    Literal,
-    List,
-    Union,
-    runtime_checkable,
-)
-import textwrap
-from pydantic import BaseModel, Field
-from pydantic_ome_ngff.base import StrictBase
-
-NodeType = Literal["array", "group"]
-
-
-class Attrs(BaseModel):
-    ...
-
-
-class Node(StrictBase):
-    node_type: NodeType
-    name: str
-    attrs: Attrs = Attrs()
-
-
-class Array(Node):
-    node_type: NodeType = Field("array", const=True)
-    shape: Tuple[int, ...]
-    dtype: str
-
-
-class Group(Node):
-    node_type: NodeType = Field("group", const=True)
-    children: List[Union[Group, Array]]
-
-
-class NodeLike(Protocol):
-    basename: str
-    attrs: Dict[str, Any]
-
-
-@runtime_checkable
-class ArrayLike(NodeLike, Protocol):
-    shape: Tuple[int, ...]
-    dtype: Any
-
-
-@runtime_checkable
-class GroupLike(NodeLike, Protocol):
-    def values(self) -> Iterable[Union[GroupLike, ArrayLike]]:
-        """
-        Iterable of the children of this group
-        """
-        ...
-
-
-def build_tree(element: Union[GroupLike, ArrayLike]) -> Union[Group, Array]:
-    """
-    Recursively parse an array-like or group-like into an Array or Group.
-    """
-    result: Union[Group, Array]
-    name = element.basename
-    attrs = Attrs(**element.attrs)
-
-    if isinstance(element, ArrayLike):
-        result = Array(
-            shape=element.shape, name=name, dtype=str(element.dtype), attrs=attrs
-        )
-    elif isinstance(element, GroupLike):
-        children = list(map(build_tree, element.values()))
-        result = Group(name=name, attrs=attrs, children=children)
-    else:
-        msg = f"Object of type {type(element)} cannot be processed."
-        raise ValueError(textwrap.fill(msg))
-    return result
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index e18cda1..4bba3a5 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -2,13 +2,12 @@
 from collections import Counter
 import textwrap
 import warnings
-from typing import Any, Dict, List, Optional, Tuple, Union, cast
-
-from pydantic import BaseModel, conlist, root_validator, validator
+from typing import Any, Dict, List, Optional, Union, cast
 
+from pydantic import BaseModel, Field, conlist, root_validator, validator
+from pydantic_zarr import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.base import VersionedBase
-from pydantic_ome_ngff.tree import Group, Attrs, Array
+from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axes import Axis, AxisType
 import pydantic_ome_ngff.v04.coordinateTransformations as ctx
@@ -151,7 +150,7 @@ def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         return axes
 
 
-class MultiscaleAttrs(Attrs):
+class MultiscaleAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -160,42 +159,37 @@ class MultiscaleAttrs(Attrs):
     multiscales: List[Multiscale]
 
 
-class MultiscaleGroup(Group):
-    attrs: MultiscaleAttrs
-
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
     @root_validator
     def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        children: List[Union[Array, Group]] = values["children"]
-        child_arrays = []
-        child_groups = []
-
-        for child in children:
-            if isinstance(child, Group):
-                child_groups.append(child)
-            else:
-                child_arrays.append(child)
-        child_array_names = [a.name for a in child_arrays]
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
+
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in child_array_names:
-                    msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, "
-                        "but no array with that name was found in the children of "
-                        "that group. All arrays in multiscale metadata must be "
-                        "children of the group."
+                if (dpath := dataset.path) not in array_items:
+                    raise ValueError(
+                        f"""
+                    Dataset {dpath} was specified in multiscale metadata, but no 
+                    array with that name was found in the items of that group. All 
+                    arrays in multiscale metadata must be items of the group.
+                    """
                     )
                     raise ValueError(textwrap.fill(msg))
         return values
 
     @root_validator
     def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        array_children: Tuple[Array, ...] = tuple(
-            filter(lambda v: hasattr(v, "shape"), values["children"])
-        )
-        multiscales: List[Multiscale] = values["attrs"].multiscales
+        attrs = values["attrs"]
+        array_items: dict[str, ArraySpec] = {
+            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+        }
+        multiscales: List[Multiscale] = attrs.multiscales
 
-        ndims = tuple(len(a.shape) for a in array_children)
+        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             msg = (
                 "All arrays must have the same dimensionality. "
diff --git a/tests/test_latest.py b/tests/test_latest.py
index 3745696..a7586e3 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -2,8 +2,8 @@
 from typing import Optional, Tuple, List, Type
 import jsonschema as jsc
 import pytest
-from pydantic import ValidationError, BaseModel
-from pydantic_ome_ngff.tree import Array
+from pydantic import ValidationError
+from pydantic_zarr import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
     MultiscaleAttrs,
@@ -284,86 +284,52 @@ def test_coordinate_transforms_invalid_elements(
 
 
 def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1,) * len(default_multiscale.datasets), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError,
-        match="must be children of the group.",
+        match="array with that name was found in the items of that group.",
     ):
-        bad_children = [
-            Array(name=d.path + "bla", shape=(1, 1, 1, 1), dtype="")
+        bad_items = {
+            d.path
+            + "x": ArraySpec(
+                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+            )
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
 
 def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1,) * len(default_multiscale.datasets), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
         # arrays with varying rank
-        bad_children = [
-            Array(name=d.path, shape=(1,) * (idx + 1), dtype="")
+        bad_items = {
+            d.path: ArraySpec(
+                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+            )
             for idx, d in enumerate(default_multiscale.datasets)
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
-        bad_children = [
-            Array(name=d.path, shape=(1,), dtype="")
+        bad_items = {
+            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
-
-
-@pytest.mark.parametrize(
-    ("fname", "key", "Class"),
-    [
-        ("image-label", "image-label", ImageLabel),
-        ("plate0", "plate", Plate),
-        ("plate1", "plate", Plate),
-        ("well0", "well", Well),
-        ("well1", "well", Well),
-        (
-            "multiscales",
-            None,
-            MultiscaleAttrs,
-        ),
-    ],
-)
-def test_examples(fname: str, key: str, Class: Type[BaseModel]):
-    obj = loader.load_obj(fname)
-    if key is not None:
-        obj = obj[key]
-    Class.parse_obj(obj)
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
diff --git a/tests/test_v04.py b/tests/test_v04.py
index 067c5c8..29d0cda 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -2,12 +2,9 @@
 from typing import Optional, Tuple, List, Type
 import jsonschema as jsc
 import pytest
-from pydantic import ValidationError, BaseModel
-from pydantic_ome_ngff.tree import Array
-from pydantic_ome_ngff.v04.imageLabel import ImageLabel
-from pydantic_ome_ngff.v04.plate import Plate
-from pydantic_ome_ngff.v04.well import Well
-from .conftest import fetch_schemas, JsonLoader
+from pydantic import ValidationError
+from pydantic_zarr import ArraySpec
+from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
     MultiscaleAttrs,
@@ -287,60 +284,51 @@ def test_coordinate_transforms_invalid_elements(
 
 
 def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=[1] * len(default_multiscale.datasets), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError,
-        match="must be children of the group",
+        match="array with that name was found in the items of that group.",
     ):
-        bad_children = [
-            Array(name=d.path + "bla", shape=(1, 1, 1, 1), dtype="")
+        bad_items = {
+            d.path
+            + "x": ArraySpec(
+                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+            )
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
 
 def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
-    good_children = [
-        Array(name=d.path, shape=(1,) * len(default_multiscale.datasets), dtype="")
+    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+    good_items = {
+        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
         for d in default_multiscale.datasets
-    ]
-    MultiscaleGroup(
-        name="",
-        attrs={"multiscales": [default_multiscale.dict()]},
-        children=good_children,
-    )
+    }
+    MultiscaleGroup(attrs=group_attrs, items=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
         # arrays with varying rank
-        bad_children = [
-            Array(name=d.path, shape=(1,) * (idx + 1), dtype="")
+        bad_items = {
+            d.path: ArraySpec(
+                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+            )
             for idx, d in enumerate(default_multiscale.datasets)
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
+        }
+        MultiscaleGroup(attrs=group_attrs, items=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
-        bad_children = [
-            Array(name=d.path, shape=(1,), dtype="")
+        bad_items = {
+            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
             for d in default_multiscale.datasets
         ]
         MultiscaleGroup(

From 64fbfa8b83de1fb999a2b20a05d3822d541f5b70 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 6 Jun 2023 12:16:35 -0400
Subject: [PATCH 18/69] chore: update type signature of version in latest
 multiscale, although the version is still untyped. also use conlist for axes.

---
 src/pydantic_ome_ngff/latest/multiscales.py | 8 ++++----
 src/pydantic_ome_ngff/v04/multiscales.py    | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 4b320e4..27047f0 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -3,7 +3,7 @@
 from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, root_validator, validator, Field
+from pydantic import BaseModel, conlist, root_validator, validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
@@ -66,10 +66,10 @@ class Multiscale(VersionedBase):
     """
 
     # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # is not properly typed by the spec...
     _version = version
-
-    version: str = version
+    # SPEC: why is this untyped?
+    version: Any = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
     name: Optional[Any]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 4bba3a5..77effa6 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -4,7 +4,7 @@
 import warnings
 from typing import Any, Dict, List, Optional, Union, cast
 
-from pydantic import BaseModel, Field, conlist, root_validator, validator
+from pydantic import BaseModel, conlist, root_validator, validator
 from pydantic_zarr import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase

From 45ce1c472b01b19e1120e3f5c6f939e974a1528e Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 8 Nov 2023 15:36:50 +0100
Subject: [PATCH 19/69] feat: update to pydantic 2 / pydantic-zarr 0.5.2

---
 poetry.lock                                   | 1713 ++++++++++++-----
 pyproject.toml                                |    6 +-
 src/pydantic_ome_ngff/latest/axes.py          |   53 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |   65 +-
 src/pydantic_ome_ngff/v04/axes.py             |   48 +-
 src/pydantic_ome_ngff/v04/cli.py              |   15 +
 .../v04/coordinateTransformations.py          |   14 +-
 src/pydantic_ome_ngff/v04/imageLabel.py       |    8 +-
 src/pydantic_ome_ngff/v04/multiscales.py      |   90 +-
 src/pydantic_ome_ngff/v04/plate.py            |   23 +-
 tests/test_latest.py                          |   45 +-
 tests/test_v04.py                             |   79 +-
 12 files changed, 1498 insertions(+), 661 deletions(-)
 create mode 100644 src/pydantic_ome_ngff/v04/cli.py

diff --git a/poetry.lock b/poetry.lock
index 40e11bb..c952835 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,21 +1,198 @@
-# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+
+[[package]]
+name = "aiobotocore"
+version = "2.7.0"
+description = "Async client for aws services using botocore and aiohttp"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "aiobotocore-2.7.0-py3-none-any.whl", hash = "sha256:aec605df77ce4635a0479b50fd849aa6b640900f7b295021ecca192e1140e551"},
+    {file = "aiobotocore-2.7.0.tar.gz", hash = "sha256:506591374cc0aee1bdf0ebe290560424a24af176dfe2ea7057fe1df97c4f0467"},
+]
+
+[package.dependencies]
+aiohttp = ">=3.7.4.post0,<4.0.0"
+aioitertools = ">=0.5.1,<1.0.0"
+botocore = ">=1.31.16,<1.31.65"
+wrapt = ">=1.10.10,<2.0.0"
+
+[package.extras]
+awscli = ["awscli (>=1.29.16,<1.29.65)"]
+boto3 = ["boto3 (>=1.28.16,<1.28.65)"]
+
+[[package]]
+name = "aiohttp"
+version = "3.8.6"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1"},
+    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1d84166673694841d8953f0a8d0c90e1087739d24632fe86b1a08819168b4566"},
+    {file = "aiohttp-3.8.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:253bf92b744b3170eb4c4ca2fa58f9c4b87aeb1df42f71d4e78815e6e8b73c9e"},
+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3fd194939b1f764d6bb05490987bfe104287bbf51b8d862261ccf66f48fb4096"},
+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6c5f938d199a6fdbdc10bbb9447496561c3a9a565b43be564648d81e1102ac22"},
+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2817b2f66ca82ee699acd90e05c95e79bbf1dc986abb62b61ec8aaf851e81c93"},
+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0fa375b3d34e71ccccf172cab401cd94a72de7a8cc01847a7b3386204093bb47"},
+    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9de50a199b7710fa2904be5a4a9b51af587ab24c8e540a7243ab737b45844543"},
+    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:e1d8cb0b56b3587c5c01de3bf2f600f186da7e7b5f7353d1bf26a8ddca57f965"},
+    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:8e31e9db1bee8b4f407b77fd2507337a0a80665ad7b6c749d08df595d88f1cf5"},
+    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:7bc88fc494b1f0311d67f29fee6fd636606f4697e8cc793a2d912ac5b19aa38d"},
+    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:ec00c3305788e04bf6d29d42e504560e159ccaf0be30c09203b468a6c1ccd3b2"},
+    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:ad1407db8f2f49329729564f71685557157bfa42b48f4b93e53721a16eb813ed"},
+    {file = "aiohttp-3.8.6-cp310-cp310-win32.whl", hash = "sha256:ccc360e87341ad47c777f5723f68adbb52b37ab450c8bc3ca9ca1f3e849e5fe2"},
+    {file = "aiohttp-3.8.6-cp310-cp310-win_amd64.whl", hash = "sha256:93c15c8e48e5e7b89d5cb4613479d144fda8344e2d886cf694fd36db4cc86865"},
+    {file = "aiohttp-3.8.6-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:6e2f9cc8e5328f829f6e1fb74a0a3a939b14e67e80832975e01929e320386b34"},
+    {file = "aiohttp-3.8.6-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:e6a00ffcc173e765e200ceefb06399ba09c06db97f401f920513a10c803604ca"},
+    {file = "aiohttp-3.8.6-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:41bdc2ba359032e36c0e9de5a3bd00d6fb7ea558a6ce6b70acedf0da86458321"},
+    {file = "aiohttp-3.8.6-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:14cd52ccf40006c7a6cd34a0f8663734e5363fd981807173faf3a017e202fec9"},
+    {file = "aiohttp-3.8.6-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:2d5b785c792802e7b275c420d84f3397668e9d49ab1cb52bd916b3b3ffcf09ad"},
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+    {file = "aiohttp-3.8.6-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:42c89579f82e49db436b69c938ab3e1559e5a4409eb8639eb4143989bc390f2f"},
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 python-versions = ">=3.7"
 files = [
@@ -30,11 +207,32 @@ docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-
 tests = ["attrs[tests-no-zope]", "zope-interface"]
 tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
 
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+python-versions = ">= 3.7"
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+
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 description = "Python package for providing Mozilla's CA Bundle."
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 optional = false
 python-versions = ">=3.6"
 files = [
@@ -44,106 +242,118 @@ files = [
 
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+version = "3.4.0"
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 [package.dependencies]
@@ -231,7 +432,6 @@ toml = ["tomli"]
 name = "distlib"
 version = "0.3.7"
 description = "Distribution utilities"
-category = "dev"
 optional = false
 python-versions = "*"
 files = [
@@ -239,28 +439,15 @@ files = [
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 ]
 
-[[package]]
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-description = "Discover and load entry points from installed packages."
-category = "main"
-optional = false
-python-versions = ">=3.6"
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-
 [[package]]
 name = "exceptiongroup"
-version = "1.1.2"
+version = "1.1.3"
 description = "Backport of PEP 654 (exception groups)"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -268,42 +455,145 @@ test = ["pytest (>=6)"]
 
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-version = "0.18"
+version = "0.19"
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-python-versions = ">=3.7"
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+gcs = ["gcsfs"]
+git = ["pygit2"]
+github = ["requests"]
+gs = ["gcsfs"]
+gui = ["panel"]
+hdfs = ["pyarrow (>=1)"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
+libarchive = ["libarchive-c"]
+oci = ["ocifs"]
+s3 = ["s3fs"]
+sftp = ["paramiko"]
+smb = ["smbprotocol"]
+ssh = ["paramiko"]
+tqdm = ["tqdm"]
 
 [[package]]
 name = "identify"
-version = "2.5.26"
+version = "2.5.31"
 description = "File identification library for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.26-py2.py3-none-any.whl", hash = "sha256:c22a8ead0d4ca11f1edd6c9418c3220669b3b7533ada0a0ffa6cc0ef85cf9b54"},
-    {file = "identify-2.5.26.tar.gz", hash = "sha256:7243800bce2f58404ed41b7c002e53d4d22bcf3ae1b7900c2d7aefd95394bf7f"},
+    {file = "identify-2.5.31-py2.py3-none-any.whl", hash = "sha256:90199cb9e7bd3c5407a9b7e81b4abec4bb9d249991c79439ec8af740afc6293d"},
+    {file = "identify-2.5.31.tar.gz", hash = "sha256:7736b3c7a28233637e3c36550646fc6389bedd74ae84cb788200cc8e2dd60b75"},
 ]
 
 [package.extras]
@@ -313,7 +603,6 @@ license = ["ukkonen"]
 name = "idna"
 version = "3.4"
 description = "Internationalized Domain Names in Applications (IDNA)"
-category = "dev"
 optional = false
 python-versions = ">=3.5"
 files = [
@@ -325,7 +614,6 @@ files = [
 name = "iniconfig"
 version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
-category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
@@ -337,7 +625,6 @@ files = [
 name = "isort"
 version = "5.12.0"
 description = "A Python utility / library to sort Python imports."
-category = "dev"
 optional = false
 python-versions = ">=3.8.0"
 files = [
@@ -351,16 +638,26 @@ pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"
 plugins = ["setuptools"]
 requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
+[[package]]
+name = "jmespath"
+version = "1.0.1"
+description = "JSON Matching Expressions"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jmespath-1.0.1-py3-none-any.whl", hash = "sha256:02e2e4cc71b5bcab88332eebf907519190dd9e6e82107fa7f83b1003a6252980"},
+    {file = "jmespath-1.0.1.tar.gz", hash = "sha256:90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe"},
+]
+
 [[package]]
 name = "jsonschema"
-version = "4.18.4"
+version = "4.19.2"
 description = "An implementation of JSON Schema validation for Python"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.18.4-py3-none-any.whl", hash = "sha256:971be834317c22daaa9132340a51c01b50910724082c2c1a2ac87eeec153a3fe"},
-    {file = "jsonschema-4.18.4.tar.gz", hash = "sha256:fb3642735399fa958c0d2aad7057901554596c63349f4f6b283c493cf692a25d"},
+    {file = "jsonschema-4.19.2-py3-none-any.whl", hash = "sha256:eee9e502c788e89cb166d4d37f43084e3b64ab405c795c03d343a4dbc2c810fc"},
+    {file = "jsonschema-4.19.2.tar.gz", hash = "sha256:c9ff4d7447eed9592c23a12ccee508baf0dd0d59650615e847feb6cdca74f392"},
 ]
 
 [package.dependencies]
@@ -377,7 +674,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 name = "jsonschema-specifications"
 version = "2023.7.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
-category = "dev"
 optional = false
 python-versions = ">=3.8"
 files = [
@@ -388,40 +684,158 @@ files = [
 [package.dependencies]
 referencing = ">=0.28.0"
 
+[[package]]
+name = "markdown-it-py"
+version = "3.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
+]
+
+[package.dependencies]
+mdurl = ">=0.1,<1.0"
+
+[package.extras]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
+]
+
+[[package]]
+name = "multidict"
+version = "6.0.4"
+description = "multidict implementation"
+optional = false
+python-versions = ">=3.7"
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 [package.dependencies]
@@ -432,14 +846,12 @@ typing-extensions = ">=4.1.0"
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
 install-types = ["pip"]
-python2 = ["typed-ast (>=1.4.0,<2)"]
 reports = ["lxml"]
 
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 version = "1.0.0"
 description = "Type system extensions for programs checked with the mypy type checker."
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 optional = false
 python-versions = ">=3.5"
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 optional = false
 python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
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@@ -464,97 +875,98 @@ setuptools = "*"
 
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-entrypoints = "*"
 numpy = ">=1.7"
 
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 msgpack = ["msgpack"]
 test = ["coverage", "flake8", "pytest", "pytest-cov"]
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 zfpy = ["zfpy (>=1.0.0)"]
 
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 description = "Core utilities for Python packages"
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 optional = false
 python-versions = ">=3.7"
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 name = "platformdirs"
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 optional = false
 python-versions = ">=3.7"
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 [package.extras]
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 [[package]]
 name = "pluggy"
-version = "1.2.0"
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 [package.extras]
@@ -579,14 +990,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
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+version = "3.5.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
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 python-versions = ">=3.8"
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 [package.dependencies]
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 [[package]]
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 description = "Python HTTP for Humans."
-category = "dev"
 optional = false
 python-versions = ">=3.7"
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 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
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+
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+
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@@ -947,14 +1552,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
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+    {file = "yarl-1.9.2.tar.gz", hash = "sha256:04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+
 [[package]]
 name = "zarr"
-version = "2.14.2"
+version = "2.16.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
-category = "main"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zarr-2.14.2-py3-none-any.whl", hash = "sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2"},
-    {file = "zarr-2.14.2.tar.gz", hash = "sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc"},
+    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
+    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
 ]
 
 [package.dependencies]
 asciitree = "*"
 fasteners = "*"
 numcodecs = ">=0.10.0"
-numpy = ">=1.20"
+numpy = ">=1.20,<1.21.0 || >1.21.0"
 
 [package.extras]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "4d1e5c2217e358fbade28531c262f70bf716a876f8d6222c3c8643ef34a9efef"
+content-hash = "d6ba84447520a466cb6cd52278784c5dfdac4c3ac0622619ac0306a55dec74c6"
diff --git a/pyproject.toml b/pyproject.toml
index f008f5c..dd93a87 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,8 +9,10 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
 python = "^3.9"
-pydantic = "^1.10.4"
-pydantic-zarr = "^0.1.3"
+pydantic-zarr = "0.5.2"
+fsspec = "^2023.10.0"
+s3fs = "^2023.10.0"
+rich = "^13.6.0"
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/src/pydantic_ome_ngff/latest/axes.py b/src/pydantic_ome_ngff/latest/axes.py
index 15d4a3c..b049c4f 100644
--- a/src/pydantic_ome_ngff/latest/axes.py
+++ b/src/pydantic_ome_ngff/latest/axes.py
@@ -1,6 +1,9 @@
-from __future__ import annotations
+import warnings
+from pydantic import model_validator
+from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-import pydantic_ome_ngff.v04.axes as axv04
+from typing import Any, Optional
+from pydantic_ome_ngff.v04.axes import AxisType, SpaceUnit, TimeUnit
 
 
 class Axis(axv04.Axis):
@@ -10,3 +13,49 @@ class Axis(axv04.Axis):
     """
 
     _version = version
+    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
+    name: Any
+    type: Optional[str]
+    unit: Optional[str]
+
+    @model_validator(mode="after")
+    def check_units(self) -> "Axis":
+        typ = self.type
+        unit = self.unit
+        if typ == AxisType.space:
+            if unit not in SpaceUnit.__members__:
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit for "
+                    f" an axis with type '{typ}''."
+                )
+                warnings.warn(msg)
+        elif typ == AxisType.time:
+            if unit not in TimeUnit.__members__:
+                msg = (
+                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                    f"with type '{typ}'."
+                )
+                warnings.warn(msg)
+        elif typ == AxisType.channel:
+            pass
+        elif typ is None:
+            msg = (
+                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
+                "that the 'type' field of an axis should be set to a string."
+            )
+            warnings.warn(msg, UserWarning)
+        else:
+            msg = (
+                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
+                " spec states that the 'type' field of an axis should be one of "
+                f"{AxisType._member_names_}."
+            )
+            warnings.warn(msg)
+
+        if unit is None:
+            msg = (
+                f"Null unit. Version {self._version} of the OME-NGFF spec states "
+                "that the `unit` field of an axis should be set to a string."
+            )
+            warnings.warn(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 27047f0..4a39cfa 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -3,23 +3,23 @@
 from typing import Any, Dict, List, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, root_validator, validator
+from pydantic import BaseModel, conlist, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import coordinateTransformations as ctx
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.axes import AxisType
 from pydantic_ome_ngff.latest.axes import Axis
-from pydantic_zarr import GroupSpec, ArraySpec
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(BaseModel):
     path: str
     coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_items=1, max_items=2
+        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
     )
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_dimensionality(
         cls,
         transforms: List[
@@ -39,7 +39,7 @@ def check_transforms_dimensionality(
             raise ValueError(textwrap.fill(msg))
         return transforms
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_types(
         cls, transforms: List[ctx.CoordinateTransform]
     ) -> List[ctx.CoordinateTransform]:
@@ -72,23 +72,23 @@ class Multiscale(VersionedBase):
     version: Any = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
-    name: Optional[Any]
+    name: Any = None
     # SPEC: not clear what this field is for, given the existence of .metadata
     # SPEC: untyped!
-    type: Optional[Any]
+    type: Any = None
     # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_items=2, max_items=5)
+    axes: conlist(Axis, min_length=2, max_length=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[
         List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
     ]
 
-    @validator("name")
+    @field_validator("name")
     def check_name(cls, name: Optional[str]) -> Optional[str]:
         if name is None:
             msg = (
@@ -99,7 +99,7 @@ def check_name(cls, name: Optional[str]) -> Optional[str]:
             warnings.warn(textwrap.fill(msg))
         return name
 
-    @validator("axes")
+    @field_validator("axes")
     def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         name_dupes = duplicates(a.name for a in axes)
         if len(name_dupes) > 0:
@@ -156,32 +156,30 @@ class MultiscaleAttrs(BaseModel):
 
 
 class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @root_validator
-    def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_arrays_exist(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if hasattr(v, "shape")
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
-                    raise ValueError(
-                        f"""
-                    Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the items of that group. All 
-                    arrays in multiscale metadata must be items of the group.
-                    """
+                    msg = (
+                        f"Dataset {dpath} was specified in multiscale metadata, but no "
+                        "array with that name was found in the items of that group. "
+                        "All arrays in multiscale metadata must be items of the group."
                     )
-                    raise ValueError(textwrap.fill(msg))
-        return values
+                    raise ValueError(msg)
+        return self
 
-    @root_validator
-    def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_array_ndim(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if hasattr(v, "shape")
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
@@ -191,7 +189,7 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                 "All arrays must have the same dimensionality. "
                 f"Got arrays with dimensionality {ndims}."
             )
-            raise ValueError(textwrap.fill(msg))
+            raise ValueError(msg)
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
@@ -209,10 +207,11 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                     )
                     if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
                         msg = (
-                            f"Transform {tform} has dimensionality {tform_dims} which "
-                            "does not match the dimensionality of the arrays in this "
-                            "group ({ndims}). Transform dimensionality must match "
-                            "array dimensionality."
+                            f"Transform {tform} has dimensionality {tform_dims} "
+                            "which does not match the dimensionality "
+                            f"of the arrays in this group ({ndims}). "
+                            "Transform dimensionality must match array "
+                            "dimensionality."
                         )
-                        raise ValueError(textwrap.fill(msg))
-        return values
+                        raise ValueError(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/axes.py b/src/pydantic_ome_ngff/v04/axes.py
index fb87f9f..dedc924 100644
--- a/src/pydantic_ome_ngff/v04/axes.py
+++ b/src/pydantic_ome_ngff/v04/axes.py
@@ -3,9 +3,8 @@
 from pydantic_ome_ngff.v04.base import version
 import warnings
 from enum import Enum
-from typing import Any, Dict, Optional
-from pydantic import validator
-import textwrap
+from typing import Any, Optional
+from pydantic import model_validator
 
 
 class AxisType(str, Enum):
@@ -81,43 +80,44 @@ class Axis(StrictVersionedBase):
     type: Optional[str]
     unit: Optional[str]
 
-    @validator("unit")
-    def check_unit(cls, unit: str, values: Dict[str, AxisType]) -> str:
-        typ = values["type"]
+    @model_validator(mode="after")
+    def check_units(self) -> "Axis":
+        typ = self.type
+        unit = self.unit
         if typ == AxisType.space:
             if unit not in SpaceUnit.__members__:
                 msg = (
-                    f'Unit "{unit}" is not recognized as a standard unit for an '
-                    f'axis with type "{typ}".'
+                    f"Unit '{unit}' is not recognized as a standard unit "
+                    f"for an axis with type '{typ}'."
                 )
-                warnings.warn(textwrap.fill(msg))
-
+                warnings.warn(msg)
         elif typ == AxisType.time:
             if unit not in TimeUnit.__members__:
                 msg = (
-                    f'Unit "{unit}" is not recognized as a standard unit for an '
-                    f'axis with type "{typ}".'
+                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                    f"with type '{typ}'."
                 )
-                warnings.warn(textwrap.fill(msg))
+                warnings.warn(msg)
         elif typ == AxisType.channel:
             pass
         elif typ is None:
             msg = (
-                f"Null axis type. Version {cls._version} of the OME-NGFF spec "
-                "states that the `type` field of an axis should be a string."
+                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
+                "that the 'type' field of an axis should be set to a string."
             )
-            warnings.warn(textwrap.fill(msg))
+            warnings.warn(msg, UserWarning)
         else:
             msg = (
-                f'Unknown axis type "{typ}". Version {cls._version} of the '
-                "OME-NGFF spec states that the `type` field of an axis should be "
-                f"one of {AxisType._member_names_}."
+                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
+                " spec states that the 'type' field of an axis should be one of "
+                f"{AxisType._member_names_}."
             )
-            warnings.warn(textwrap.fill(msg))
+            warnings.warn(msg)
+
         if unit is None:
             msg = (
-                f"Null unit. Version {cls._version} of the OME-NGFF spec states "
-                "that the `unit` field of an axis should be a string."
+                f"Null unit. Version {self._version} of the OME-NGFF spec states "
+                "that the `unit` field of an axis should be set to a string."
             )
-            warnings.warn(textwrap.fill(msg))
-        return unit
+            warnings.warn(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/cli.py b/src/pydantic_ome_ngff/v04/cli.py
new file mode 100644
index 0000000..6d9af11
--- /dev/null
+++ b/src/pydantic_ome_ngff/v04/cli.py
@@ -0,0 +1,15 @@
+import sys
+from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+import zarr
+from pydantic import ValidationError
+from rich import print_json, print
+
+if __name__ == "__main__":
+    path: str = sys.argv[1]
+    group = zarr.open(path, mode="r")
+    try:
+        result = MultiscaleGroup.from_zarr(group).model_dump_json(indent=2)
+        print_json(result)
+    except ValidationError as e:
+        result = e
+        print(result)
diff --git a/src/pydantic_ome_ngff/v04/coordinateTransformations.py b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
index bfca241..f28663c 100644
--- a/src/pydantic_ome_ngff/v04/coordinateTransformations.py
+++ b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
@@ -1,7 +1,5 @@
-from __future__ import annotations
-import textwrap
-from typing import List, Literal, Union
-from pydantic import BaseModel
+from typing import Literal, Sequence, Union
+from pydantic_ome_ngff.base import StrictBase
 
 
 class IdentityTransform(BaseModel):
@@ -35,8 +33,8 @@ class VectorTranslationTransform(BaseModel):
     """
 
     type: Literal["translation"] = "translation"
-    translation: List[
-        float
+    translation: Sequence[
+        Union[float, int]
     ]  # SPEC: redundant field name -- we already know it's translation
 
 
@@ -47,7 +45,9 @@ class VectorScaleTransform(BaseModel):
     """
 
     type: Literal["scale"] = "scale"
-    scale: List[float]  # SPEC: redundant field name -- we already know it's scale
+    scale: Sequence[
+        Union[float, int]
+    ]  # SPEC: redundant field name -- we already know it's scale
 
 
 def get_transform_ndim(
diff --git a/src/pydantic_ome_ngff/v04/imageLabel.py b/src/pydantic_ome_ngff/v04/imageLabel.py
index b8627ac..8ddff66 100644
--- a/src/pydantic_ome_ngff/v04/imageLabel.py
+++ b/src/pydantic_ome_ngff/v04/imageLabel.py
@@ -1,8 +1,8 @@
 from __future__ import annotations
 import warnings
 from typing import List, Optional, Tuple
-import textwrap
-from pydantic import BaseModel, Field, validator
+
+from pydantic import BaseModel, Field, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.base import version
@@ -37,7 +37,7 @@ class ImageLabel(VersionedBase):
     properties: Optional[List[Properties]]
     source: Optional[Source]
 
-    @validator("version")
+    @field_validator("version")
     def check_version(cls, ver: str) -> str:
         if ver is None:
             msg = f"""
@@ -48,7 +48,7 @@ def check_version(cls, ver: str) -> str:
             warnings.warn(textwrap.fill(msg))
         return ver
 
-    @validator("colors")
+    @field_validator("colors")
     def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
             msg = f"""
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 77effa6..7871109 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -4,8 +4,8 @@
 import warnings
 from typing import Any, Dict, List, Optional, Union, cast
 
-from pydantic import BaseModel, conlist, root_validator, validator
-from pydantic_zarr import GroupSpec, ArraySpec
+from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -16,10 +16,10 @@
 class MultiscaleDataset(BaseModel):
     path: str
     coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_items=1, max_items=2
+        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
     )
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_dimensionality(
         cls,
         transforms: List[
@@ -36,10 +36,10 @@ def check_transforms_dimensionality(
                 "Elements of coordinateTransformations must have the same "
                 f"dimensionality. Got elements with dimensionality = {ndims}."
             )
-            raise ValueError(textwrap.fill(msg))
+            raise ValueError(msg)
         return transforms
 
-    @validator("coordinateTransformations")
+    @field_validator("coordinateTransformations")
     def check_transforms_types(
         cls,
         transforms: List[
@@ -51,15 +51,14 @@ def check_transforms_types(
                 "The first element of coordinateTransformations must be a scale "
                 f"transform. Got {tform} instead."
             )
-            raise ValueError(textwrap.fill(msg))
+            raise ValueError(msg)
         if len(transforms) == 2:
             if (tform := transforms[1].type) != "translation":
                 msg = (
                     "The second element of coordinateTransformations must be a "
-                    f"translation transform. Got {tform} instead."
+                    f"translation transform. got {tform} instead."
                 )
-                raise ValueError(textwrap.fill(msg))
-
+                raise ValueError(msg)
         return transforms
 
 
@@ -76,34 +75,34 @@ class Multiscale(VersionedBase):
     version: Optional[Any] = version
     # SPEC: why is this nullable instead of reserving the empty string
     # SPEC: untyped!
-    name: Optional[Any]
+    name: Optional[Any] = None
     # SPEC: not clear what this field is for, given the existence of .metadata
     # SPEC: untyped!
-    type: Optional[Any]
+    type: Any = None
     # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
     # SPEC: should not exist at top level and instead
     # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_items=2, max_items=5)
+    axes: conlist(Axis, min_length=2, max_length=5)
     # SPEC: should not live here, and if it is here,
     # it should default to an empty list instead of being nullable
     coordinateTransformations: Optional[
         List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ]
+    ] = None
 
-    @validator("name")
+    @field_validator("name")
     def check_name(cls, name: str) -> str:
         if name is None:
             msg = (
-                f"The name field was set to `None`. Version {cls._version} of the "
-                "OME-NGFF spec states that the `name` field of a Multiscales object "
-                "should not be None."
+                f"The name field was set to None. Version {cls._version} "
+                "of the OME-NGFF spec states that the `name` field of a Multiscales "
+                "object should not be None."
             )
-            warnings.warn(textwrap.fill(msg))
+            warnings.warn(msg)
         return name
 
-    @validator("axes")
+    @field_validator("axes")
     def check_axes(cls, axes: List[Axis]) -> List[Axis]:
         name_dupes = duplicates(a.name for a in axes)
         if len(name_dupes) > 0:
@@ -156,36 +155,35 @@ class MultiscaleAttrs(BaseModel):
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: List[Multiscale]
+    multiscales: conlist(Multiscale, min_length=1)
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @root_validator
-    def check_arrays_exist(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
+    @model_validator(mode="after")
+    def check_arrays_exist(self) -> "MultiscaleGroup":
+
+        attrs = self.attributes
+        array_items: dict[str, dict[str, Any]] = {
+            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
-                    raise ValueError(
-                        f"""
-                    Dataset {dpath} was specified in multiscale metadata, but no 
-                    array with that name was found in the items of that group. All 
-                    arrays in multiscale metadata must be items of the group.
-                    """
+                    msg = (
+                        f"Dataset {dpath} was specified in multiscale metadata, but no "
+                        "array with that name was found in the items of that group. "
+                        "All arrays in multiscale metadata must be items of the group."
                     )
-                    raise ValueError(textwrap.fill(msg))
-        return values
+                    raise ValueError(msg)
+        return self
 
-    @root_validator
-    def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
-        attrs = values["attrs"]
+    @model_validator(mode="after")
+    def check_array_ndim(self) -> "MultiscaleGroup":
+        attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
-            k: v for k, v in values["items"].items() if hasattr(v, "shape")
+            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
         multiscales: List[Multiscale] = attrs.multiscales
 
@@ -195,7 +193,7 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                 "All arrays must have the same dimensionality. "
                 f"Got arrays with dimensionality {ndims}."
             )
-            raise ValueError(textwrap.fill(msg))
+            raise ValueError(msg)
 
         # check that each transform has compatible rank
         for multiscale in multiscales:
@@ -212,10 +210,10 @@ def check_array_ndim(cls, values: Dict[str, Any]) -> Dict[str, Any]:
                     )
                     if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
                         msg = (
-                            f"Transform {tform} has dimensionality {tform_dims} which "
-                            "does not match the dimensionality of the arrays in this "
-                            "group ({ndims}). Transform dimensionality must match "
-                            "array dimensionality."
+                            f"Transform {tform} has dimensionality {tform_dims} "
+                            "which does notmatch the dimensionality of the arrays "
+                            f"in this group ({ndims}). Transform dimensionality "
+                            "must match array dimensionality."
                         )
-                        raise ValueError(textwrap.fill(msg))
-        return values
+                        raise ValueError(msg)
+        return self
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 3f0fe48..4309514 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -3,13 +3,14 @@
 
 from pydantic import BaseModel, PositiveInt, NonNegativeInt
 from pydantic_ome_ngff.base import VersionedBase
-
 from pydantic_ome_ngff.v04.base import version
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
+from typing import Union
 
 
 class Acquisition(BaseModel):
-    id: NonNegativeInt
-    name: Optional[str]
+    id: PositiveInt
+    name: Optional[str] = None
     maximumfieldcount: PositiveInt
 
 
@@ -17,14 +18,14 @@ class Entry(BaseModel):
     name: str
 
 
-class Well(BaseModel):
+class WellMeta(BaseModel):
     # must be {rowName}/{columnName}
     path: str
     rowIndex: NonNegativeInt
     columnIndex: NonNegativeInt
 
 
-class Plate(VersionedBase):
+class PlateMeta(VersionedBase):
     """
     Plate metadata
     see https://ngff.openmicroscopy.org/0.4/#plate-md
@@ -34,9 +35,17 @@ class Plate(VersionedBase):
     # is not required by the spec...
     _version = version
     version: Optional[str] = version
-    name: Optional[str]
+    name: Optional[str] = None
     acquisitions: List[Acquisition]
     columns: List[Entry]
     rows: List[Entry]
     field_count: PositiveInt
-    wells: List[Well]
+    wells: List[WellMeta]
+
+
+class PlateAttributes(BaseModel):
+    plate: PlateMeta
+
+
+class PlateGroup(GroupSpec[PlateAttributes, Union[GroupSpec, ArraySpec]]):
+    ...
diff --git a/tests/test_latest.py b/tests/test_latest.py
index a7586e3..e1be221 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -3,7 +3,7 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_zarr import ArraySpec
+from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
     MultiscaleAttrs,
@@ -185,7 +185,7 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
 
 
 @pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
-def test_multiscale_axis_length(num_axes: int):
+def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
@@ -207,7 +207,7 @@ def test_multiscale_axis_length(num_axes: int):
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="type=value_error.list"):
+    with pytest.raises(ValidationError, match="List should have"):
         Multiscale(
             name="foo",
             axes=axes,
@@ -250,10 +250,10 @@ def test_coordinate_transforms_invalid_ndims():
         ],
     ),
 )
-def test_coordinate_transforms_invalid_lenght(
+def test_coordinate_transforms_invalid_length(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
-    with pytest.raises(ValidationError, match="ensure this value has at most 2 items"):
+) -> None:
+    with pytest.raises(ValidationError, match="List should have at most 2 items"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -276,20 +276,22 @@ def test_coordinate_transforms_invalid_lenght(
 )
 def test_coordinate_transforms_invalid_elements(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
+) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -298,21 +300,23 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
         bad_items = {
             d.path
             + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
 
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -320,16 +324,19 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
         # arrays with varying rank
         bad_items = {
             d.path: ArraySpec(
-                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+                shape=(1,) * (idx + 1),
+                dtype="uint8",
+                chunks=(1,) * (idx + 1),
+                attributes={},
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
+            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
diff --git a/tests/test_v04.py b/tests/test_v04.py
index 29d0cda..a354283 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -3,7 +3,7 @@
 import jsonschema as jsc
 import pytest
 from pydantic import ValidationError
-from pydantic_zarr import ArraySpec
+from pydantic_zarr.v2 import ArraySpec
 from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
@@ -136,7 +136,7 @@ def test_multiscale_unique_axis_names():
         ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
+def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
@@ -185,7 +185,7 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
 
 
 @pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
-def test_multiscale_axis_length(num_axes: int):
+def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
@@ -207,7 +207,7 @@ def test_multiscale_axis_length(num_axes: int):
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="type=value_error.list"):
+    with pytest.raises(ValidationError, match="List should have"):
         Multiscale(
             name="foo",
             axes=axes,
@@ -223,7 +223,7 @@ def test_multiscale_axis_length(num_axes: int):
         )
 
 
-def test_coordinate_transforms_invalid_ndims():
+def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
         VectorScaleTransform(scale=(1, 1)),
         VectorTranslationTransform(translation=(1, 1, 1)),
@@ -250,10 +250,12 @@ def test_coordinate_transforms_invalid_ndims():
         ],
     ),
 )
-def test_coordinate_transforms_invalid_lenght(
+def test_coordinate_transforms_invalid_length(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
-    with pytest.raises(ValidationError, match="ensure this value has at most 2 items"):
+) -> None:
+    with pytest.raises(
+        ValidationError, match="List should have at most 2 items after validation, not"
+    ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -276,20 +278,22 @@ def test_coordinate_transforms_invalid_lenght(
 )
 def test_coordinate_transforms_invalid_elements(
     transforms: Tuple[CoordinateTransform, CoordinateTransform]
-):
+) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -298,20 +302,22 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale):
         bad_items = {
             d.path
             + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={}
+                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
+def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
     group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
     good_items = {
-        d.path: ArraySpec(shape=(1, 1, 1, 1), dtype="", chunks=(1, 1, 1, 1), attrs={})
+        d.path: ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attrs=group_attrs, items=good_items)
+    MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -319,42 +325,19 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale):
         # arrays with varying rank
         bad_items = {
             d.path: ArraySpec(
-                shape=(1,) * (idx + 1), dtype="", chunks=(1,) * (idx + 1), attrs={}
+                shape=(1,) * (idx + 1),
+                dtype="uint8",
+                chunks=(1,) * (idx + 1),
+                attributes={},
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attrs=group_attrs, items=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="", chunks=(1,), attrs={})
+            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
-        ]
-        MultiscaleGroup(
-            name="",
-            attrs={"multiscales": [default_multiscale.dict()]},
-            children=bad_children,
-        )
-
-
-@pytest.mark.parametrize(
-    ("fname", "key", "Class"),
-    [
-        ("image-label", "image-label", ImageLabel),
-        ("plate0", "plate", Plate),
-        ("plate1", "plate", Plate),
-        ("well0", "well", Well),
-        ("well1", "well", Well),
-        (
-            "multiscales",
-            None,
-            MultiscaleAttrs,
-        ),
-    ],
-)
-def test_examples(fname: str, key: str, Class: Type[BaseModel]):
-    obj = loader.load_obj(fname)
-    if key is not None:
-        obj = obj[key]
-    Class.parse_obj(obj)
+        }
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)

From 41bdf3fe14ba85225686bd4a3e03783d7e8d227d Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 8 Nov 2023 15:42:54 +0100
Subject: [PATCH 20/69] feat: pointless renaming

---
 src/pydantic_ome_ngff/latest/__init__.py |  4 ++--
 src/pydantic_ome_ngff/latest/plate.py    |  4 ++--
 src/pydantic_ome_ngff/latest/well.py     |  4 ++--
 src/pydantic_ome_ngff/v04/__init__.py    |  4 ++--
 src/pydantic_ome_ngff/v04/well.py        |  2 +-
 tests/test_latest.py                     | 10 +++++-----
 6 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index aa98389..1f72baa 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,6 +1,6 @@
 from pydantic_ome_ngff.latest.axes import Axis  # noqa
 from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
 from pydantic_ome_ngff.latest.imageLabel import ImageLabel  # noqa
-from pydantic_ome_ngff.latest.well import Well  # noqa
-from pydantic_ome_ngff.latest.plate import Plate  # noqa
+from pydantic_ome_ngff.latest.well import WellMeta  # noqa
+from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.latest.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index 4e7a54b..e462b11 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -3,10 +3,10 @@
 
 
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.plate import Plate as PlateV04
+from pydantic_ome_ngff.v04.plate import PlateMeta as PlateMetaV04
 
 
-class Plate(PlateV04):
+class PlateMeta(PlateMetaV04):
     """
     Plate metadata.
     See https://ngff.openmicroscopy.org/latest/#plate-md
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index 350d63b..b36a2d0 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,10 +1,10 @@
 from __future__ import annotations
 from typing import Optional
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.well import Well as WellV04
+from pydantic_ome_ngff.v04.well import WellMeta as WellMetaV04
 
 
-class Well(WellV04):
+class WellMeta(WellMetaV04):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/latest/#well-md
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index e69208d..da6b4d7 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -2,6 +2,6 @@
 from pydantic_ome_ngff.v04.coordinateTransformations import CoordinateTransform  # noqa
 from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
 from pydantic_ome_ngff.v04.imageLabel import ImageLabel  # noqa
-from pydantic_ome_ngff.v04.well import Well  # noqa
-from pydantic_ome_ngff.v04.plate import Plate  # noqa
+from pydantic_ome_ngff.v04.well import WellMeta  # noqa
+from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.v04.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 9c602f2..9ba2a6f 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -12,7 +12,7 @@ class Image(BaseModel):
     acquisition: Optional[int]
 
 
-class Well(VersionedBase):
+class WellMeta(VersionedBase):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/0.4/#well-md
diff --git a/tests/test_latest.py b/tests/test_latest.py
index e1be221..f799ed9 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -25,7 +25,7 @@
 
 
 @pytest.fixture
-def default_multiscale():
+def default_multiscale() -> Multiscale:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -70,12 +70,12 @@ def default_multiscale():
     return multi
 
 
-def test_multiscale(default_multiscale):
+def test_multiscale(default_multiscale: Multiscale) -> None:
     base_schema, strict_schema = fetch_schemas("latest", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
 
 
-def test_multiscale_unique_axis_names():
+def test_multiscale_unique_axis_names() -> None:
 
     axes = [
         Axis(name="y", type="space", unit="meter"),
@@ -136,7 +136,7 @@ def test_multiscale_unique_axis_names():
         ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]):
+def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
@@ -223,7 +223,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
 
 
-def test_coordinate_transforms_invalid_ndims():
+def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
         VectorScaleTransform(scale=(1, 1)),
         VectorTranslationTransform(translation=(1, 1, 1)),

From 6dab0a8226832cd2a9a403586b95df0c193a3ec9 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Dec 2023 15:12:27 +0100
Subject: [PATCH 21/69] feat: big refactor: split validators into separate
 functions, rename transforms, etc

---
 .pre-commit-config.yaml                       |  14 +-
 src/pydantic_ome_ngff/latest/__init__.py      |   4 +-
 src/pydantic_ome_ngff/latest/axes.py          |  61 ----
 src/pydantic_ome_ngff/latest/axis.py          |  10 +
 .../latest/{imageLabel.py => label.py}        |   4 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |   7 +-
 ...dinateTransformations.py => transforms.py} |  21 +-
 src/pydantic_ome_ngff/v04/__init__.py         |   6 +-
 .../v04/{axes.py => axis.py}                  |  78 +++---
 src/pydantic_ome_ngff/v04/cli.py              |  15 -
 .../v04/coordinateTransformations.py          |  73 -----
 .../v04/{imageLabel.py => label.py}           |   0
 src/pydantic_ome_ngff/v04/multiscales.py      | 260 +++++++++---------
 src/pydantic_ome_ngff/v04/plate.py            |  21 +-
 src/pydantic_ome_ngff/v04/transforms.py       | 114 ++++++++
 src/pydantic_ome_ngff/v04/well.py             |  30 +-
 tests/test_latest.py                          |  19 +-
 tests/test_v04.py                             | 100 ++++---
 18 files changed, 418 insertions(+), 419 deletions(-)
 delete mode 100644 src/pydantic_ome_ngff/latest/axes.py
 create mode 100644 src/pydantic_ome_ngff/latest/axis.py
 rename src/pydantic_ome_ngff/latest/{imageLabel.py => label.py} (73%)
 rename src/pydantic_ome_ngff/latest/{coordinateTransformations.py => transforms.py} (75%)
 rename src/pydantic_ome_ngff/v04/{axes.py => axis.py} (57%)
 delete mode 100644 src/pydantic_ome_ngff/v04/cli.py
 delete mode 100644 src/pydantic_ome_ngff/v04/coordinateTransformations.py
 rename src/pydantic_ome_ngff/v04/{imageLabel.py => label.py} (100%)
 create mode 100644 src/pydantic_ome_ngff/v04/transforms.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index db3e79d..2c2a769 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,18 +5,16 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/psf/black
-    rev: 22.12.0
-    hooks:
-    - id: black
-      language_version: python3.9
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
     - id: check-yaml
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.245'
+    rev: v0.1.8
     hooks:
+      # Run the linter.
       - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
\ No newline at end of file
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index 1f72baa..fb9e90e 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,6 +1,6 @@
-from pydantic_ome_ngff.latest.axes import Axis  # noqa
+from pydantic_ome_ngff.latest.axis import Axis  # noqa
 from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.latest.imageLabel import ImageLabel  # noqa
+from pydantic_ome_ngff.latest.label import ImageLabel  # noqa
 from pydantic_ome_ngff.latest.well import WellMeta  # noqa
 from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.latest.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/latest/axes.py b/src/pydantic_ome_ngff/latest/axes.py
deleted file mode 100644
index b049c4f..0000000
--- a/src/pydantic_ome_ngff/latest/axes.py
+++ /dev/null
@@ -1,61 +0,0 @@
-import warnings
-from pydantic import model_validator
-from pydantic_ome_ngff.base import StrictVersionedBase
-from pydantic_ome_ngff.latest.base import version
-from typing import Any, Optional
-from pydantic_ome_ngff.v04.axes import AxisType, SpaceUnit, TimeUnit
-
-
-class Axis(axv04.Axis):
-    """
-    Axis metadata.
-    See https://ngff.openmicroscopy.org/latest/#axes-md
-    """
-
-    _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: Any
-    type: Optional[str]
-    unit: Optional[str]
-
-    @model_validator(mode="after")
-    def check_units(self) -> "Axis":
-        typ = self.type
-        unit = self.unit
-        if typ == AxisType.space:
-            if unit not in SpaceUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for "
-                    f" an axis with type '{typ}''."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.time:
-            if unit not in TimeUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                    f"with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.channel:
-            pass
-        elif typ is None:
-            msg = (
-                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
-                "that the 'type' field of an axis should be set to a string."
-            )
-            warnings.warn(msg, UserWarning)
-        else:
-            msg = (
-                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
-                " spec states that the 'type' field of an axis should be one of "
-                f"{AxisType._member_names_}."
-            )
-            warnings.warn(msg)
-
-        if unit is None:
-            msg = (
-                f"Null unit. Version {self._version} of the OME-NGFF spec states "
-                "that the `unit` field of an axis should be set to a string."
-            )
-            warnings.warn(msg)
-        return self
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
new file mode 100644
index 0000000..fbd8459
--- /dev/null
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -0,0 +1,10 @@
+from pydantic_ome_ngff.v04 import Axis as AxisV04
+
+
+class Axis(AxisV04):
+    """
+    Axis metadata.
+    See https://ngff.openmicroscopy.org/latest/#axes-md
+
+    Note: this metadata is unchanged from version 0.4 of the spec.
+    """
diff --git a/src/pydantic_ome_ngff/latest/imageLabel.py b/src/pydantic_ome_ngff/latest/label.py
similarity index 73%
rename from src/pydantic_ome_ngff/latest/imageLabel.py
rename to src/pydantic_ome_ngff/latest/label.py
index c1f78d3..0f7784d 100644
--- a/src/pydantic_ome_ngff/latest/imageLabel.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -1,6 +1,4 @@
-from __future__ import annotations
-from typing import Optional
-from pydantic_ome_ngff.v04.imageLabel import ImageLabel as ImageLabelV04
+from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
 from pydantic_ome_ngff.latest.base import version
 
 
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 4a39cfa..084d508 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -6,10 +6,10 @@
 from pydantic import BaseModel, conlist, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.latest import coordinateTransformations as ctx
+from pydantic_ome_ngff.latest import transforms as ctx
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.v04.axes import AxisType
-from pydantic_ome_ngff.latest.axes import Axis
+from pydantic_ome_ngff.v04.axis import AxisType
+from pydantic_ome_ngff.latest.axis import Axis
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
@@ -199,7 +199,6 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for dataset in multiscale.datasets:
                 tforms.extend(dataset.coordinateTransformations)
             for tform in tforms:
-
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
                         Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
diff --git a/src/pydantic_ome_ngff/latest/coordinateTransformations.py b/src/pydantic_ome_ngff/latest/transforms.py
similarity index 75%
rename from src/pydantic_ome_ngff/latest/coordinateTransformations.py
rename to src/pydantic_ome_ngff/latest/transforms.py
index ee0203a..3a69cea 100644
--- a/src/pydantic_ome_ngff/latest/coordinateTransformations.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,31 +1,38 @@
 from __future__ import annotations
 import textwrap
 from typing import Union
-import pydantic_ome_ngff.v04.coordinateTransformations as ctx
+import pydantic_ome_ngff.v04.transforms as ctx
 
 
-class IdentityTransform(ctx.IdentityTransform):
+class IdentityTransform(ctx.Identity):
     """
     An identity transform with no parameters.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathTransform(ctx.PathTransform):
+class PathScale(ctx.PathScale):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorTranslationTransform(ctx.VectorTranslationTransform):
+class PathTranslation(ctx.PathTranslation):
+    """ "
+    A coordinateTransform with at "path" field.
+    See https://ngff.openmicroscopy.org/latest/#trafo-md
+    """
+
+
+class VectorTranslationTransform(ctx.VectorTranslation):
     """
     A translation transform with a `translate` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorScaleTransform(ctx.VectorScaleTransform):
+class VectorScaleTransform(ctx.VectorScale):
     """
     A scale transform with a `scale` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
@@ -51,6 +58,6 @@ def get_transform_ndim(
         raise ValueError(textwrap.fill(msg))
 
 
-ScaleTransform = Union[VectorScaleTransform, PathTransform]
-TranslationTransform = Union[VectorTranslationTransform, PathTransform]
+ScaleTransform = Union[VectorScaleTransform, PathScale]
+TranslationTransform = Union[VectorTranslationTransform, PathTranslation]
 CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index da6b4d7..ffd00cb 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -1,7 +1,7 @@
-from pydantic_ome_ngff.v04.axes import Axis  # noqa
-from pydantic_ome_ngff.v04.coordinateTransformations import CoordinateTransform  # noqa
+from pydantic_ome_ngff.v04.axis import Axis  # noqa
+from pydantic_ome_ngff.v04.transforms import Transform  # noqa
 from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.v04.imageLabel import ImageLabel  # noqa
+from pydantic_ome_ngff.v04.label import ImageLabel  # noqa
 from pydantic_ome_ngff.v04.well import WellMeta  # noqa
 from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
 from pydantic_ome_ngff.v04.base import version  # noqa
diff --git a/src/pydantic_ome_ngff/v04/axes.py b/src/pydantic_ome_ngff/v04/axis.py
similarity index 57%
rename from src/pydantic_ome_ngff/v04/axes.py
rename to src/pydantic_ome_ngff/v04/axis.py
index dedc924..3baa42d 100644
--- a/src/pydantic_ome_ngff/v04/axes.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -3,8 +3,6 @@
 from pydantic_ome_ngff.v04.base import version
 import warnings
 from enum import Enum
-from typing import Any, Optional
-from pydantic import model_validator
 
 
 class AxisType(str, Enum):
@@ -76,48 +74,48 @@ class Axis(StrictVersionedBase):
 
     _version = version
     # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: Any
-    type: Optional[str]
-    unit: Optional[str]
+    name: str
+    type: str | None
+    unit: str | None
 
-    @model_validator(mode="after")
-    def check_units(self) -> "Axis":
-        typ = self.type
-        unit = self.unit
-        if typ == AxisType.space:
-            if unit not in SpaceUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit "
-                    f"for an axis with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.time:
-            if unit not in TimeUnit.__members__:
-                msg = (
-                    f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                    f"with type '{typ}'."
-                )
-                warnings.warn(msg)
-        elif typ == AxisType.channel:
-            pass
-        elif typ is None:
-            msg = (
-                f"Null axis type. Version {self._version} of the OME-NGFF spec states "
-                "that the 'type' field of an axis should be set to a string."
-            )
-            warnings.warn(msg, UserWarning)
-        else:
+
+def check_unit(model: Axis) -> "Axis":
+    typ = model.type
+    unit = model.unit
+    if typ == AxisType.space:
+        if unit not in SpaceUnit.__members__:
             msg = (
-                f"Unknown axis type '{typ}'. Version {self._version} of the OME-NGFF "
-                " spec states that the 'type' field of an axis should be one of "
-                f"{AxisType._member_names_}."
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
-
-        if unit is None:
+    elif typ == AxisType.time:
+        if unit not in TimeUnit.__members__:
             msg = (
-                f"Null unit. Version {self._version} of the OME-NGFF spec states "
-                "that the `unit` field of an axis should be set to a string."
+                f"Unit '{unit}' is not recognized as a standard unit for an axis "
+                f"with type '{typ}'."
             )
             warnings.warn(msg)
-        return self
+    elif typ == AxisType.channel:
+        pass
+    elif typ is None:
+        msg = (
+            f"Null axis type. Version {model._version} of the OME-NGFF spec states "
+            "that the 'type' field of an axis should be set to a string."
+        )
+        warnings.warn(msg, UserWarning)
+    else:
+        msg = (
+            f"Unknown axis type '{typ}'. Version {model._version} of the OME-NGFF "
+            " spec states that the 'type' field of an axis should be one of "
+            f"{AxisType._member_names_}."
+        )
+        warnings.warn(msg)
+
+    if unit is None:
+        msg = (
+            f"Null unit. Version {model._version} of the OME-NGFF spec states "
+            "that the `unit` field of an axis should be set to a string."
+        )
+        warnings.warn(msg)
+    return model
diff --git a/src/pydantic_ome_ngff/v04/cli.py b/src/pydantic_ome_ngff/v04/cli.py
deleted file mode 100644
index 6d9af11..0000000
--- a/src/pydantic_ome_ngff/v04/cli.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import sys
-from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
-import zarr
-from pydantic import ValidationError
-from rich import print_json, print
-
-if __name__ == "__main__":
-    path: str = sys.argv[1]
-    group = zarr.open(path, mode="r")
-    try:
-        result = MultiscaleGroup.from_zarr(group).model_dump_json(indent=2)
-        print_json(result)
-    except ValidationError as e:
-        result = e
-        print(result)
diff --git a/src/pydantic_ome_ngff/v04/coordinateTransformations.py b/src/pydantic_ome_ngff/v04/coordinateTransformations.py
deleted file mode 100644
index f28663c..0000000
--- a/src/pydantic_ome_ngff/v04/coordinateTransformations.py
+++ /dev/null
@@ -1,73 +0,0 @@
-from typing import Literal, Sequence, Union
-from pydantic_ome_ngff.base import StrictBase
-
-
-class IdentityTransform(BaseModel):
-    """
-    An identity transform with no parameters.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    # SPEC why does this exist, as opposed to translation by 0 or scale by 1?
-    type: str = "identity"
-
-
-class PathTransform(BaseModel):
-    """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    # SPEC: the existence of this type is a massive sinkhole in the spec
-    # translate and scale are both so simple that nobody should be using a path
-    # argument to refer to some remote resource representing a translation
-    # or a scale transform
-    type: Union[Literal["scale"], Literal["translation"]]
-    path: str
-
-
-class VectorTranslationTransform(BaseModel):
-    """
-    A translation transform with a `translate` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    type: Literal["translation"] = "translation"
-    translation: Sequence[
-        Union[float, int]
-    ]  # SPEC: redundant field name -- we already know it's translation
-
-
-class VectorScaleTransform(BaseModel):
-    """
-    A scale transform with a `scale` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
-    """
-
-    type: Literal["scale"] = "scale"
-    scale: Sequence[
-        Union[float, int]
-    ]  # SPEC: redundant field name -- we already know it's scale
-
-
-def get_transform_ndim(
-    transform: Union[VectorScaleTransform, VectorTranslationTransform],
-) -> int:
-    """
-    Get the dimensionality of a vector transform (scale or translation).
-    """
-    if transform.type == "scale" and hasattr(transform, "scale"):
-        return len(transform.scale)
-    elif transform.type == "translation" and hasattr(transform, "translation"):
-        return len(transform.translation)
-    else:
-        msg = (
-            f"Transform must be either VectorScaleTransform or "
-            f"VectorTranslationTransform. Got {type(transform)} instead."
-        )
-        raise ValueError(textwrap.fill(msg))
-
-
-ScaleTransform = Union[VectorScaleTransform, PathTransform]
-TranslationTransform = Union[VectorTranslationTransform, PathTransform]
-CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
diff --git a/src/pydantic_ome_ngff/v04/imageLabel.py b/src/pydantic_ome_ngff/v04/label.py
similarity index 100%
rename from src/pydantic_ome_ngff/v04/imageLabel.py
rename to src/pydantic_ome_ngff/v04/label.py
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 7871109..39e7f10 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,65 +1,136 @@
 from __future__ import annotations
 from collections import Counter
-import textwrap
-import warnings
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Annotated, Any, Dict, List, Optional, Sequence, Union, cast
 
-from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic import AfterValidator, BaseModel, conlist, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
-from pydantic_ome_ngff.v04.axes import Axis, AxisType
-import pydantic_ome_ngff.v04.coordinateTransformations as ctx
+from pydantic_ome_ngff.v04.axis import Axis, AxisType
+import pydantic_ome_ngff.v04.transforms as ctx
 
+VALID_NDIM = (2, 3, 4, 5)
 
-class MultiscaleDataset(BaseModel):
-    path: str
-    coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
-    )
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_dimensionality(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        ndims = []
-        for tx in transforms:
-            # this repeated conditional logic around transforms is so awful.
-            if type(tx) in (ctx.VectorScaleTransform, ctx.VectorTranslationTransform):
-                ndims.append(ctx.get_transform_ndim(tx))
-        if len(set(ndims)) > 1:
-            msg = (
-                "Elements of coordinateTransformations must have the same "
-                f"dimensionality. Got elements with dimensionality = {ndims}."
-            )
-            raise ValueError(msg)
-        return transforms
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_types(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        if (tform := transforms[0].type) != "scale":
+
+def ensure_scale_translation(
+    transforms: Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]],
+) -> Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]]:
+    """
+    Ensure that
+        - the first element is a scale transformation
+        - the second element is a translation transform
+    """
+    if len(transforms) == 0:
+        raise ValueError("Invalid transforms: got 0, expected 1 or 2")
+
+    maybe_scale = transforms[0]
+    if maybe_scale.type != "scale":
+        msg = (
+            "The first element of coordinateTransformations must be a scale "
+            f"transform. Got {maybe_scale} instead."
+        )
+        raise ValueError(msg)
+    if len(transforms) == 2:
+        maybe_trans = transforms[1]
+        if (maybe_trans.type) != "translation":
             msg = (
-                "The first element of coordinateTransformations must be a scale "
-                f"transform. Got {tform} instead."
+                "The second element of coordinateTransformations must be a "
+                f"translation transform. Got {maybe_trans} instead."
             )
             raise ValueError(msg)
-        if len(transforms) == 2:
-            if (tform := transforms[1].type) != "translation":
-                msg = (
-                    "The second element of coordinateTransformations must be a "
-                    f"translation transform. got {tform} instead."
-                )
-                raise ValueError(msg)
-        return transforms
+    else:
+        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        raise ValueError(msg)
+    return transforms
+
+
+def ensure_transforms_length(
+    transforms: Sequence[ctx.VectorScale | ctx.VectorTranslation],
+) -> Sequence[ctx.VectorScale | ctx.VectorTranslation]:
+    if (num_tx := len(transforms)) not in (1, 2):
+        msg = f"Invalid number of transforms: got {num_tx}, expected 1 or 2"
+        raise ValueError(msg)
+    return transforms
+
+
+class MultiscaleDataset(StrictBase):
+    """
+    A single entry in the multiscales.datasets list.
+    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+
+    Attributes:
+    ----------
+    path: str
+        The path to the zarr array that stores the image described by this metadata.
+        This path should be relative to the group that contains this metadata.
+    coordinateTransformations: Union[ctx.ScaleTransform, ctx.TranslationTransform]
+        The coordinate transformations for this image.
+    """
+
+    path: str
+    coordinateTransformations: Annotated[
+        List[ctx.Scale | ctx.Translation],
+        AfterValidator(ensure_transforms_length),
+        AfterValidator(ensure_scale_translation),
+        AfterValidator(ctx.ensure_dimensionality),
+    ]
+
+
+def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that there are between 2 and 5 axes (inclusive)
+    """
+    if (len_axes := len(axes)) not in VALID_NDIM:
+        msg = f"Incorrect number of axes provided ({len_axes}). Only 2, 3, 4, or 5 axes are allowed."
+        raise ValueError(msg)
+    return axes
+
+
+def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that the names of the axes are unique
+    """
+    name_dupes = duplicates(a.name for a in axes)
+    if len(name_dupes) > 0:
+        msg = f"Axis names must be unique. Axis names {tuple(name_dupes.keys())} are repeated."
+        raise ValueError(msg)
+    return axes
+
+
+def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
+    """
+    Ensure that the following conditions hold:
+        - there are only 2 or 3 axes with type "space"
+        - the axes with type "space" are last in the list of axes
+        - there is only 1 axis with type "time"
+        - there is only 1 axis with type "channel"
+        - there is only 1 axis with a custom type
+    """
+    axis_types = [ax.type for ax in axes]
+    type_census = Counter(axis_types)
+    num_spaces = type_census["space"]
+    if num_spaces < 2 or num_spaces > 3:
+        msg = f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes are allowed."
+        raise ValueError(msg)
+
+    elif not all(a == "space" for a in axis_types[-num_spaces:]):
+        msg = f"Space axes must come last. Got axes with order: {axis_types}."
+        raise ValueError(msg)
+
+    if (num_times := type_census["time"]) > 1:
+        msg = f"Invalid number of time axes: {num_times}. Only 1 time axis is allowed."
+        raise ValueError(msg)
+
+    if (num_channels := type_census["channel"]) > 1:
+        msg = f"Invalid number of channel axes: {num_channels}. Only 1 channel axis is allowed."
+        raise ValueError(msg)
+
+    custom_axes = set(axis_types) - set(AxisType._member_names_)
+    if (num_custom := len(custom_axes)) > 1:
+        msg = f"Invalid number of custom axes: {num_custom}. Only 1 custom axis is allowed."
+        raise ValueError(msg)
+    return axes
 
 
 class Multiscale(VersionedBase):
@@ -71,82 +142,19 @@ class Multiscale(VersionedBase):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    # SPEC: why is this optional? why is it untyped?
-    version: Optional[Any] = version
-    # SPEC: why is this nullable instead of reserving the empty string
-    # SPEC: untyped!
-    name: Optional[Any] = None
-    # SPEC: not clear what this field is for, given the existence of .metadata
-    # SPEC: untyped!
+    version: Any = version
+    name: Any = None
     type: Any = None
-    # SPEC: should default to empty dict instead of None
     metadata: Optional[Dict[str, Any]] = None
     datasets: List[MultiscaleDataset]
-    # SPEC: should not exist at top level and instead
-    # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_length=2, max_length=5)
-    # SPEC: should not live here, and if it is here,
-    # it should default to an empty list instead of being nullable
-    coordinateTransformations: Optional[
-        List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ] = None
-
-    @field_validator("name")
-    def check_name(cls, name: str) -> str:
-        if name is None:
-            msg = (
-                f"The name field was set to None. Version {cls._version} "
-                "of the OME-NGFF spec states that the `name` field of a Multiscales "
-                "object should not be None."
-            )
-            warnings.warn(msg)
-        return name
-
-    @field_validator("axes")
-    def check_axes(cls, axes: List[Axis]) -> List[Axis]:
-        name_dupes = duplicates(a.name for a in axes)
-        if len(name_dupes) > 0:
-            msg = (
-                f"Axis names must be unique. Axis names {tuple(name_dupes.keys())} "
-                "are repeated."
-            )
-            raise ValueError(textwrap.fill(msg))
-        axis_types = [ax.type for ax in axes]
-        type_census = Counter(axis_types)
-        num_spaces = type_census["space"]
-        if num_spaces < 2 or num_spaces > 3:
-            msg = (
-                f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space "
-                "axes are allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
+    axes: Annotated[
+        List[Axis],
+        AfterValidator(ensure_axis_length),
+        AfterValidator(ensure_axis_names),
+        AfterValidator(ensure_axis_types),
+    ]
 
-        elif not all(a == "space" for a in axis_types[-num_spaces:]):
-            msg = f"Space axes must come last. Got axes with order: {axis_types}"
-            raise ValueError(textwrap.fill(msg))
-
-        if (num_times := type_census["time"]) > 1:
-            msg = (
-                f"Invalid number of time axes: {num_times}. "
-                "Only 1 time axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-
-        if (num_channels := type_census["channel"]) > 1:
-            msg = (
-                f"Invalid number of channel axes: {num_channels}. "
-                "Only 1 channel axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-
-        custom_axes = set(axis_types) - set(AxisType._member_names_)
-        if len(custom_axes) > 1:
-            msg = (
-                f"Invalid number of custom axes: {custom_axes}. "
-                "Only 1 custom axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-        return axes
+    coordinateTransformations: List[ctx.Scale | ctx.Translation] | None = None
 
 
 class MultiscaleAttrs(BaseModel):
@@ -161,11 +169,11 @@ class MultiscaleAttrs(BaseModel):
 class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
-
         attrs = self.attributes
-        array_items: dict[str, dict[str, Any]] = {
+        array_items: dict[str, dict[str, ArraySpec]] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
+
         multiscales: List[Multiscale] = attrs.multiscales
 
         for multiscale in multiscales:
@@ -205,10 +213,10 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for tform in tforms:
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
-                        Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
+                        Union[ctx.VectorScale, ctx.VectorTranslation],
                         tform,
                     )
-                    if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
+                    if (tform_dims := ctx.ndim(tform)) not in set(ndims):
                         msg = (
                             f"Transform {tform} has dimensionality {tform_dims} "
                             "which does notmatch the dimensionality of the arrays "
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 4309514..cc8ddef 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,12 +1,14 @@
 from __future__ import annotations
 from typing import List, Optional
 
-from pydantic import BaseModel, PositiveInt, NonNegativeInt
+from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
+from pydantic_ome_ngff.v04.well import WellGroup
+
 
 class Acquisition(BaseModel):
     id: PositiveInt
@@ -31,8 +33,7 @@ class PlateMeta(VersionedBase):
     see https://ngff.openmicroscopy.org/0.4/#plate-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # the version here as a private class attribute because the version is not required by the spec
     _version = version
     version: Optional[str] = version
     name: Optional[str] = None
@@ -47,5 +48,15 @@ class PlateAttributes(BaseModel):
     plate: PlateMeta
 
 
-class PlateGroup(GroupSpec[PlateAttributes, Union[GroupSpec, ArraySpec]]):
-    ...
+class PlateGroup(GroupSpec[PlateAttributes, Union[WellGroup, GroupSpec, ArraySpec]]):
+    @field_validator("members", mode="after")
+    @classmethod
+    def contains_well(
+        cls, members: Union[WellGroup, GroupSpec, ArraySpec]
+    ) -> Union[WellGroup, GroupSpec, ArraySpec]:
+        """
+        Check that .members contains a WellGroup
+        """
+        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+            raise ValidationError
+        return members
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
new file mode 100644
index 0000000..52c23a3
--- /dev/null
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -0,0 +1,114 @@
+from __future__ import annotations
+
+from typing import Literal, Sequence, Tuple, Union
+from pydantic_ome_ngff.base import StrictBase
+
+
+class Identity(StrictBase):
+    """
+    An identity transform. It has no parameters, and no valid use according to the spec.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: str = "identity"
+
+
+class PathTranslation(StrictBase):
+    """
+    A coordinateTransform with a `path` field.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"] = "translation"
+    path: str
+
+
+class PathScale(StrictBase):
+    """
+    A coordinateTransform with a `path` field.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"] = "scale"
+    path: str
+
+
+class VectorTranslation(StrictBase):
+    """
+    A translation transform with a `translate` field that is a vector.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["translation"] = "translation"
+    translation: Sequence[float | int]
+
+
+class VectorScale(StrictBase):
+    """
+    A scale transform with a `scale` field that is a vector.
+    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    """
+
+    type: Literal["scale"] = "scale"
+    scale: Sequence[float | int]
+
+
+def ndim(
+    transform: Union[VectorScale, VectorTranslation],
+) -> int:
+    """
+    Get the dimensionality of a vector transform (scale or translation).
+    """
+    if hasattr(transform, "scale"):
+        return len(transform.scale)
+    elif hasattr(transform, "translation"):
+        return len(transform.translation)
+    else:
+        msg = (
+            "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
+            f"Got {type(transform)} instead."
+        )
+        raise ValueError(msg)
+
+
+def scale_translation(
+    scale: Sequence[float], translation: Sequence[float]
+) -> Tuple[Scale, Translation]:
+    """
+    Create a scale and transformation transformation from a scale and a translation parameter
+    """
+    len_scale = len(scale)
+    len_translation = len(translation)
+    if len_scale < 1:
+        msg = f"Not enough values in scale. Got {len_scale}"
+        raise ValueError(msg)
+    if len_translation < 1:
+        msg = f"Not enough values in `tranlsation`. Got {len_translation}"
+        raise ValueError(msg)
+    if len_translation != len_scale:
+        msg = (
+            f"Length of `scale` and `translation` do not match. `scale` has length = {len_scale}"
+            f"but `translation` has length = {len_translation}"
+        )
+        raise ValueError(msg)
+
+    return (VectorScale(scale=scale), VectorTranslation(translation=translation))
+
+
+Scale = VectorScale | PathScale
+Translation = VectorTranslation | PathTranslation
+Transform = Scale | Translation
+
+
+def ensure_dimensionality(
+    transforms: Sequence[VectorScale | VectorTranslation],
+) -> Sequence[VectorScale | VectorTranslation]:
+    ndims = tuple(ndim(tx) for tx in transforms)
+    ndims_set = set(ndims)
+    if len(ndims_set) > 1:
+        msg = (
+            "The transforms have inconsistent dimensionality. "
+            f"Got transforms with dimensionality = {ndims}."
+        )
+        raise ValueError(msg)
+    return transforms
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 9ba2a6f..bf883d0 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,10 +1,11 @@
-from __future__ import annotations
-from typing import List, Optional
+from typing import List, Optional, Union
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ValidationError, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 
 from pydantic_ome_ngff.v04.base import version
+from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class Image(BaseModel):
@@ -18,8 +19,27 @@ class WellMeta(VersionedBase):
     See https://ngff.openmicroscopy.org/0.4/#well-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    # the version here as a private class attribute because the version is not required by the spec
     _version = version
     version: Optional[str] = version
     images: List[Image]
+
+
+class WellAttributes(BaseModel):
+    well: WellMeta
+
+
+class WellGroup(
+    GroupSpec[WellAttributes, Union[MultiscaleGroup, GroupSpec, ArraySpec]]
+):
+    @field_validator("members", mode="after")
+    @classmethod
+    def contains_well(
+        cls, members: Union[MultiscaleGroup, GroupSpec, ArraySpec]
+    ) -> Union[MultiscaleGroup, GroupSpec, ArraySpec]:
+        """
+        Check that .members contains a MultiscaleGroup
+        """
+        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+            raise ValidationError
+        return members
diff --git a/tests/test_latest.py b/tests/test_latest.py
index f799ed9..f33c65d 100644
--- a/tests/test_latest.py
+++ b/tests/test_latest.py
@@ -10,18 +10,13 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
-from pydantic_ome_ngff.latest.well import Well
-from pydantic_ome_ngff.latest.plate import Plate
-from pydantic_ome_ngff.latest.imageLabel import ImageLabel
-from pydantic_ome_ngff.latest.coordinateTransformations import (
+from pydantic_ome_ngff.latest.transforms import (
     CoordinateTransform,
     VectorScaleTransform,
     VectorTranslationTransform,
 )
-from pydantic_ome_ngff.latest.axes import Axis
-from .conftest import fetch_schemas, JsonLoader
-
-loader = JsonLoader("latest")
+from pydantic_ome_ngff.latest.axis import Axis
+from .conftest import fetch_schemas
 
 
 @pytest.fixture
@@ -76,7 +71,6 @@ def test_multiscale(default_multiscale: Multiscale) -> None:
 
 
 def test_multiscale_unique_axis_names() -> None:
-
     axes = [
         Axis(name="y", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -251,7 +245,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[CoordinateTransform, CoordinateTransform],
 ) -> None:
     with pytest.raises(ValidationError, match="List should have at most 2 items"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
@@ -275,7 +269,7 @@ def test_coordinate_transforms_invalid_length(
     ),
 )
 def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[CoordinateTransform, CoordinateTransform],
 ) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
@@ -298,8 +292,7 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
         match="array with that name was found in the items of that group.",
     ):
         bad_items = {
-            d.path
-            + "x": ArraySpec(
+            d.path + "x": ArraySpec(
                 shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets
diff --git a/tests/test_v04.py b/tests/test_v04.py
index a354283..33a2850 100644
--- a/tests/test_v04.py
+++ b/tests/test_v04.py
@@ -11,18 +11,18 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
-from pydantic_ome_ngff.v04.coordinateTransformations import (
-    CoordinateTransform,
-    VectorScaleTransform,
-    VectorTranslationTransform,
+from pydantic_ome_ngff.v04.transforms import (
+    Transform,
+    VectorScale,
+    VectorTranslation,
 )
-from pydantic_ome_ngff.v04.axes import Axis
+from pydantic_ome_ngff.v04.axis import Axis
 
 loader = JsonLoader("v04")
 
 
 @pytest.fixture
-def default_multiscale():
+def default_multiscale() -> Multiscale:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -34,13 +34,13 @@ def default_multiscale():
         MultiscaleDataset(
             path=f"path{idx}",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -56,7 +56,7 @@ def default_multiscale():
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(
+            VectorScale(
                 scale=[
                     1,
                 ]
@@ -67,14 +67,12 @@ def default_multiscale():
     return multi
 
 
-def test_multiscale(default_multiscale):
+def test_multiscale(default_multiscale: Multiscale) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
-    # breakpoint()
-    jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
+    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
 
-def test_multiscale_unique_axis_names():
-
+def test_multiscale_unique_axis_names() -> None:
     axes = [
         Axis(name="y", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -86,8 +84,8 @@ def test_multiscale_unique_axis_names():
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -97,7 +95,7 @@ def test_multiscale_unique_axis_names():
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(scale=[1, 1, 1]),
+            VectorScale(scale=[1, 1, 1]),
         ],
     )
 
@@ -110,8 +108,8 @@ def test_multiscale_unique_axis_names():
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -122,7 +120,7 @@ def test_multiscale_unique_axis_names():
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
+                VectorScale(scale=[1, 1, 1]),
             ],
         )
 
@@ -132,11 +130,9 @@ def test_multiscale_unique_axis_names():
     (
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-        (None, "space", "space", None),
-        ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
@@ -152,13 +148,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -168,13 +164,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         )
     ]
     # TODO: make some axis-specifc exceptions
-    with pytest.raises(ValidationError):
+    with pytest.raises(ValidationError, match="Space axes must come last."):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -192,13 +188,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -207,13 +203,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="List should have"):
+    with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -225,10 +221,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
 
 def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
-        VectorScaleTransform(scale=(1, 1)),
-        VectorTranslationTransform(translation=(1, 1, 1)),
+        VectorScale(scale=(1, 1)),
+        VectorTranslation(translation=(1, 1, 1)),
     ]
-    with pytest.raises(ValidationError, match="Got elements with dimensionality"):
+    with pytest.raises(
+        ValidationError,
+        match="The transforms have inconsistent dimensionality.",  # noqa
+    ):
         MultiscaleDataset(path="foo", coordinateTransformations=tforms)
 
 
@@ -236,26 +235,20 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ]
-        * 3,
+            VectorScale(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+        ],
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-        [
-            VectorScaleTransform(scale=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ],
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: List[Transform],
 ) -> None:
-    with pytest.raises(
-        ValidationError, match="List should have at most 2 items after validation, not"
-    ):
+    with pytest.raises(ValidationError, match="expected 1 or 2"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -263,21 +256,21 @@ def test_coordinate_transforms_invalid_length(
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
 def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform]
+    transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
         ValidationError, match="element of coordinateTransformations must be a"
@@ -300,8 +293,7 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
         match="array with that name was found in the items of that group.",
     ):
         bad_items = {
-            d.path
-            + "x": ArraySpec(
+            d.path + "x": ArraySpec(
                 shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
             )
             for d in default_multiscale.datasets

From fb777cbf243e2bafb1fe1d2f725884cd23b6b0ea Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 1 Jan 2024 17:56:08 +0100
Subject: [PATCH 22/69] feat: use python 3.10 as baseline, refactor the test
 suite a bit, use inheritance more for the latest classes, start looking at
 coverage and adjusting things accordingly

---
 poetry.lock                                   | 1473 +++++++++--------
 pyproject.toml                                |   32 +-
 src/pydantic_ome_ngff/base.py                 |    2 +-
 src/pydantic_ome_ngff/latest/axis.py          |    5 +-
 src/pydantic_ome_ngff/latest/multiscales.py   |  220 +--
 src/pydantic_ome_ngff/latest/transforms.py    |   41 +-
 src/pydantic_ome_ngff/v04/axis.py             |   49 +-
 src/pydantic_ome_ngff/v04/label.py            |   64 +-
 src/pydantic_ome_ngff/v04/multiscales.py      |  103 +-
 src/pydantic_ome_ngff/v04/transforms.py       |   18 +-
 src/pydantic_ome_ngff/v04/well.py             |    1 +
 tests/latest/__init__.py                      |    0
 .../test_multiscales.py}                      |  121 +-
 tests/v04/__init__.py                         |    0
 tests/v04/test_axis.py                        |   17 +
 tests/v04/test_label.py                       |   25 +
 .../{test_v04.py => v04/test_multiscales.py}  |   35 +-
 17 files changed, 1095 insertions(+), 1111 deletions(-)
 create mode 100644 tests/latest/__init__.py
 rename tests/{test_latest.py => latest/test_multiscales.py} (75%)
 create mode 100644 tests/v04/__init__.py
 create mode 100644 tests/v04/test_axis.py
 create mode 100644 tests/v04/test_label.py
 rename tests/{test_v04.py => v04/test_multiscales.py} (93%)

diff --git a/poetry.lock b/poetry.lock
index c952835..c295b29 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,133 +1,121 @@
-# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.7.0"
+version = "2.9.0"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.7.0-py3-none-any.whl", hash = "sha256:aec605df77ce4635a0479b50fd849aa6b640900f7b295021ecca192e1140e551"},
-    {file = "aiobotocore-2.7.0.tar.gz", hash = "sha256:506591374cc0aee1bdf0ebe290560424a24af176dfe2ea7057fe1df97c4f0467"},
+    {file = "aiobotocore-2.9.0-py3-none-any.whl", hash = "sha256:acf5e49644e6e434b9ecc26284ae7e05d557effbdcdd8185e2eb08925f011853"},
+    {file = "aiobotocore-2.9.0.tar.gz", hash = "sha256:4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.31.16,<1.31.65"
+botocore = ">=1.33.2,<1.33.14"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.29.16,<1.29.65)"]
-boto3 = ["boto3 (>=1.28.16,<1.28.65)"]
+awscli = ["awscli (>=1.31.2,<1.31.14)"]
+boto3 = ["boto3 (>=1.33.2,<1.33.14)"]
 
 [[package]]
 name = "aiohttp"
-version = "3.8.6"
+version = "3.9.1"
 description = "Async http client/server framework (asyncio)"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8"
 files = [
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1"},
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1d84166673694841d8953f0a8d0c90e1087739d24632fe86b1a08819168b4566"},
-    {file = "aiohttp-3.8.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:253bf92b744b3170eb4c4ca2fa58f9c4b87aeb1df42f71d4e78815e6e8b73c9e"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3fd194939b1f764d6bb05490987bfe104287bbf51b8d862261ccf66f48fb4096"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:6c5f938d199a6fdbdc10bbb9447496561c3a9a565b43be564648d81e1102ac22"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2817b2f66ca82ee699acd90e05c95e79bbf1dc986abb62b61ec8aaf851e81c93"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:0fa375b3d34e71ccccf172cab401cd94a72de7a8cc01847a7b3386204093bb47"},
-    {file = "aiohttp-3.8.6-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:9de50a199b7710fa2904be5a4a9b51af587ab24c8e540a7243ab737b45844543"},
-    {file = "aiohttp-3.8.6-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:e1d8cb0b56b3587c5c01de3bf2f600f186da7e7b5f7353d1bf26a8ddca57f965"},
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-    {file = "aiohttp-3.8.6-cp310-cp310-win_amd64.whl", hash = "sha256:93c15c8e48e5e7b89d5cb4613479d144fda8344e2d886cf694fd36db4cc86865"},
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 ]
 
 [package.dependencies]
 aiosignal = ">=1.1.2"
-async-timeout = ">=4.0.0a3,<5.0"
+async-timeout = {version = ">=4.0,<5.0", markers = "python_version < \"3.11\""}
 attrs = ">=17.3.0"
-charset-normalizer = ">=2.0,<4.0"
 frozenlist = ">=1.1.1"
 multidict = ">=4.5,<7.0"
 yarl = ">=1.0,<2.0"
 
 [package.extras]
-speedups = ["Brotli", "aiodns", "cchardet"]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
 
 [[package]]
 name = "aioitertools"
@@ -140,9 +128,6 @@ files = [
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 ]
 
-[package.dependencies]
-typing_extensions = {version = ">=4.0", markers = "python_version < \"3.10\""}
-
 [[package]]
 name = "aiosignal"
 version = "1.3.1"
@@ -191,53 +176,51 @@ files = [
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "botocore"
-version = "1.31.64"
+version = "1.33.13"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
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 ]
 
 [package.dependencies]
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 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = [
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-    {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""},
-]
+urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.16.26)"]
+crt = ["awscrt (==0.19.17)"]
 
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2023.11.17"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -363,63 +346,63 @@ files = [
 
 [[package]]
 name = "coverage"
-version = "7.3.2"
+version = "7.4.0"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -430,24 +413,24 @@ toml = ["tomli"]
 
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 python-versions = ">=3.8"
 files = [
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 [package.extras]
@@ -587,13 +586,13 @@ tqdm = ["tqdm"]
 
 [[package]]
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-version = "2.5.31"
+version = "2.5.33"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
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 [package.extras]
@@ -601,13 +600,13 @@ license = ["ukkonen"]
 
 [[package]]
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-version = "3.4"
+version = "3.6"
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 [[package]]
@@ -623,20 +622,17 @@ files = [
 
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+version = "5.13.2"
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-plugins = ["setuptools"]
-requirements-deprecated-finder = ["pip-api", "pipreqs"]
+colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jmespath"
@@ -651,13 +647,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.2"
+version = "4.20.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -672,17 +668,17 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
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 python-versions = ">=3.8"
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 [package.dependencies]
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "markdown-it-py"
@@ -804,38 +800,38 @@ files = [
 
 [[package]]
 name = "mypy"
-version = "1.6.1"
+version = "1.8.0"
 description = "Optional static typing for Python"
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -846,6 +842,7 @@ typing-extensions = ">=4.1.0"
 [package.extras]
 dmypy = ["psutil (>=4.0)"]
 install-types = ["pip"]
+mypyc = ["setuptools (>=50)"]
 reports = ["lxml"]
 
 [[package]]
@@ -915,36 +912,47 @@ zfpy = ["zfpy (>=1.0.0)"]
 
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 [[package]]
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 [[package]]
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 python-versions = ">=3.8"
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@@ -1508,31 +1516,15 @@ files = [
 
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@@ -1552,19 +1544,19 @@ zstd = ["zstandard (>=0.18.0)"]
 
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+    {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
+    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
 ]
 
 [package.dependencies]
@@ -1764,5 +1767,5 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.9"
-content-hash = "d6ba84447520a466cb6cd52278784c5dfdac4c3ac0622619ac0306a55dec74c6"
+python-versions = "^3.10"
+content-hash = "ee46872069c5871528c57be240af3e1e784f1130e07bf77eff4c00621f71004e"
diff --git a/pyproject.toml b/pyproject.toml
index dd93a87..0009a83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ readme = "README.md"
 packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.10"
 pydantic-zarr = "0.5.2"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
@@ -47,4 +47,32 @@ disallow_untyped_defs = true
 init_forbid_extra = true
 init_typed = true
 warn_required_dynamic_aliases = true
-warn_untyped_fields = true
\ No newline at end of file
+warn_untyped_fields = true
+
+
+[tool.coverage.run]
+source = ['src']
+branch = true
+context = '${CONTEXT}'
+
+[tool.coverage.report]
+precision = 2
+exclude_lines = [
+    'pragma: no cover',
+    'raise NotImplementedError',
+    'if TYPE_CHECKING:',
+    'if typing.TYPE_CHECKING:',
+    '@overload',
+    '@typing.overload',
+    '\(Protocol\):$',
+    'typing.assert_never',
+    'assert_never',
+]
+
+[tool.coverage.paths]
+source = [
+    'src/'
+]
+
+[tool.coverage.html]
+directory = "htmlcov"
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index bc4ac4a..3dca3ec 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -1,7 +1,7 @@
 from pydantic import BaseModel, Extra
 
 
-class StrictBase(BaseModel):
+class StrictBase(BaseModel, extra='forbid'):
     """
     A pydantic basemodel that refuses extra fields.
     """
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
index fbd8459..9e5c8ac 100644
--- a/src/pydantic_ome_ngff/latest/axis.py
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -1,7 +1,8 @@
-from pydantic_ome_ngff.v04 import Axis as AxisV04
+import pydantic_ome_ngff.v04.axis as axisV04
 
+AxisType = axisV04.AxisType
 
-class Axis(AxisV04):
+class Axis(axisV04.Axis):
     """
     Axis metadata.
     See https://ngff.openmicroscopy.org/latest/#axes-md
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 084d508..cd0df53 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,216 +1,60 @@
 from __future__ import annotations
 from collections import Counter
-from typing import Any, Dict, List, Optional, Union, cast
+from typing import Any, Dict, List, Literal, Optional, Union, cast
 import warnings
 
-from pydantic import BaseModel, conlist, model_validator, field_validator
+from pydantic import BaseModel, model_validator, field_validator
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.latest import transforms as ctx
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.v04.axis import AxisType
-from pydantic_ome_ngff.latest.axis import Axis
+from pydantic_ome_ngff.latest.axis import AxisType, Axis
+import pydantic_ome_ngff.v04.multiscales as msv04
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
-class MultiscaleDataset(BaseModel):
-    path: str
-    coordinateTransformations: conlist(
-        Union[ctx.ScaleTransform, ctx.TranslationTransform], min_length=1, max_length=2
-    )
-
-    @field_validator("coordinateTransformations")
-    def check_transforms_dimensionality(
-        cls,
-        transforms: List[
-            Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]
-        ],
-    ) -> List[Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform]]:
-        ndims = []
-        for tx in transforms:
-            # this repeated conditional logic around transforms is so awful.
-            if type(tx) in (ctx.VectorScaleTransform, ctx.VectorTranslationTransform):
-                ndims.append(ctx.get_transform_ndim(tx))
-        if len(set(ndims)) > 1:
-            msg = (
-                "Elements of coordinateTransformations must have the same "
-                f"dimensionality. Got elements with dimensionality = {ndims}."
-            )
-            raise ValueError(textwrap.fill(msg))
-        return transforms
+class MultiscaleDataset(msv04.MultiscaleDataset):
+    """
+    A single entry in the multiscales.datasets list.
+    See https://ngff.openmicroscopy.org/latest/#multiscale-md
 
-    @field_validator("coordinateTransformations")
-    def check_transforms_types(
-        cls, transforms: List[ctx.CoordinateTransform]
-    ) -> List[ctx.CoordinateTransform]:
-        if (tform := transforms[0].type) != "scale":
-            msg = (
-                "The first element of coordinateTransformations must be a scale "
-                f"transform. Got {tform} instead."
-            )
-            raise ValueError(textwrap.fill(msg))
-        if len(transforms) == 2:
-            if (tform := transforms[1].type) != "translation":
-                msg = (
-                    "The second element of coordinateTransformations must be a "
-                    f"translation transform. Got {tform} instead."
-                )
-                raise ValueError(textwrap.fill(msg))
-        return transforms
+    Note that this class is unchanged from the v04 counterpart.
 
+    Attributes:
+    ----------
+    path: str
+        The path to the zarr array that stores the image described by this metadata.
+        This path should be relative to the group that contains this metadata.
+    coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
+        The coordinate transformations for this image.
+    """
+    ...
 
-class Multiscale(VersionedBase):
+class Multiscale(msv04.Multiscale):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
-
-    # we need to put the version here as a private class attribute because the version
-    # is not properly typed by the spec...
     _version = version
-    # SPEC: why is this untyped?
-    version: Any = version
-    # SPEC: why is this nullable instead of reserving the empty string
-    # SPEC: untyped!
-    name: Any = None
-    # SPEC: not clear what this field is for, given the existence of .metadata
-    # SPEC: untyped!
-    type: Any = None
-    # SPEC: should default to empty dict instead of None
-    metadata: Optional[Dict[str, Any]] = None
-    datasets: List[MultiscaleDataset]
-    # SPEC: should not exist at top level and instead
-    # live in dataset metadata or in .datasets
-    axes: conlist(Axis, min_length=2, max_length=5)
-    # SPEC: should not live here, and if it is here,
-    # it should default to an empty list instead of being nullable
-    coordinateTransformations: Optional[
-        List[Union[ctx.ScaleTransform, ctx.TranslationTransform]]
-    ]
-
-    @field_validator("name")
-    def check_name(cls, name: Optional[str]) -> Optional[str]:
-        if name is None:
-            msg = (
-                f"The name field was set to `None`. Version {cls._version} of the "
-                "OME-NGFF spec states that the `name` field of a Multiscales object "
-                "should not be None."
-            )
-            warnings.warn(textwrap.fill(msg))
-        return name
-
-    @field_validator("axes")
-    def check_axes(cls, axes: List[Axis]) -> List[Axis]:
-        name_dupes = duplicates(a.name for a in axes)
-        if len(name_dupes) > 0:
-            msg = (
-                f"Axis names must be unique. Axis names {tuple(name_dupes.keys())} "
-                "are repeated."
-            )
-            raise ValueError(textwrap.fill(msg))
-        axis_types = tuple(ax.type for ax in axes)
-        type_census = Counter(axis_types)
-        num_spaces = type_census["space"]
-        if num_spaces < 2 or num_spaces > 3:
-            msg = (
-                f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space "
-                "axes are allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
+    version: Literal['0.5-dev'] = version
 
-        elif not all(a == "space" for a in axis_types[-num_spaces:]):
-            msg = f"Space axes must come last. Got axes with order: {axis_types}"
-            raise ValueError(textwrap.fill(msg))
-
-        if (num_times := type_census["time"]) > 1:
-            msg = (
-                f"Invalid number of time axes: {num_times}. "
-                "Only 1 time axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-
-        if (num_channels := type_census["channel"]) > 1:
-            msg = (
-                f"Invalid number of channel axes: {num_channels}. "
-                "Only 1 channel axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-
-        custom_axes = set(axis_types) - set(AxisType._member_names_)
-        if len(custom_axes) > 1:
-            msg = (
-                f"Invalid number of custom axes: {custom_axes}. "
-                "Only 1 custom axis is allowed."
-            )
-            raise ValueError(textwrap.fill(msg))
-        return axes
-
-
-class MultiscaleAttrs(BaseModel):
+class MultiscaleAttrs(msv04.MultiscaleAttrs):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
-    multiscales: List[Multiscale]
-
-
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Any]):
-    @model_validator(mode="after")
-    def check_arrays_exist(self) -> "MultiscaleGroup":
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if hasattr(v, "shape")
-        }
-        multiscales: List[Multiscale] = attrs.multiscales
-
-        for multiscale in multiscales:
-            for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in array_items:
-                    msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, but no "
-                        "array with that name was found in the items of that group. "
-                        "All arrays in multiscale metadata must be items of the group."
-                    )
-                    raise ValueError(msg)
-        return self
+class MultiscaleGroup(msv04.MultiscaleGroup):
+     """
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
-    @model_validator(mode="after")
-    def check_array_ndim(self) -> "MultiscaleGroup":
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if hasattr(v, "shape")
-        }
-        multiscales: List[Multiscale] = attrs.multiscales
+    Attributes
+    ----------
 
-        ndims = tuple(len(a.shape) for a in array_items.values())
-        if len(set(ndims)) > 1:
-            msg = (
-                "All arrays must have the same dimensionality. "
-                f"Got arrays with dimensionality {ndims}."
-            )
-            raise ValueError(msg)
+    attributes: MultiscaleAttrs
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
+        values are allowed.
+    members Dict[Str, ArraySpec | GroupSpec]:
+        The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
-        # check that each transform has compatible rank
-        for multiscale in multiscales:
-            tforms = []
-            if multiscale.coordinateTransformations is not None:
-                tforms.extend(multiscale.coordinateTransformations)
-            for dataset in multiscale.datasets:
-                tforms.extend(dataset.coordinateTransformations)
-            for tform in tforms:
-                if hasattr(tform, "scale") or hasattr(tform, "translation"):
-                    tform = cast(
-                        Union[ctx.VectorScaleTransform, ctx.VectorTranslationTransform],
-                        tform,
-                    )
-                    if (tform_dims := ctx.get_transform_ndim(tform)) not in set(ndims):
-                        msg = (
-                            f"Transform {tform} has dimensionality {tform_dims} "
-                            "which does not match the dimensionality "
-                            f"of the arrays in this group ({ndims}). "
-                            "Transform dimensionality must match array "
-                            "dimensionality."
-                        )
-                        raise ValueError(msg)
-        return self
+    """
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index 3a69cea..f72b263 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,63 +1,46 @@
 from __future__ import annotations
 import textwrap
 from typing import Union
-import pydantic_ome_ngff.v04.transforms as ctx
+import pydantic_ome_ngff.v04.transforms as tx
 
-
-class IdentityTransform(ctx.Identity):
+class Identity(tx.Identity):
     """
     An identity transform with no parameters.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathScale(ctx.PathScale):
+class PathScale(tx.PathScale):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class PathTranslation(ctx.PathTranslation):
+class PathTranslation(tx.PathTranslation):
     """ "
     A coordinateTransform with at "path" field.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorTranslationTransform(ctx.VectorTranslation):
+class VectorTranslation(tx.VectorTranslation):
     """
     A translation transform with a `translate` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
 
-class VectorScaleTransform(ctx.VectorScale):
+class VectorScale(tx.VectorScale):
     """
     A scale transform with a `scale` field that is a vector.
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+Scale = Union[VectorScale, PathScale]
+Translation = Union[VectorTranslation, PathTranslation]
+Transform = Union[Scale, Translation, Identity]
 
-def get_transform_ndim(
-    transform: Union[VectorScaleTransform, VectorTranslationTransform],
-) -> int:
-    """
-    Get the dimensionality of a vector transform (scale or translation).
-    """
-    if transform.type == "scale" and hasattr(transform, "scale"):
-        return len(transform.scale)
-    elif transform.type == "translation" and hasattr(transform, "translation"):
-        return len(transform.translation)
-    else:
-        msg = (
-            f"Transform must be either VectorScaleTransform or "
-            f"VectorTranslationTransform. Got {type(transform)} instead."
-        )
-
-        raise ValueError(textwrap.fill(msg))
-
-
-ScaleTransform = Union[VectorScaleTransform, PathScale]
-TranslationTransform = Union[VectorTranslationTransform, PathTranslation]
-CoordinateTransform = Union[ScaleTransform, TranslationTransform, IdentityTransform]
+scale_translation = tx.scale_translation
+ensure_dimensionality = tx.ensure_dimensionality
+ndim = tx.ndim
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 3baa42d..3932a35 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,4 +1,8 @@
 from __future__ import annotations
+from typing import Annotated
+
+from pydantic import AfterValidator, model_validator
+
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 import warnings
@@ -66,41 +70,34 @@ class TimeUnit(str, Enum):
     zettasecond = "zettasecond"
 
 
-class Axis(StrictVersionedBase):
+def check_type_unit(model: Axis) -> "Axis":
     """
-    Axis metadata.
-    See https://ngff.openmicroscopy.org/0.4/#axes-md
+    Check that the `unit` attribute of an `Axis` object is valid. This function emits warnings when the units of an `Axis` object
+    are spec-compliant but go against a "SHOULD" statement in the spec.
     """
 
-    _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
-    name: str
-    type: str | None
-    unit: str | None
-
-
-def check_unit(model: Axis) -> "Axis":
     typ = model.type
     unit = model.unit
+
     if typ == AxisType.space:
-        if unit not in SpaceUnit.__members__:
+        if unit not in [e.value for e in SpaceUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
     elif typ == AxisType.time:
-        if unit not in TimeUnit.__members__:
+        if unit not in [e.value for e in TimeUnit]:
             msg = (
-                f"Unit '{unit}' is not recognized as a standard unit for an axis "
-                f"with type '{typ}'."
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
             )
             warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
         msg = (
-            f"Null axis type. Version {model._version} of the OME-NGFF spec states "
+            f"The `type` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the 'type' field of an axis should be set to a string."
         )
         warnings.warn(msg, UserWarning)
@@ -114,8 +111,26 @@ def check_unit(model: Axis) -> "Axis":
 
     if unit is None:
         msg = (
-            f"Null unit. Version {model._version} of the OME-NGFF spec states "
+            f"The `unit` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the `unit` field of an axis should be set to a string."
         )
         warnings.warn(msg)
     return model
+
+
+
+class Axis(StrictVersionedBase):
+    """
+    Axis metadata.
+    See https://ngff.openmicroscopy.org/0.4/#axes-md
+    """
+
+    _version = version
+    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
+    name: str
+    type: str | None
+    unit: str | None
+
+    @model_validator(mode='after')
+    def check_type_unit(self):
+        return check_type_unit(self)
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 8ddff66..45a29de 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -1,24 +1,29 @@
 from __future__ import annotations
 import warnings
-from typing import List, Optional, Tuple
+from typing import List, Optional, Tuple, Annotated
 
 from pydantic import BaseModel, Field, field_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.base import version
 
+ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
+RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
 
 class Color(BaseModel):
-    label_value: int = Field(..., alias="label-value")
-    rgba: Optional[Tuple[int, int, int, int]]
+    """
+    a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
+    """
+    label_value: int = Field(..., serialization_alias="label-value")
+    rgba: RGBA | None
 
 
 class Source(BaseModel):
-    image: Optional[str] = "../../"
+    image: str | None = "../../"
 
 
 class Properties(BaseModel):
-    label_value: int = Field(..., alias="label-value")
+    label_value: int = Field(..., serialization_alias="label-value")
 
 
 class ImageLabel(VersionedBase):
@@ -27,43 +32,40 @@ class ImageLabel(VersionedBase):
     See https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # field is not required by the spec...
     _version = version
 
-    # SPEC: version is either unset or a string?
     version: Optional[str] = version
-    colors: Optional[List[Color]]
-    properties: Optional[List[Properties]]
-    source: Optional[Source]
-
+    colors: List[Color] | None = None
+    properties: Properties | None = None
+    source: Source | None = None
+    
     @field_validator("version")
-    def check_version(cls, ver: str) -> str:
+    @classmethod
+    def check_version(cls, ver: str | None) -> str:
         if ver is None:
-            msg = f"""
-            The field "version" is "None". Version {cls._version} of
-            the OME-NGFF spec states that "version" must either be unset or the string
-            "{cls._version}"
-            """
-            warnings.warn(textwrap.fill(msg))
+            msg = (
+                f"The `version` attribute is `None`. Version {cls._version} of "
+                f"the OME-NGFF spec states that `version` must either be unset or the string {cls._version}"
+            )
+            warnings.warn(msg, stacklevel=1)
+
         return ver
 
     @field_validator("colors")
+    @classmethod
     def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
-            msg = f"""
-            The field "colors" is "None". Version {cls._version} of
-            the OME-NGFF spec states that "colors" should be a list of label
-            descriptors.
-            """
-            warnings.warn(textwrap.fill(msg))
+            msg = (
+                f"The field `colors` is `None`. Version {cls._version} of"
+                "the OME-NGFF spec states that `colors` should be a list of label descriptors.")
+            warnings.warn(msg, stacklevel=1)
         else:
             dupes = duplicates(x.label_value for x in colors)
-            if len(dupes) > 1:
-                msg = f"""
-                    Duplicated label-value: {tuple(dupes.keys())}.
-                    label-values must be unique across elements of `colors`
-                    """
-                raise ValueError(textwrap.fill(msg))
+            if len(dupes) > 0:
+                msg = (
+                    f"Duplicated label-value: {tuple(dupes.keys())}."
+                    "label-values must be unique across elements of `colors`."
+                )
+                raise ValueError(msg)
 
         return colors
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 39e7f10..0ee2306 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,33 +1,35 @@
 from __future__ import annotations
 from collections import Counter
-from typing import Annotated, Any, Dict, List, Optional, Sequence, Union, cast
+from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 
-from pydantic import AfterValidator, BaseModel, conlist, model_validator
+from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
-import pydantic_ome_ngff.v04.transforms as ctx
+import pydantic_ome_ngff.v04.transforms as tx
 
 VALID_NDIM = (2, 3, 4, 5)
 
 
 def ensure_scale_translation(
-    transforms: Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]],
-) -> Sequence[Union[ctx.VectorScale, ctx.VectorTranslation]]:
+    transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
+) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
     Ensure that
         - the first element is a scale transformation
-        - the second element is a translation transform
+        - the second element, if present, is a translation transform
+        - there are only 1 or 2 transforms
     """
-    if len(transforms) == 0:
-        raise ValueError("Invalid transforms: got 0, expected 1 or 2")
+
+    if len(transforms) == 0 or len(transforms) > 2:
+        raise ValueError(f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2")
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
         msg = (
-            "The first element of coordinateTransformations must be a scale "
+            "The first element of `coordinateTransformations` must be a scale "
             f"transform. Got {maybe_scale} instead."
         )
         raise ValueError(msg)
@@ -35,19 +37,17 @@ def ensure_scale_translation(
         maybe_trans = transforms[1]
         if (maybe_trans.type) != "translation":
             msg = (
-                "The second element of coordinateTransformations must be a "
+                "The second element of `coordinateTransformations` must be a "
                 f"translation transform. Got {maybe_trans} instead."
             )
             raise ValueError(msg)
-    else:
-        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
-        raise ValueError(msg)
+
     return transforms
 
 
 def ensure_transforms_length(
-    transforms: Sequence[ctx.VectorScale | ctx.VectorTranslation],
-) -> Sequence[ctx.VectorScale | ctx.VectorTranslation]:
+    transforms: Sequence[tx.VectorScale | tx.VectorTranslation],
+) -> Sequence[tx.VectorScale | tx.VectorTranslation]:
     if (num_tx := len(transforms)) not in (1, 2):
         msg = f"Invalid number of transforms: got {num_tx}, expected 1 or 2"
         raise ValueError(msg)
@@ -64,16 +64,16 @@ class MultiscaleDataset(StrictBase):
     path: str
         The path to the zarr array that stores the image described by this metadata.
         This path should be relative to the group that contains this metadata.
-    coordinateTransformations: Union[ctx.ScaleTransform, ctx.TranslationTransform]
+    coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
     """
 
     path: str
     coordinateTransformations: Annotated[
-        List[ctx.Scale | ctx.Translation],
+        List[tx.Scale | tx.Translation],
         AfterValidator(ensure_transforms_length),
         AfterValidator(ensure_scale_translation),
-        AfterValidator(ctx.ensure_dimensionality),
+        AfterValidator(tx.ensure_dimensionality),
     ]
 
 
@@ -137,15 +137,28 @@ class Multiscale(VersionedBase):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
-    """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
+    Attributes
+    ----------
+
+    name: Any
+        The name for this multiscale image. Optional. Defaults to `None`.
+    type: Any
+        The type of the multiscale image. Optional. Defaults to `None`.
+    metadata: Dict[str, Any] | None
+        Metadata for this multiscale image. Optional. Defaults to `None`.
+    datasets: List[MultiscaleDataset]
+        A collection of descriptions of arrays that collectively comprise this multiscale image.
+    axes: List[Axis]
+        A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
+    coordinateTransformations: List[tx.Scale, tx.Translation]
+
+    """
     _version = version
     version: Any = version
     name: Any = None
     type: Any = None
-    metadata: Optional[Dict[str, Any]] = None
+    metadata: Dict[str, Any] | None = None
     datasets: List[MultiscaleDataset]
     axes: Annotated[
         List[Axis],
@@ -154,7 +167,7 @@ class Multiscale(VersionedBase):
         AfterValidator(ensure_axis_types),
     ]
 
-    coordinateTransformations: List[ctx.Scale | ctx.Translation] | None = None
+    coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
 class MultiscaleAttrs(BaseModel):
@@ -163,37 +176,57 @@ class MultiscaleAttrs(BaseModel):
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: conlist(Multiscale, min_length=1)
+    multiscales: Annotated[List[Multiscale], Field(..., min_length=1)]
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, Union[ArraySpec, GroupSpec]]):
+class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
+    """
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
+
+    Attributes
+    ----------
+
+    attributes: MultiscaleAttrs
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
+        values are allowed.
+    members Dict[Str, ArraySpec | GroupSpec]:
+        The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
+
+    """
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
+        """
+        Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
+
+        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is 
+        allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
+        """
         attrs = self.attributes
         array_items: dict[str, dict[str, ArraySpec]] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
 
-        multiscales: List[Multiscale] = attrs.multiscales
-
-        for multiscale in multiscales:
+        for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
                 if (dpath := dataset.path) not in array_items:
                     msg = (
                         f"Dataset {dpath} was specified in multiscale metadata, but no "
                         "array with that name was found in the items of that group. "
-                        "All arrays in multiscale metadata must be items of the group."
+                        "All arrays referenced in multiscale metadata must be items of the group."
                     )
                     raise ValueError(msg)
         return self
 
     @model_validator(mode="after")
     def check_array_ndim(self) -> "MultiscaleGroup":
+        """
+        Check that all the arrays referenced by the `multiscales` metadata have the same
+        dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
+        """
         attrs = self.attributes
         array_items: dict[str, ArraySpec] = {
             k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
         }
-        multiscales: List[Multiscale] = attrs.multiscales
 
         ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
@@ -204,7 +237,7 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             raise ValueError(msg)
 
         # check that each transform has compatible rank
-        for multiscale in multiscales:
+        for multiscale in attrs.multiscales:
             tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
@@ -213,15 +246,15 @@ def check_array_ndim(self) -> "MultiscaleGroup":
             for tform in tforms:
                 if hasattr(tform, "scale") or hasattr(tform, "translation"):
                     tform = cast(
-                        Union[ctx.VectorScale, ctx.VectorTranslation],
+                        Union[tx.VectorScale, tx.VectorTranslation],
                         tform,
                     )
-                    if (tform_dims := ctx.ndim(tform)) not in set(ndims):
+                    if (tform_dims := tx.ndim(tform)) not in set(ndims):
                         msg = (
                             f"Transform {tform} has dimensionality {tform_dims} "
-                            "which does notmatch the dimensionality of the arrays "
+                            "which does not match the dimensionality of the arrays "
                             f"in this group ({ndims}). Transform dimensionality "
                             "must match array dimensionality."
                         )
                         raise ValueError(msg)
-        return self
+        return self
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 52c23a3..33a79b2 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -61,14 +61,15 @@ def ndim(
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
-    elif hasattr(transform, "translation"):
+    
+    if hasattr(transform, "translation"):
         return len(transform.translation)
-    else:
-        msg = (
-            "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
-            f"Got {type(transform)} instead."
-        )
-        raise ValueError(msg)
+
+    msg = (
+        "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
+        f"Got {type(transform)} instead."
+    )
+    raise ValueError(msg)
 
 
 def scale_translation(
@@ -103,6 +104,9 @@ def scale_translation(
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
+    """
+    Ensure that the elements of `Sequence[VectorTransform]`
+    """
     ndims = tuple(ndim(tx) for tx in transforms)
     ndims_set = set(ndims)
     if len(ndims_set) > 1:
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index bf883d0..bd7cd9e 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from typing import List, Optional, Union
 
 from pydantic import BaseModel, ValidationError, field_validator
diff --git a/tests/latest/__init__.py b/tests/latest/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_latest.py b/tests/latest/test_multiscales.py
similarity index 75%
rename from tests/test_latest.py
rename to tests/latest/test_multiscales.py
index f33c65d..859114c 100644
--- a/tests/test_latest.py
+++ b/tests/latest/test_multiscales.py
@@ -1,8 +1,8 @@
 from __future__ import annotations
-from typing import Optional, Tuple, List, Type
-import jsonschema as jsc
-import pytest
+from typing import List, Optional, Tuple
 from pydantic import ValidationError
+import pytest
+import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
     Multiscale,
@@ -10,13 +10,14 @@
     MultiscaleDataset,
     MultiscaleGroup,
 )
+
 from pydantic_ome_ngff.latest.transforms import (
-    CoordinateTransform,
-    VectorScaleTransform,
-    VectorTranslationTransform,
+    Transform,
+    VectorScale,
+    VectorTranslation,
 )
 from pydantic_ome_ngff.latest.axis import Axis
-from .conftest import fetch_schemas
+from tests.conftest import fetch_schemas
 
 
 @pytest.fixture
@@ -32,13 +33,13 @@ def default_multiscale() -> Multiscale:
         MultiscaleDataset(
             path=f"path{idx}",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -54,7 +55,7 @@ def default_multiscale() -> Multiscale:
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(
+            VectorScale(
                 scale=[
                     1,
                 ]
@@ -66,8 +67,8 @@ def default_multiscale() -> Multiscale:
 
 
 def test_multiscale(default_multiscale: Multiscale) -> None:
-    base_schema, strict_schema = fetch_schemas("latest", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.dict()]}, strict_schema)
+    _, strict_schema = fetch_schemas("latest", schema_name="image")
+    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -76,12 +77,14 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
 
+    # this should be fine
+
     datasets = [
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -91,7 +94,7 @@ def test_multiscale_unique_axis_names() -> None:
         axes=axes,
         datasets=datasets,
         coordinateTransformations=[
-            VectorScaleTransform(scale=[1, 1, 1]),
+            VectorScale(scale=[1, 1, 1]),
         ],
     )
 
@@ -104,8 +107,8 @@ def test_multiscale_unique_axis_names() -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
-                VectorTranslationTransform(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1, 1]),
+                VectorTranslation(translation=[0, 0, 0]),
             ],
         )
     ]
@@ -116,7 +119,7 @@ def test_multiscale_unique_axis_names() -> None:
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(scale=[1, 1, 1]),
+                VectorScale(scale=[1, 1, 1]),
             ],
         )
 
@@ -126,11 +129,9 @@ def test_multiscale_unique_axis_names() -> None:
     (
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-        (None, "space", "space", None),
-        ("time", "time"),
     ),
 )
-def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
@@ -146,13 +147,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -162,13 +163,13 @@ def test_multiscale_semantic_axis_order(axis_types: List[Optional[str]]) -> None
         )
     ]
     # TODO: make some axis-specifc exceptions
-    with pytest.raises(ValidationError):
+    with pytest.raises(ValidationError, match="Space axes must come last."):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -186,13 +187,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         MultiscaleDataset(
             path="path",
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-                VectorTranslationTransform(
+                VectorTranslation(
                     translation=[
                         0,
                     ]
@@ -201,13 +202,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             ],
         )
     ]
-    with pytest.raises(ValidationError, match="List should have"):
+    with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
         Multiscale(
             name="foo",
             axes=axes,
             datasets=datasets,
             coordinateTransformations=[
-                VectorScaleTransform(
+                VectorScale(
                     scale=[
                         1,
                     ]
@@ -219,10 +220,13 @@ def test_multiscale_axis_length(num_axes: int) -> None:
 
 def test_coordinate_transforms_invalid_ndims() -> None:
     tforms = [
-        VectorScaleTransform(scale=(1, 1)),
-        VectorTranslationTransform(translation=(1, 1, 1)),
+        VectorScale(scale=(1, 1)),
+        VectorTranslation(translation=(1, 1, 1)),
     ]
-    with pytest.raises(ValidationError, match="Got elements with dimensionality"):
+    with pytest.raises(
+        ValidationError,
+        match="The transforms have inconsistent dimensionality.",  # noqa
+    ):
         MultiscaleDataset(path="foo", coordinateTransformations=tforms)
 
 
@@ -230,24 +234,20 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ]
-        * 3,
+            VectorScale(scale=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
+        ],
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-        [
-            VectorScaleTransform(scale=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorTranslationTransform(translation=(1, 1, 1)),
-        ],
     ),
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform],
+    transforms: List[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="List should have at most 2 items"):
+    with pytest.raises(ValidationError, match="expected 1 or 2"):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -255,24 +255,38 @@ def test_coordinate_transforms_invalid_length(
     "transforms",
     (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
+            VectorTranslation(translation=(1, 1, 1)),
         ]
         * 2,
         [
-            VectorScaleTransform(scale=(1, 1, 1)),
-        ]
-        * 2,
+            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
+        ],
+    ),
+)
+def test_coordinate_transforms_invalid_first_element(
+    transforms: Tuple[Transform, Transform],
+) -> None:
+    with pytest.raises(
+        ValidationError, match="The first element of `coordinateTransformations` must be a"
+    ):
+        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+
+
+@pytest.mark.parametrize(
+    "transforms",
+    (
         [
-            VectorTranslationTransform(translation=(1, 1, 1)),
-            VectorScaleTransform(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
-def test_coordinate_transforms_invalid_elements(
-    transforms: Tuple[CoordinateTransform, CoordinateTransform],
+def test_coordinate_transforms_invalid_second_element(
+    transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="element of coordinateTransformations must be a"
+        ValidationError, match="The second element of `coordinateTransformations` must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -308,7 +322,6 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
         )
         for d in default_multiscale.datasets
     }
-
     MultiscaleGroup(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
@@ -332,4 +345,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
diff --git a/tests/v04/__init__.py b/tests/v04/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
new file mode 100644
index 0000000..778d0ba
--- /dev/null
+++ b/tests/v04/test_axis.py
@@ -0,0 +1,17 @@
+import pytest
+
+from pydantic_ome_ngff.v04.axis import Axis
+
+@pytest.mark.parametrize(
+        'axis_type, unit', [
+            ('space', 'second'), 
+            ('time', 'meter'), 
+            ('space', None),
+            (None, None),
+            ('foo', None)
+            ])
+
+def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
+    with pytest.warns(UserWarning):
+        Axis(name='axis', type=axis_type, unit=unit)
+
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
new file mode 100644
index 0000000..31f784d
--- /dev/null
+++ b/tests/v04/test_label.py
@@ -0,0 +1,25 @@
+from typing import List
+import pytest
+from pydantic import ValidationError
+
+
+from pydantic_ome_ngff.v04.label import Color, ImageLabel
+
+@pytest.mark.parametrize('version', ('0.4', None))
+def test_imagelabel_version(version: str | None) -> None:
+    if version is None:
+        with pytest.warns(UserWarning):
+            model = ImageLabel(version=version)
+    else:
+        model = ImageLabel(version=version)
+    assert model.version == version
+
+@pytest.mark.parametrize('colors', (None, 
+                                    [Color(label_value=10, rgba=[0,0,0,0]), Color(label_value=10, rgba=[0,0,0,0])]))
+def test_imagelabel_colors(colors: List[Color] | None):
+    if colors is None:
+        with pytest.warns(UserWarning):
+            model = ImageLabel(colors=colors)
+    else:
+        with pytest.raises(ValidationError, match='Duplicated label-value'):
+            model=ImageLabel(colors=colors)
\ No newline at end of file
diff --git a/tests/test_v04.py b/tests/v04/test_multiscales.py
similarity index 93%
rename from tests/test_v04.py
rename to tests/v04/test_multiscales.py
index 33a2850..ec1f4e1 100644
--- a/tests/test_v04.py
+++ b/tests/v04/test_multiscales.py
@@ -1,22 +1,23 @@
 from __future__ import annotations
-from typing import Optional, Tuple, List, Type
-import jsonschema as jsc
-import pytest
+from typing import List, Optional, Tuple
 from pydantic import ValidationError
+import pytest
+import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
-from .conftest import fetch_schemas
 from pydantic_ome_ngff.v04.multiscales import (
     Multiscale,
     MultiscaleAttrs,
     MultiscaleDataset,
     MultiscaleGroup,
 )
+
 from pydantic_ome_ngff.v04.transforms import (
     Transform,
     VectorScale,
     VectorTranslation,
 )
 from pydantic_ome_ngff.v04.axis import Axis
+from tests.conftest import fetch_schemas
 
 loader = JsonLoader("v04")
 
@@ -260,20 +261,34 @@ def test_coordinate_transforms_invalid_length(
         ]
         * 2,
         [
+            VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
-        ]
-        * 2,
+        ],
+    ),
+)
+def test_coordinate_transforms_invalid_first_element(
+    transforms: Tuple[Transform, Transform],
+) -> None:
+    with pytest.raises(
+        ValidationError, match="The first element of `coordinateTransformations` must be a"
+    ):
+        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+
+
+@pytest.mark.parametrize(
+    "transforms",
+    (
         [
-            VectorTranslation(translation=(1, 1, 1)),
+            VectorScale(scale=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
     ),
 )
-def test_coordinate_transforms_invalid_elements(
+def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="element of coordinateTransformations must be a"
+        ValidationError, match="The second element of `coordinateTransformations` must be a"
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -332,4 +347,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file

From 02e09eed428d7cc5029cc79f1fc1bcd49b21bdfb Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 1 Jan 2024 17:57:14 +0100
Subject: [PATCH 23/69] lint

---
 src/pydantic_ome_ngff/base.py               |  4 ++--
 src/pydantic_ome_ngff/latest/axis.py        |  1 +
 src/pydantic_ome_ngff/latest/multiscales.py | 22 +++++++++------------
 src/pydantic_ome_ngff/latest/transforms.py  |  2 ++
 src/pydantic_ome_ngff/v04/axis.py           |  6 ++----
 src/pydantic_ome_ngff/v04/label.py          |  7 +++++--
 src/pydantic_ome_ngff/v04/multiscales.py    | 10 +++++++---
 src/pydantic_ome_ngff/v04/transforms.py     |  2 +-
 tests/latest/test_multiscales.py            |  8 +++++---
 tests/v04/test_axis.py                      | 21 ++++++++++----------
 tests/v04/test_label.py                     | 22 +++++++++++++++------
 tests/v04/test_multiscales.py               |  8 +++++---
 12 files changed, 66 insertions(+), 47 deletions(-)

diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index 3dca3ec..4678c2d 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -1,7 +1,7 @@
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel
 
 
-class StrictBase(BaseModel, extra='forbid'):
+class StrictBase(BaseModel, extra="forbid"):
     """
     A pydantic basemodel that refuses extra fields.
     """
diff --git a/src/pydantic_ome_ngff/latest/axis.py b/src/pydantic_ome_ngff/latest/axis.py
index 9e5c8ac..f44723a 100644
--- a/src/pydantic_ome_ngff/latest/axis.py
+++ b/src/pydantic_ome_ngff/latest/axis.py
@@ -2,6 +2,7 @@
 
 AxisType = axisV04.AxisType
 
+
 class Axis(axisV04.Axis):
     """
     Axis metadata.
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index cd0df53..f7e24bd 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,16 +1,7 @@
-from __future__ import annotations
-from collections import Counter
-from typing import Any, Dict, List, Literal, Optional, Union, cast
-import warnings
+from typing import Literal
 
-from pydantic import BaseModel, model_validator, field_validator
-from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.latest import transforms as ctx
-from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.latest.axis import AxisType, Axis
 import pydantic_ome_ngff.v04.multiscales as msv04
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class MultiscaleDataset(msv04.MultiscaleDataset):
@@ -28,15 +19,19 @@ class MultiscaleDataset(msv04.MultiscaleDataset):
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
     """
+
     ...
 
+
 class Multiscale(msv04.Multiscale):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
+
     _version = version
-    version: Literal['0.5-dev'] = version
+    version: Literal["0.5-dev"] = version
+
 
 class MultiscaleAttrs(msv04.MultiscaleAttrs):
     """
@@ -44,8 +39,9 @@ class MultiscaleAttrs(msv04.MultiscaleAttrs):
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
+
 class MultiscaleGroup(msv04.MultiscaleGroup):
-     """
+    """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
     Attributes
@@ -57,4 +53,4 @@ class MultiscaleGroup(msv04.MultiscaleGroup):
     members Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
-    """
\ No newline at end of file
+    """
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index f72b263..68c087f 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -3,6 +3,7 @@
 from typing import Union
 import pydantic_ome_ngff.v04.transforms as tx
 
+
 class Identity(tx.Identity):
     """
     An identity transform with no parameters.
@@ -37,6 +38,7 @@ class VectorScale(tx.VectorScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+
 Scale = Union[VectorScale, PathScale]
 Translation = Union[VectorTranslation, PathTranslation]
 Transform = Union[Scale, Translation, Identity]
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 3932a35..d780f2a 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,7 +1,6 @@
 from __future__ import annotations
-from typing import Annotated
 
-from pydantic import AfterValidator, model_validator
+from pydantic import model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -118,7 +117,6 @@ def check_type_unit(model: Axis) -> "Axis":
     return model
 
 
-
 class Axis(StrictVersionedBase):
     """
     Axis metadata.
@@ -131,6 +129,6 @@ class Axis(StrictVersionedBase):
     type: str | None
     unit: str | None
 
-    @model_validator(mode='after')
+    @model_validator(mode="after")
     def check_type_unit(self):
         return check_type_unit(self)
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 45a29de..8106e08 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -10,10 +10,12 @@
 ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
 RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
 
+
 class Color(BaseModel):
     """
     a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
     """
+
     label_value: int = Field(..., serialization_alias="label-value")
     rgba: RGBA | None
 
@@ -38,7 +40,7 @@ class ImageLabel(VersionedBase):
     colors: List[Color] | None = None
     properties: Properties | None = None
     source: Source | None = None
-    
+
     @field_validator("version")
     @classmethod
     def check_version(cls, ver: str | None) -> str:
@@ -57,7 +59,8 @@ def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
         if colors is None:
             msg = (
                 f"The field `colors` is `None`. Version {cls._version} of"
-                "the OME-NGFF spec states that `colors` should be a list of label descriptors.")
+                "the OME-NGFF spec states that `colors` should be a list of label descriptors."
+            )
             warnings.warn(msg, stacklevel=1)
         else:
             dupes = duplicates(x.label_value for x in colors)
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 0ee2306..c139c49 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -24,7 +24,9 @@ def ensure_scale_translation(
     """
 
     if len(transforms) == 0 or len(transforms) > 2:
-        raise ValueError(f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2")
+        raise ValueError(
+            f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        )
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
@@ -154,6 +156,7 @@ class Multiscale(VersionedBase):
     coordinateTransformations: List[tx.Scale, tx.Translation]
 
     """
+
     _version = version
     version: Any = version
     name: Any = None
@@ -193,12 +196,13 @@ class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "MultiscaleGroup":
         """
         Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
 
-        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is 
+        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is
         allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
         """
         attrs = self.attributes
@@ -257,4 +261,4 @@ def check_array_ndim(self) -> "MultiscaleGroup":
                             "must match array dimensionality."
                         )
                         raise ValueError(msg)
-        return self
\ No newline at end of file
+        return self
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 33a79b2..729b5f3 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -61,7 +61,7 @@ def ndim(
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
-    
+
     if hasattr(transform, "translation"):
         return len(transform.translation)
 
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 859114c..68e6f77 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -268,7 +268,8 @@ def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The first element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The first element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -286,7 +287,8 @@ def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The second element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The second element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -345,4 +347,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
index 778d0ba..968c507 100644
--- a/tests/v04/test_axis.py
+++ b/tests/v04/test_axis.py
@@ -2,16 +2,17 @@
 
 from pydantic_ome_ngff.v04.axis import Axis
 
-@pytest.mark.parametrize(
-        'axis_type, unit', [
-            ('space', 'second'), 
-            ('time', 'meter'), 
-            ('space', None),
-            (None, None),
-            ('foo', None)
-            ])
 
+@pytest.mark.parametrize(
+    "axis_type, unit",
+    [
+        ("space", "second"),
+        ("time", "meter"),
+        ("space", None),
+        (None, None),
+        ("foo", None),
+    ],
+)
 def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
     with pytest.warns(UserWarning):
-        Axis(name='axis', type=axis_type, unit=unit)
-
+        Axis(name="axis", type=axis_type, unit=unit)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index 31f784d..7636620 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -5,7 +5,8 @@
 
 from pydantic_ome_ngff.v04.label import Color, ImageLabel
 
-@pytest.mark.parametrize('version', ('0.4', None))
+
+@pytest.mark.parametrize("version", ("0.4", None))
 def test_imagelabel_version(version: str | None) -> None:
     if version is None:
         with pytest.warns(UserWarning):
@@ -14,12 +15,21 @@ def test_imagelabel_version(version: str | None) -> None:
         model = ImageLabel(version=version)
     assert model.version == version
 
-@pytest.mark.parametrize('colors', (None, 
-                                    [Color(label_value=10, rgba=[0,0,0,0]), Color(label_value=10, rgba=[0,0,0,0])]))
+
+@pytest.mark.parametrize(
+    "colors",
+    (
+        None,
+        [
+            Color(label_value=10, rgba=[0, 0, 0, 0]),
+            Color(label_value=10, rgba=[0, 0, 0, 0]),
+        ],
+    ),
+)
 def test_imagelabel_colors(colors: List[Color] | None):
     if colors is None:
         with pytest.warns(UserWarning):
-            model = ImageLabel(colors=colors)
+            ImageLabel(colors=colors)
     else:
-        with pytest.raises(ValidationError, match='Duplicated label-value'):
-            model=ImageLabel(colors=colors)
\ No newline at end of file
+        with pytest.raises(ValidationError, match="Duplicated label-value"):
+            ImageLabel(colors=colors)
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index ec1f4e1..8c96ddb 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -270,7 +270,8 @@ def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The first element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The first element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -288,7 +289,8 @@ def test_coordinate_transforms_invalid_second_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
-        ValidationError, match="The second element of `coordinateTransformations` must be a"
+        ValidationError,
+        match="The second element of `coordinateTransformations` must be a",
     ):
         MultiscaleDataset(path="foo", coordinateTransformations=transforms)
 
@@ -347,4 +349,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
\ No newline at end of file
+        MultiscaleGroup(attributes=group_attrs, members=bad_items)

From 675992f03e92ae0c1c79d551fe529455bc263df4 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 9 Jan 2024 15:49:32 +0100
Subject: [PATCH 24/69] feat: use a tighter module-local name convention for
 specialized GroupSpec instances, and expand ImageLabel metadata

---
 src/pydantic_ome_ngff/latest/__init__.py    |   2 +-
 src/pydantic_ome_ngff/latest/label.py       |   2 +-
 src/pydantic_ome_ngff/latest/multiscales.py |   8 +-
 src/pydantic_ome_ngff/latest/plate.py       |   4 +-
 src/pydantic_ome_ngff/latest/well.py        |   2 +-
 src/pydantic_ome_ngff/v04/__init__.py       |  24 ++--
 src/pydantic_ome_ngff/v04/axis.py           |  32 +++--
 src/pydantic_ome_ngff/v04/label.py          | 128 ++++++++++++++------
 src/pydantic_ome_ngff/v04/multiscales.py    |  21 ++--
 src/pydantic_ome_ngff/v04/plate.py          |  24 ++--
 src/pydantic_ome_ngff/v04/well.py           |  21 ++--
 tests/latest/test_multiscales.py            |  60 ++++-----
 tests/v04/test_label.py                     |  35 +++++-
 tests/v04/test_multiscales.py               |  60 ++++-----
 14 files changed, 250 insertions(+), 173 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index fb9e90e..1bccf6f 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,5 +1,5 @@
 from pydantic_ome_ngff.latest.axis import Axis  # noqa
-from pydantic_ome_ngff.latest.multiscales import Multiscale  # noqa
+from pydantic_ome_ngff.latest.multiscales import MultiscaleMetadata  # noqa
 from pydantic_ome_ngff.latest.label import ImageLabel  # noqa
 from pydantic_ome_ngff.latest.well import WellMeta  # noqa
 from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
diff --git a/src/pydantic_ome_ngff/latest/label.py b/src/pydantic_ome_ngff/latest/label.py
index 0f7784d..18e6697 100644
--- a/src/pydantic_ome_ngff/latest/label.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -11,4 +11,4 @@ class ImageLabel(ImageLabelV04):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index f7e24bd..1064f47 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -4,7 +4,7 @@
 import pydantic_ome_ngff.v04.multiscales as msv04
 
 
-class MultiscaleDataset(msv04.MultiscaleDataset):
+class Dataset(msv04.Dataset):
     """
     A single entry in the multiscales.datasets list.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -23,7 +23,7 @@ class MultiscaleDataset(msv04.MultiscaleDataset):
     ...
 
 
-class Multiscale(msv04.Multiscale):
+class MultiscaleMetadata(msv04.MultiscaleMetadata):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
@@ -33,14 +33,14 @@ class Multiscale(msv04.Multiscale):
     version: Literal["0.5-dev"] = version
 
 
-class MultiscaleAttrs(msv04.MultiscaleAttrs):
+class GroupAttrs(msv04.GroupAttrs):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/latest/#multiscale-md
     """
 
 
-class MultiscaleGroup(msv04.MultiscaleGroup):
+class Group(msv04.Group):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.5-dev.
 
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index e462b11..75a6d6e 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -3,7 +3,7 @@
 
 
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.plate import PlateMeta as PlateMetaV04
+from pydantic_ome_ngff.v04.plate import PlateMetadata as PlateMetaV04
 
 
 class PlateMeta(PlateMetaV04):
@@ -12,7 +12,5 @@ class PlateMeta(PlateMetaV04):
     See https://ngff.openmicroscopy.org/latest/#plate-md
     """
 
-    # we need to put the version here as a private class attribute because the version
-    # is not required by the spec...
     _version = version
     version: Optional[str] = version
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index b36a2d0..43a579e 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 from typing import Optional
 from pydantic_ome_ngff.latest.base import version
-from pydantic_ome_ngff.v04.well import WellMeta as WellMetaV04
+from pydantic_ome_ngff.v04.well import WellMetadata as WellMetaV04
 
 
 class WellMeta(WellMetaV04):
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index ffd00cb..f63d655 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -1,7 +1,17 @@
-from pydantic_ome_ngff.v04.axis import Axis  # noqa
-from pydantic_ome_ngff.v04.transforms import Transform  # noqa
-from pydantic_ome_ngff.v04.multiscales import Multiscale  # noqa
-from pydantic_ome_ngff.v04.label import ImageLabel  # noqa
-from pydantic_ome_ngff.v04.well import WellMeta  # noqa
-from pydantic_ome_ngff.v04.plate import PlateMeta  # noqa
-from pydantic_ome_ngff.v04.base import version  # noqa
+from pydantic_ome_ngff.v04.axis import Axis
+from pydantic_ome_ngff.v04.transforms import Transform
+from pydantic_ome_ngff.v04.multiscales import MultiscaleMetadata
+from pydantic_ome_ngff.v04.label import ImageLabel
+from pydantic_ome_ngff.v04.well import WellMetadata
+from pydantic_ome_ngff.v04.plate import PlateMetadata
+from pydantic_ome_ngff.v04.base import version
+
+__all__ = [
+    "Axis",
+    "Transform",
+    "MultiscaleMetadata",
+    "ImageLabel",
+    "WellMetadata",
+    "PlateMetadata",
+    "version",
+]
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index d780f2a..21e0731 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -69,29 +69,28 @@ class TimeUnit(str, Enum):
     zettasecond = "zettasecond"
 
 
-def check_type_unit(model: Axis) -> "Axis":
+def check_type_unit(model: Axis) -> Axis:
     """
-    Check that the `unit` attribute of an `Axis` object is valid. This function emits warnings when the units of an `Axis` object
+    Check that the `unit` attribute of an `Axis` object is valid.
+    This function emits warnings when the units of an `Axis` object
     are spec-compliant but go against a "SHOULD" statement in the spec.
     """
 
     typ = model.type
     unit = model.unit
 
-    if typ == AxisType.space:
-        if unit not in [e.value for e in SpaceUnit]:
-            msg = (
-                f"Unit '{unit}' is not recognized as a standard unit "
-                f"for an axis with type '{typ}'."
-            )
-            warnings.warn(msg)
-    elif typ == AxisType.time:
-        if unit not in [e.value for e in TimeUnit]:
-            msg = (
-                f"Unit '{unit}' is not recognized as a standard unit "
-                f"for an axis with type '{typ}'."
-            )
-            warnings.warn(msg)
+    if typ == AxisType.space and unit not in [e.value for e in SpaceUnit]:
+        msg = (
+            f"Unit '{unit}' is not recognized as a standard unit "
+            f"for an axis with type '{typ}'."
+        )
+        warnings.warn(msg)
+    elif typ == AxisType.time and unit not in [e.value for e in TimeUnit]:
+        msg = (
+            f"Unit '{unit}' is not recognized as a standard unit "
+            f"for an axis with type '{typ}'."
+        )
+        warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -124,7 +123,6 @@ class Axis(StrictVersionedBase):
     """
 
     _version = version
-    # SPEC: this should almost certainly be a string, but the spec doesn't specify the type: https://github.com/ome/ngff/blob/ee4d5dab677636a28f1f65c248a751e279a0d1fe/0.4/index.bs#L243
     name: str
     type: str | None
     unit: str | None
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 8106e08..436d3c8 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -1,11 +1,13 @@
 from __future__ import annotations
 import warnings
-from typing import List, Optional, Tuple, Annotated
+from typing import List, Literal, Optional, Tuple, Annotated
 
-from pydantic import BaseModel, Field, field_validator
+from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.utils import duplicates
-from pydantic_ome_ngff.v04.base import version
+from pydantic_ome_ngff.v04.base import version as NGFF_VERSION
+
+import pydantic_ome_ngff.v04.multiscales as multiscales
 
 ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
 RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
@@ -17,58 +19,104 @@ class Color(BaseModel):
     """
 
     label_value: int = Field(..., serialization_alias="label-value")
-    rgba: RGBA | None
+    rgba: Optional[RGBA]
 
 
 class Source(BaseModel):
-    image: str | None = "../../"
+    # todo: add validation that this path resolves to something
+    image: Optional[str] = "../../"
 
 
-class Properties(BaseModel):
+class Property(BaseModel):
     label_value: int = Field(..., serialization_alias="label-value")
 
 
+def parse_colors(colors: List[Color] | None) -> List[Color] | None:
+    if colors is None:
+        msg = (
+            f"The field `colors` is `None`. Version {NGFF_VERSION} of"
+            "the OME-NGFF spec states that `colors` should be a list of label descriptors."
+        )
+        warnings.warn(msg, stacklevel=1)
+    else:
+        dupes = duplicates(x.label_value for x in colors)
+        if len(dupes) > 0:
+            msg = (
+                f"Duplicated label-value: {tuple(dupes.keys())}."
+                "label-values must be unique across elements of `colors`."
+            )
+            raise ValueError(msg)
+
+    return colors
+
+
+def parse_version(version: Literal["0.4"] | None) -> Literal["0.4"] | None:
+    if version is None:
+        msg = (
+            f"The `version` attribute is `None`. Version {NGFF_VERSION} of "
+            f"the OME-NGFF spec states that `version` must either be unset or the string {NGFF_VERSION}"
+        )
+        warnings.warn(msg, stacklevel=1)
+    return version
+
+
+def parse_imagelabel(model: ImageLabel):
+    """
+    check that label_values are consistent across properties and colors
+    """
+    if model.colors is not None and model.properties is not None:
+        prop_label_value = [prop.label_value for prop in model.properties]
+        color_label_value = [color.label_value for color in model.colors]
+
+        prop_label_value_set = set(prop_label_value)
+        color_label_value_set = set(color_label_value)
+        if color_label_value_set != prop_label_value_set:
+            msg = (
+                "Inconsistent `label_value` attributes in `colors` and `properties`."
+                f"The `properties` attributes have `label_values` {prop_label_value}, "
+                f"The `colors` attributes have `label_values` {color_label_value}, "
+            )
+            raise ValueError(msg)
+    return model
+
+
 class ImageLabel(VersionedBase):
     """
     image-label metadata.
     See https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
-    _version = version
+    _version: Literal["0.4"] = NGFF_VERSION
 
-    version: Optional[str] = version
-    colors: List[Color] | None = None
-    properties: Properties | None = None
-    source: Source | None = None
+    version: Annotated[
+        Literal["0.4"] | None, AfterValidator(parse_version)
+    ] = NGFF_VERSION
+    colors: Annotated[Optional[List[Color]], AfterValidator(parse_colors)] = None
+    properties: Optional[List[Property]] = None
+    source: Optional[Source] = None
 
-    @field_validator("version")
-    @classmethod
-    def check_version(cls, ver: str | None) -> str:
-        if ver is None:
-            msg = (
-                f"The `version` attribute is `None`. Version {cls._version} of "
-                f"the OME-NGFF spec states that `version` must either be unset or the string {cls._version}"
-            )
-            warnings.warn(msg, stacklevel=1)
+    @model_validator(mode="after")
+    def parse_model(self):
+        return parse_imagelabel(self)
 
-        return ver
 
-    @field_validator("colors")
-    @classmethod
-    def check_colors(cls, colors: Optional[List[Color]]) -> Optional[List[Color]]:
-        if colors is None:
-            msg = (
-                f"The field `colors` is `None`. Version {cls._version} of"
-                "the OME-NGFF spec states that `colors` should be a list of label descriptors."
-            )
-            warnings.warn(msg, stacklevel=1)
-        else:
-            dupes = duplicates(x.label_value for x in colors)
-            if len(dupes) > 0:
-                msg = (
-                    f"Duplicated label-value: {tuple(dupes.keys())}."
-                    "label-values must be unique across elements of `colors`."
-                )
-                raise ValueError(msg)
-
-        return colors
+class GroupAttrs(multiscales.GroupAttrs):
+    """
+    Attributes for a Zarr group that contains `image-label` metadata.
+    Inherits from `v04.multiscales.MultiscaleAttrs`.
+
+    See https://ngff.openmicroscopy.org/0.4/#label-md
+
+    Attributes
+    ----------
+    image_label: `ImageLabel`
+        Image label metadata.
+    multiscales: List[v04.multiscales.Multiscales]
+        Multiscale image metadata.
+    """
+
+    image_label: Annotated[ImageLabel, Field(..., serialization_alias="image-label")]
+
+
+class Group(multiscales.Group):
+    attributes: GroupAttrs
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index c139c49..8bdb470 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -56,7 +56,7 @@ def ensure_transforms_length(
     return transforms
 
 
-class MultiscaleDataset(StrictBase):
+class Dataset(StrictBase):
     """
     A single entry in the multiscales.datasets list.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -135,7 +135,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     return axes
 
 
-class Multiscale(VersionedBase):
+class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
@@ -162,7 +162,7 @@ class Multiscale(VersionedBase):
     name: Any = None
     type: Any = None
     metadata: Dict[str, Any] | None = None
-    datasets: List[MultiscaleDataset]
+    datasets: Annotated[List[Dataset], Field(..., min_length=1)]
     axes: Annotated[
         List[Axis],
         AfterValidator(ensure_axis_length),
@@ -173,16 +173,16 @@ class Multiscale(VersionedBase):
     coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
-class MultiscaleAttrs(BaseModel):
+class GroupAttrs(BaseModel):
     """
     Attributes of a multiscale group.
     See https://ngff.openmicroscopy.org/0.4/#multiscale-md
     """
 
-    multiscales: Annotated[List[Multiscale], Field(..., min_length=1)]
+    multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
 
 
-class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
+class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
 
@@ -190,20 +190,19 @@ class MultiscaleGroup(GroupSpec[MultiscaleAttrs, ArraySpec | GroupSpec]):
     ----------
 
     attributes: MultiscaleAttrs
-        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`. Extra
-        values are allowed.
+        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`.
     members Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
 
     @model_validator(mode="after")
-    def check_arrays_exist(self) -> "MultiscaleGroup":
+    def check_arrays_exist(self) -> "Group":
         """
         Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
 
         Note that this is currently too strict, since it will not check for arrays in subgroups, but this is
-        allowed by the spec. I will implement tree-flattening over in pydantic-zarr to fix this.
+        allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
         array_items: dict[str, dict[str, ArraySpec]] = {
@@ -222,7 +221,7 @@ def check_arrays_exist(self) -> "MultiscaleGroup":
         return self
 
     @model_validator(mode="after")
-    def check_array_ndim(self) -> "MultiscaleGroup":
+    def check_array_ndim(self) -> "Group":
         """
         Check that all the arrays referenced by the `multiscales` metadata have the same
         dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index cc8ddef..e2633f6 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -7,7 +7,7 @@
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
-from pydantic_ome_ngff.v04.well import WellGroup
+import pydantic_ome_ngff.v04.well as well
 
 
 class Acquisition(BaseModel):
@@ -20,14 +20,14 @@ class Entry(BaseModel):
     name: str
 
 
-class WellMeta(BaseModel):
+class WellMetadata(BaseModel):
     # must be {rowName}/{columnName}
     path: str
     rowIndex: NonNegativeInt
     columnIndex: NonNegativeInt
 
 
-class PlateMeta(VersionedBase):
+class PlateMetadata(VersionedBase):
     """
     Plate metadata
     see https://ngff.openmicroscopy.org/0.4/#plate-md
@@ -35,28 +35,28 @@ class PlateMeta(VersionedBase):
 
     # the version here as a private class attribute because the version is not required by the spec
     _version = version
-    version: Optional[str] = version
-    name: Optional[str] = None
+    version: str | None = version
+    name: str | None = None
     acquisitions: List[Acquisition]
     columns: List[Entry]
     rows: List[Entry]
     field_count: PositiveInt
-    wells: List[WellMeta]
+    wells: List[WellMetadata]
 
 
-class PlateAttributes(BaseModel):
-    plate: PlateMeta
+class GroupAttrs(BaseModel):
+    plate: PlateMetadata
 
 
-class PlateGroup(GroupSpec[PlateAttributes, Union[WellGroup, GroupSpec, ArraySpec]]):
+class Group(GroupSpec[GroupAttrs, Union[well.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
     def contains_well(
-        cls, members: Union[WellGroup, GroupSpec, ArraySpec]
-    ) -> Union[WellGroup, GroupSpec, ArraySpec]:
+        cls, members: Union[Group, GroupSpec, ArraySpec]
+    ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a WellGroup
         """
-        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+        if not any(map(lambda v: isinstance(v, Group), members.values())):
             raise ValidationError
         return members
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index bd7cd9e..170c3db 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -5,7 +5,7 @@
 from pydantic_ome_ngff.base import VersionedBase
 
 from pydantic_ome_ngff.v04.base import version
-from pydantic_ome_ngff.v04.multiscales import MultiscaleGroup
+import pydantic_ome_ngff.v04.multiscales as multiscales
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
@@ -14,33 +14,30 @@ class Image(BaseModel):
     acquisition: Optional[int]
 
 
-class WellMeta(VersionedBase):
+class WellMetadata(VersionedBase):
     """
     Well metadata.
     See https://ngff.openmicroscopy.org/0.4/#well-md
     """
 
-    # the version here as a private class attribute because the version is not required by the spec
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
     images: List[Image]
 
 
-class WellAttributes(BaseModel):
-    well: WellMeta
+class GroupAttrs(BaseModel):
+    well: WellMetadata
 
 
-class WellGroup(
-    GroupSpec[WellAttributes, Union[MultiscaleGroup, GroupSpec, ArraySpec]]
-):
+class Group(GroupSpec[GroupAttrs, Union[multiscales.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
     def contains_well(
-        cls, members: Union[MultiscaleGroup, GroupSpec, ArraySpec]
-    ) -> Union[MultiscaleGroup, GroupSpec, ArraySpec]:
+        cls, members: Union[Group, GroupSpec, ArraySpec]
+    ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a MultiscaleGroup
         """
-        if not any(map(lambda v: isinstance(v, WellGroup), members.values())):
+        if not any(map(lambda v: isinstance(v, Group), members.values())):
             raise ValidationError
         return members
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 68e6f77..c938301 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -5,10 +5,10 @@
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.latest.multiscales import (
-    Multiscale,
-    MultiscaleAttrs,
-    MultiscaleDataset,
-    MultiscaleGroup,
+    MultiscaleMetadata,
+    GroupAttrs,
+    Dataset,
+    Group,
 )
 
 from pydantic_ome_ngff.latest.transforms import (
@@ -21,7 +21,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> Multiscale:
+def default_multiscale() -> MultiscaleMetadata:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -30,7 +30,7 @@ def default_multiscale() -> Multiscale:
     rank = len(axes)
     num_datasets = 3
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path=f"path{idx}",
             coordinateTransformations=[
                 VectorScale(
@@ -50,7 +50,7 @@ def default_multiscale() -> Multiscale:
         for idx in range(num_datasets)
     ]
 
-    multi = Multiscale(
+    multi = MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -66,7 +66,7 @@ def default_multiscale() -> Multiscale:
     return multi
 
 
-def test_multiscale(default_multiscale: Multiscale) -> None:
+def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     _, strict_schema = fetch_schemas("latest", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
@@ -80,7 +80,7 @@ def test_multiscale_unique_axis_names() -> None:
     # this should be fine
 
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -89,7 +89,7 @@ def test_multiscale_unique_axis_names() -> None:
         )
     ]
 
-    Multiscale(
+    MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -104,7 +104,7 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -114,7 +114,7 @@ def test_multiscale_unique_axis_names() -> None:
     ]
 
     with pytest.raises(ValidationError, match="Axis names must be unique."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -144,7 +144,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
 
     rank = len(axes)
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -164,7 +164,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     # TODO: make some axis-specifc exceptions
     with pytest.raises(ValidationError, match="Space axes must come last."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -184,7 +184,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -203,7 +203,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -227,7 +227,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
         ValidationError,
         match="The transforms have inconsistent dimensionality.",  # noqa
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=tforms)
+        Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
@@ -248,7 +248,7 @@ def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -271,7 +271,7 @@ def test_coordinate_transforms_invalid_first_element(
         ValidationError,
         match="The first element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -290,18 +290,20 @@ def test_coordinate_transforms_invalid_second_element(
         ValidationError,
         match="The second element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_exist(
+    default_multiscale: MultiscaleMetadata,
+) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -313,18 +315,18 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -339,7 +341,7 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
@@ -347,4 +349,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index 7636620..e2c4523 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -1,19 +1,42 @@
-from typing import List
+from typing import List, Literal
 import pytest
 from pydantic import ValidationError
+from pydantic_ome_ngff.v04 import version as NGFF_VERSION
 
+from pydantic_ome_ngff.v04.label import Color, ImageLabel, Property
 
-from pydantic_ome_ngff.v04.label import Color, ImageLabel
 
+@pytest.mark.parametrize("version", (None, "0.4"))
+def test_imagelabel(version: Literal["0.4"] | None):
+    color = Color(label_value=1, rgba=[0, 0, 0, 0])
+    model = ImageLabel(colors=[color], version=version)
+    dumped = model.model_dump()
 
-@pytest.mark.parametrize("version", ("0.4", None))
+    assert dumped["colors"] == [color.model_dump()]
+    # check that if the version is None, then we didn't write it out
+    if version == "0.4":
+        assert dumped["version"] == NGFF_VERSION
+
+
+def test_properties_colors_match():
+    color = Color(label_value=0, rgba=(0, 0, 0, 0))
+    prop = Property(label_value=1)
+
+    with pytest.raises(
+        ValidationError,
+        match="Inconsistent `label_value` attributes in `colors` and `properties`.",
+    ):
+        ImageLabel(colors=[color], properties=[prop])
+
+
+@pytest.mark.parametrize("version", ("0.5", None))
 def test_imagelabel_version(version: str | None) -> None:
     if version is None:
         with pytest.warns(UserWarning):
-            model = ImageLabel(version=version)
+            _ = ImageLabel(version=version)
     else:
-        model = ImageLabel(version=version)
-    assert model.version == version
+        with pytest.raises(ValidationError, match="Input should be '0.4'"):
+            _ = ImageLabel(version=version)
 
 
 @pytest.mark.parametrize(
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 8c96ddb..c1a0ce7 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -5,10 +5,10 @@
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.v04.multiscales import (
-    Multiscale,
-    MultiscaleAttrs,
-    MultiscaleDataset,
-    MultiscaleGroup,
+    MultiscaleMetadata,
+    GroupAttrs,
+    Dataset,
+    Group,
 )
 
 from pydantic_ome_ngff.v04.transforms import (
@@ -23,7 +23,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> Multiscale:
+def default_multiscale() -> MultiscaleMetadata:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -32,7 +32,7 @@ def default_multiscale() -> Multiscale:
     rank = len(axes)
     num_datasets = 3
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path=f"path{idx}",
             coordinateTransformations=[
                 VectorScale(
@@ -52,7 +52,7 @@ def default_multiscale() -> Multiscale:
         for idx in range(num_datasets)
     ]
 
-    multi = Multiscale(
+    multi = MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -68,7 +68,7 @@ def default_multiscale() -> Multiscale:
     return multi
 
 
-def test_multiscale(default_multiscale: Multiscale) -> None:
+def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
     jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
 
@@ -82,7 +82,7 @@ def test_multiscale_unique_axis_names() -> None:
     # this should be fine
 
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -91,7 +91,7 @@ def test_multiscale_unique_axis_names() -> None:
         )
     ]
 
-    Multiscale(
+    MultiscaleMetadata(
         name="foo",
         axes=axes,
         datasets=datasets,
@@ -106,7 +106,7 @@ def test_multiscale_unique_axis_names() -> None:
         Axis(name="x", type="space", unit="meter"),
     ]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(scale=[1, 1, 1]),
@@ -116,7 +116,7 @@ def test_multiscale_unique_axis_names() -> None:
     ]
 
     with pytest.raises(ValidationError, match="Axis names must be unique."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -146,7 +146,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
 
     rank = len(axes)
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -166,7 +166,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     ]
     # TODO: make some axis-specifc exceptions
     with pytest.raises(ValidationError, match="Space axes must come last."):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -186,7 +186,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
     datasets = [
-        MultiscaleDataset(
+        Dataset(
             path="path",
             coordinateTransformations=[
                 VectorScale(
@@ -205,7 +205,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
-        Multiscale(
+        MultiscaleMetadata(
             name="foo",
             axes=axes,
             datasets=datasets,
@@ -229,7 +229,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
         ValidationError,
         match="The transforms have inconsistent dimensionality.",  # noqa
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=tforms)
+        Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
@@ -250,7 +250,7 @@ def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -273,7 +273,7 @@ def test_coordinate_transforms_invalid_first_element(
         ValidationError,
         match="The first element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
 @pytest.mark.parametrize(
@@ -292,18 +292,20 @@ def test_coordinate_transforms_invalid_second_element(
         ValidationError,
         match="The second element of `coordinateTransformations` must be a",
     ):
-        MultiscaleDataset(path="foo", coordinateTransformations=transforms)
+        Dataset(path="foo", coordinateTransformations=transforms)
 
 
-def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_exist(
+    default_multiscale: MultiscaleMetadata,
+) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError,
@@ -315,18 +317,18 @@ def test_multiscale_group_datasets_exist(default_multiscale: Multiscale) -> None
             )
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
-    group_attrs = MultiscaleAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
+    group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
             shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
         )
         for d in default_multiscale.datasets
     }
-    MultiscaleGroup(attributes=group_attrs, members=good_items)
+    Group(attributes=group_attrs, members=good_items)
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
@@ -341,7 +343,7 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
@@ -349,4 +351,4 @@ def test_multiscale_group_datasets_rank(default_multiscale: Multiscale) -> None:
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
             for d in default_multiscale.datasets
         }
-        MultiscaleGroup(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=bad_items)

From 2825b07ac8d87f6df19a7029390234d4012bf3b9 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Sun, 4 Feb 2024 17:16:57 +0100
Subject: [PATCH 25/69] begin adding docs and convenience function for
 multiscale creation

---
 docs/api/v04/axis.md                        |  1 +
 docs/api/v04/label.md                       |  1 +
 docs/api/v04/multiscales.md                 |  1 +
 docs/api/v04/plate.md                       |  1 +
 docs/api/v04/transforms.md                  |  1 +
 docs/index.md                               | 17 ++++
 src/pydantic_ome_ngff/latest/multiscales.py |  2 +-
 src/pydantic_ome_ngff/v04/axis.py           | 46 +++++++----
 src/pydantic_ome_ngff/v04/label.py          |  2 +-
 src/pydantic_ome_ngff/v04/multiscales.py    | 87 ++++++++++++++-------
 src/pydantic_ome_ngff/v04/plate.py          |  4 +-
 src/pydantic_ome_ngff/v04/transforms.py     | 74 ++++++++++++++----
 src/pydantic_ome_ngff/v04/well.py           |  4 +-
 13 files changed, 176 insertions(+), 65 deletions(-)
 create mode 100644 docs/api/v04/axis.md
 create mode 100644 docs/api/v04/label.md
 create mode 100644 docs/api/v04/multiscales.md
 create mode 100644 docs/api/v04/plate.md
 create mode 100644 docs/api/v04/transforms.md
 create mode 100644 docs/index.md

diff --git a/docs/api/v04/axis.md b/docs/api/v04/axis.md
new file mode 100644
index 0000000..5f1cec1
--- /dev/null
+++ b/docs/api/v04/axis.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.axis
\ No newline at end of file
diff --git a/docs/api/v04/label.md b/docs/api/v04/label.md
new file mode 100644
index 0000000..fa0d46d
--- /dev/null
+++ b/docs/api/v04/label.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.label
\ No newline at end of file
diff --git a/docs/api/v04/multiscales.md b/docs/api/v04/multiscales.md
new file mode 100644
index 0000000..f520758
--- /dev/null
+++ b/docs/api/v04/multiscales.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.multiscales
\ No newline at end of file
diff --git a/docs/api/v04/plate.md b/docs/api/v04/plate.md
new file mode 100644
index 0000000..add6722
--- /dev/null
+++ b/docs/api/v04/plate.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.plate
\ No newline at end of file
diff --git a/docs/api/v04/transforms.md b/docs/api/v04/transforms.md
new file mode 100644
index 0000000..8a9a01f
--- /dev/null
+++ b/docs/api/v04/transforms.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.transforms
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..000ea34
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,17 @@
+# Welcome to MkDocs
+
+For full documentation visit [mkdocs.org](https://www.mkdocs.org).
+
+## Commands
+
+* `mkdocs new [dir-name]` - Create a new project.
+* `mkdocs serve` - Start the live-reloading docs server.
+* `mkdocs build` - Build the documentation site.
+* `mkdocs -h` - Print help message and exit.
+
+## Project layout
+
+    mkdocs.yml    # The configuration file.
+    docs/
+        index.md  # The documentation homepage.
+        ...       # Other markdown pages, images and other files.
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 1064f47..8f43d4d 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -14,7 +14,7 @@ class Dataset(msv04.Dataset):
     Attributes:
     ----------
     path: str
-        The path to the zarr array that stores the image described by this metadata.
+        The path to the Zarr array that stores the image described by this metadata.
         This path should be relative to the group that contains this metadata.
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 21e0731..8e6a511 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -9,6 +9,9 @@
 
 
 class AxisType(str, Enum):
+    """
+    String enum representing the three axis types (`space`, `time`, `channel`) defined in the specification.
+    """
     space = "space"
     time = "time"
     channel = "channel"
@@ -72,25 +75,27 @@ class TimeUnit(str, Enum):
 def check_type_unit(model: Axis) -> Axis:
     """
     Check that the `unit` attribute of an `Axis` object is valid.
-    This function emits warnings when the units of an `Axis` object
-    are spec-compliant but go against a "SHOULD" statement in the spec.
+    This function emits warnings when the `unit` attribute of of an `Axis` object
+    is spec-compliant but contravenes a "SHOULD" statement in the spec.
     """
 
     typ = model.type
     unit = model.unit
 
-    if typ == AxisType.space and unit not in [e.value for e in SpaceUnit]:
-        msg = (
-            f"Unit '{unit}' is not recognized as a standard unit "
-            f"for an axis with type '{typ}'."
-        )
-        warnings.warn(msg)
-    elif typ == AxisType.time and unit not in [e.value for e in TimeUnit]:
-        msg = (
-            f"Unit '{unit}' is not recognized as a standard unit "
-            f"for an axis with type '{typ}'."
-        )
-        warnings.warn(msg)
+    if typ == AxisType.space:
+         if unit not in [e.value for e in SpaceUnit]:
+            msg = (
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
+            )
+            warnings.warn(msg)
+    elif typ == AxisType.time:
+        if unit not in [e.value for e in TimeUnit]:
+            msg = (
+                f"Unit '{unit}' is not recognized as a standard unit "
+                f"for an axis with type '{typ}'."
+            )
+            warnings.warn(msg)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -119,7 +124,18 @@ def check_type_unit(model: Axis) -> Axis:
 class Axis(StrictVersionedBase):
     """
     Axis metadata.
-    See https://ngff.openmicroscopy.org/0.4/#axes-md
+
+    See [https://ngff.openmicroscopy.org/0.4/#axes-md](https://ngff.openmicroscopy.org/0.4/#axes-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+
+    name: str
+        The name for this axis.
+    type: str | None
+        The type for this axis, e.g. `space`.
+    unit: str | None
+        The unit of measure associated with the interval defined by this axis.
     """
 
     _version = version
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 436d3c8..95ef442 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -15,7 +15,7 @@
 
 class Color(BaseModel):
     """
-    a label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
+    A label value and RGBA as defined in https://ngff.openmicroscopy.org/0.4/#label-md
     """
 
     label_value: int = Field(..., serialization_alias="label-value")
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 8bdb470..32f7bde 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -9,24 +9,21 @@
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
+import numpy.typing as npt
 
 VALID_NDIM = (2, 3, 4, 5)
 
-
 def ensure_scale_translation(
     transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
 ) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
-    Ensure that
-        - the first element is a scale transformation
-        - the second element, if present, is a translation transform
-        - there are only 1 or 2 transforms
+    Ensures that the first element is a scale transformation, the second element, 
+    if present, is a translation transform, and that there are only 1 or 2 transforms.
     """
 
     if len(transforms) == 0 or len(transforms) > 2:
-        raise ValueError(
-            f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
-        )
+        msg = f"Invalid number of transforms: got {len(transforms)}, expected 1 or 2"
+        raise ValueError(msg)
 
     maybe_scale = transforms[0]
     if maybe_scale.type != "scale":
@@ -58,16 +55,17 @@ def ensure_transforms_length(
 
 class Dataset(StrictBase):
     """
-    A single entry in the multiscales.datasets list.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    A single entry in the `multiscales.datasets` list.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
-    Attributes:
+    Attributes
     ----------
     path: str
-        The path to the zarr array that stores the image described by this metadata.
-        This path should be relative to the group that contains this metadata.
+        The path to the Zarr array that stores the image described by this metadata. This path should be relative to the group that contains this metadata.
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
+
     """
 
     path: str
@@ -81,7 +79,7 @@ class Dataset(StrictBase):
 
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that there are between 2 and 5 axes (inclusive)
+    Ensures that there are between 2 and 5 axes (inclusive)
     """
     if (len_axes := len(axes)) not in VALID_NDIM:
         msg = f"Incorrect number of axes provided ({len_axes}). Only 2, 3, 4, or 5 axes are allowed."
@@ -91,7 +89,7 @@ def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that the names of the axes are unique
+    Ensures that the names of the axes are unique.
     """
     name_dupes = duplicates(a.name for a in axes)
     if len(name_dupes) > 0:
@@ -102,12 +100,13 @@ def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-    Ensure that the following conditions hold:
-        - there are only 2 or 3 axes with type "space"
-        - the axes with type "space" are last in the list of axes
-        - there is only 1 axis with type "time"
-        - there is only 1 axis with type "channel"
-        - there is only 1 axis with a custom type
+        Ensures that the following conditions are true:
+
+        - there are only 2 or 3 axes with type `space`
+        - the axes with type `space` are last in the list of axes
+        - there is only 1 axis with type `time`
+        - there is only 1 axis with type `channel`
+        - there is only 1 axis with a type that is not `space`, `time`, or `channel`
     """
     axis_types = [ax.type for ax in axes]
     type_census = Counter(axis_types)
@@ -138,7 +137,8 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
 class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
     ----------
@@ -154,7 +154,8 @@ class MultiscaleMetadata(StrictVersionedBase):
     axes: List[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
     coordinateTransformations: List[tx.Scale, tx.Translation]
-
+        Coordinate transformations that express a scaling and translation shared by all elements of 
+        `datasets`.
     """
 
     _version = version
@@ -169,14 +170,19 @@ class MultiscaleMetadata(StrictVersionedBase):
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
     ]
-
     coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
 
 
 class GroupAttrs(BaseModel):
     """
-    Attributes of a multiscale group.
-    See https://ngff.openmicroscopy.org/0.4/#multiscale-md
+    A model of the required attributes of a Zarr group that implements OME-NGFF Multiscales metadata.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.    
+    
+    Attributes
+    ----------
+    multiscales: List[MultiscaleMetadata]
+        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image. 
     """
 
     multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
@@ -184,7 +190,9 @@ class GroupAttrs(BaseModel):
 
 class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
-    A model of a Zarr group that implements OME-NGFF Multiscales metadata, version 0.4.
+    A model of a Zarr group that implements OME-NGFF Multiscales metadata.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
     ----------
@@ -195,6 +203,31 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+    @classmethod
+    def from_arrays(
+        cls, 
+        arrays: npt.NDArray[Any],
+        paths: Sequence[str],
+        transforms: Sequence[Sequence[tx.Transform]],
+        axes: Sequence[Axis],
+        *, 
+        name: str | None = None, 
+        type: str | None = None, 
+        metadata: Dict[str, Any] | None = None,
+        top_level_transforms: List[tx.Transform] | None = None, 
+        **kwargs):
+            """
+            Create a `Group` from a sequence of arrays + spatial metadata.
+            """
+            members = {key: ArraySpec.from_array(arr, **kwargs) for key, arr in zip(paths, arrays, strict=True)}
+            multimeta = MultiscaleMetadata(
+                name=name, 
+                type=type,
+                metadata=metadata,
+                axes=axes,
+                datasets=[Dataset(path=path, coordinateTransformations=txs) for path, txs in zip(paths, transforms, strict=True)],
+                coordinateTransformations=top_level_transforms)
+            return cls(members=members, attributes=multimeta)
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index e2633f6..659838f 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -51,12 +51,12 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, Union[well.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
-    def contains_well(
+    def contains_well_group(
         cls, members: Union[Group, GroupSpec, ArraySpec]
     ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a WellGroup
         """
-        if not any(map(lambda v: isinstance(v, Group), members.values())):
+        if not any(map(lambda v: isinstance(v, well.Group), members.values())):
             raise ValidationError
         return members
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 729b5f3..adf5af1 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -6,17 +6,34 @@
 
 class Identity(StrictBase):
     """
-    An identity transform. It has no parameters, and no valid use according to the spec.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    An identity transform. It has no parameters other than `type`, and no valid use according to the spec.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+
+    type: Literal["identity"]
+        The string "identity".
+
     """
 
-    type: str = "identity"
+    type: Literal["identity"] = "identity"
 
 
 class PathTranslation(StrictBase):
     """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A translation transformation with a `path` field. The spec states that `path` should resolve to "binary data".
+
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+    
+    Attributes
+    ----------
+
+    type: Literal["translation"]
+        The string "translation".
+    path: str
+        A string reference to something that can be interpreted as defining a translation transformation.
     """
 
     type: Literal["translation"] = "translation"
@@ -25,8 +42,16 @@ class PathTranslation(StrictBase):
 
 class PathScale(StrictBase):
     """
-    A coordinateTransform with a `path` field.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A scaling transformation with a `path` field. The spec states that `path` should resolve to "binary data".
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["scale"]
+        The string "scale".
+    path: str
+        A string reference to something that can be interpreted as defining a scaling transformation.
     """
 
     type: Literal["scale"] = "scale"
@@ -35,8 +60,16 @@ class PathScale(StrictBase):
 
 class VectorTranslation(StrictBase):
     """
-    A translation transform with a `translate` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A translation transformation defined by a sequence of numbers.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["translation"]
+        The string "translation".
+    translation: Sequence[float | int]
+        A sequence of numbers that define an N-dimensional translation transformation.
     """
 
     type: Literal["translation"] = "translation"
@@ -45,8 +78,16 @@ class VectorTranslation(StrictBase):
 
 class VectorScale(StrictBase):
     """
-    A scale transform with a `scale` field that is a vector.
-    See https://ngff.openmicroscopy.org/0.4/#trafo-md
+    A scaling transformation defined by a sequence of numbers.
+    
+    See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
+
+    Attributes
+    ----------
+    type: Literal["scale"]
+        The string "scale".
+    scale: Sequence[float | int]
+        A sequence of numbers that define an  N-dimensional scaling transformation.
     """
 
     type: Literal["scale"] = "scale"
@@ -57,7 +98,7 @@ def ndim(
     transform: Union[VectorScale, VectorTranslation],
 ) -> int:
     """
-    Get the dimensionality of a vector transform (scale or translation).
+    Get the dimensionality of a `VectorScale` or `VectorTranslation`.
     """
     if hasattr(transform, "scale"):
         return len(transform.scale)
@@ -76,15 +117,15 @@ def scale_translation(
     scale: Sequence[float], translation: Sequence[float]
 ) -> Tuple[Scale, Translation]:
     """
-    Create a scale and transformation transformation from a scale and a translation parameter
+    Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
     """
     len_scale = len(scale)
     len_translation = len(translation)
     if len_scale < 1:
-        msg = f"Not enough values in scale. Got {len_scale}"
+        msg = f"Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation < 1:
-        msg = f"Not enough values in `tranlsation`. Got {len_translation}"
+        msg = f"Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation != len_scale:
         msg = (
@@ -100,12 +141,11 @@ def scale_translation(
 Translation = VectorTranslation | PathTranslation
 Transform = Scale | Translation
 
-
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
     """
-    Ensure that the elements of `Sequence[VectorTransform]`
+    Ensures that the elements in the input sequence define transformations with identical dimensionality.
     """
     ndims = tuple(ndim(tx) for tx in transforms)
     ndims_set = set(ndims)
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 170c3db..c9c6780 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -32,12 +32,12 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, Union[multiscales.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
-    def contains_well(
+    def contains_multiscale_group(
         cls, members: Union[Group, GroupSpec, ArraySpec]
     ) -> Union[Group, GroupSpec, ArraySpec]:
         """
         Check that .members contains a MultiscaleGroup
         """
-        if not any(map(lambda v: isinstance(v, Group), members.values())):
+        if not any(map(lambda v: isinstance(v, multiscales.Group), members.values())):
             raise ValidationError
         return members

From c502b36d4fa5026a4d3740eff27b638c6779f85e Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 12 Feb 2024 12:05:05 +0100
Subject: [PATCH 26/69] docs: add mkdocs.yml

---
 mkdocs.yml     |  63 ++++
 poetry.lock    | 896 ++++++++++++++++++++++++++++++++++++++++---------
 pyproject.toml |   7 +
 3 files changed, 808 insertions(+), 158 deletions(-)
 create mode 100644 mkdocs.yml

diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..a358917
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,63 @@
+site_name: pydantic-ome-ngff
+site_url: https://janeliascicomp.github.io/pydantic-ome-ngff/
+site_author: Davis Bennett
+site_description: >-
+  Pydantic models for the OME-NGFF file format.
+
+# Repository
+repo_name: janeliascicomp/pydantic-ome-ngff
+repo_url: https://github.com/janeliascicomp/pydantic-zarr
+
+# Copyright
+copyright: Copyright &copy; 2016 - 2023 HHMI / Janelia
+
+theme:
+  features:
+    - navigation.expand
+  name: material
+  palette: 
+  # Palette toggle for light mode
+  - scheme: default
+    toggle:
+      icon: material/brightness-7 
+      name: Switch to dark mode
+
+  # Palette toggle for dark mode
+  - scheme: slate
+    toggle:
+      icon: material/brightness-4
+      name: Switch to light mode
+
+nav:
+    - About: index.md
+    - API:
+      - v04:
+        - api/v04/multiscales.md
+        - api/v04/axis.md
+        - api/v04/transforms.md
+
+plugins:
+- mkdocstrings:
+    handlers:
+        python:
+          options:
+            docstring_style: numpy
+            members_order: source
+            separate_signature: true
+            filters: ["!^_"]
+            docstring_options:
+              ignore_init_summary: true
+            merge_init_into_class: true
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - toc:
+      baselevel: 2
+      toc_depth: 4
+      permalink: "#"
diff --git a/poetry.lock b/poetry.lock
index c295b29..132606d 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,24 +2,24 @@
 
 [[package]]
 name = "aiobotocore"
-version = "2.9.0"
+version = "2.11.1"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.9.0-py3-none-any.whl", hash = "sha256:acf5e49644e6e434b9ecc26284ae7e05d557effbdcdd8185e2eb08925f011853"},
-    {file = "aiobotocore-2.9.0.tar.gz", hash = "sha256:4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e"},
+    {file = "aiobotocore-2.11.1-py3-none-any.whl", hash = "sha256:904a7ad7cc8671d662cfd596906dafe839118ea2a66332c37908e3dcfdee1e45"},
+    {file = "aiobotocore-2.11.1.tar.gz", hash = "sha256:0b095af50da2d6f94e93ca959e2a4876f0f0d84d534b61b21d8e050832d04ab6"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.33.2,<1.33.14"
+botocore = ">=1.33.2,<1.34.28"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.31.2,<1.31.14)"]
-boto3 = ["boto3 (>=1.33.2,<1.33.14)"]
+awscli = ["awscli (>=1.31.2,<1.32.28)"]
+boto3 = ["boto3 (>=1.33.2,<1.34.28)"]
 
 [[package]]
 name = "aiohttp"
@@ -193,15 +193,75 @@ tests = ["attrs[tests-no-zope]", "zope-interface"]
 tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
 tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "black"
+version = "24.1.0"
+description = "The uncompromising code formatter."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "black-24.1.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:94d5280d020dadfafc75d7cae899609ed38653d3f5e82e7ce58f75e76387ed3d"},
+    {file = "black-24.1.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:aaf9aa85aaaa466bf969e7dd259547f4481b712fe7ee14befeecc152c403ee05"},
+    {file = "black-24.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ec489cae76eac3f7573629955573c3a0e913641cafb9e3bfc87d8ce155ebdb29"},
+    {file = "black-24.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:a5a0100b4bdb3744dd68412c3789f472d822dc058bb3857743342f8d7f93a5a7"},
+    {file = "black-24.1.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:6cc5a6ba3e671cfea95a40030b16a98ee7dc2e22b6427a6f3389567ecf1b5262"},
+    {file = "black-24.1.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:e0e367759062dcabcd9a426d12450c6d61faf1704a352a49055a04c9f9ce8f5a"},
+    {file = "black-24.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:be305563ff4a2dea813f699daaffac60b977935f3264f66922b1936a5e492ee4"},
+    {file = "black-24.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:6a8977774929b5db90442729f131221e58cc5d8208023c6af9110f26f75b6b20"},
+    {file = "black-24.1.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:d74d4d0da276fbe3b95aa1f404182562c28a04402e4ece60cf373d0b902f33a0"},
+    {file = "black-24.1.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:39addf23f7070dbc0b5518cdb2018468ac249d7412a669b50ccca18427dba1f3"},
+    {file = "black-24.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:827a7c0da520dd2f8e6d7d3595f4591aa62ccccce95b16c0e94bb4066374c4c2"},
+    {file = "black-24.1.0-cp312-cp312-win_amd64.whl", hash = "sha256:0cd59d01bf3306ff7e3076dd7f4435fcd2fafe5506a6111cae1138fc7de52382"},
+    {file = "black-24.1.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:bf8dd261ee82df1abfb591f97e174345ab7375a55019cc93ad38993b9ff5c6ad"},
+    {file = "black-24.1.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:82d9452aeabd51d1c8f0d52d4d18e82b9f010ecb30fd55867b5ff95904f427ff"},
+    {file = "black-24.1.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9aede09f72b2a466e673ee9fca96e4bccc36f463cac28a35ce741f0fd13aea8b"},
+    {file = "black-24.1.0-cp38-cp38-win_amd64.whl", hash = "sha256:780f13d03066a7daf1707ec723fdb36bd698ffa29d95a2e7ef33a8dd8fe43b5c"},
+    {file = "black-24.1.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:a15670c650668399c4b5eae32e222728185961d6ef6b568f62c1681d57b381ba"},
+    {file = "black-24.1.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:1e0fa70b8464055069864a4733901b31cbdbe1273f63a24d2fa9d726723d45ac"},
+    {file = "black-24.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7fa8d9aaa22d846f8c0f7f07391148e5e346562e9b215794f9101a8339d8b6d8"},
+    {file = "black-24.1.0-cp39-cp39-win_amd64.whl", hash = "sha256:f0dfbfbacfbf9cd1fac7a5ddd3e72510ffa93e841a69fcf4a6358feab1685382"},
+    {file = "black-24.1.0-py3-none-any.whl", hash = "sha256:5134a6f6b683aa0a5592e3fd61dd3519d8acd953d93e2b8b76f9981245b65594"},
+    {file = "black-24.1.0.tar.gz", hash = "sha256:30fbf768cd4f4576598b1db0202413fafea9a227ef808d1a12230c643cefe9fc"},
+]
+
+[package.dependencies]
+click = ">=8.0.0"
+mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
+pathspec = ">=0.9.0"
+platformdirs = ">=2"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
+
+[package.extras]
+colorama = ["colorama (>=0.4.3)"]
+d = ["aiohttp (>=3.7.4)", "aiohttp (>=3.7.4,!=3.9.0)"]
+jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
+uvloop = ["uvloop (>=0.15.2)"]
+
 [[package]]
 name = "botocore"
-version = "1.33.13"
+version = "1.34.27"
 description = "Low-level, data-driven core of boto 3."
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
-    {file = "botocore-1.33.13-py3-none-any.whl", hash = "sha256:aeadccf4b7c674c7d47e713ef34671b834bc3e89723ef96d994409c9f54666e6"},
-    {file = "botocore-1.33.13.tar.gz", hash = "sha256:fb577f4cb175605527458b04571451db1bd1a2036976b626206036acd4496617"},
+    {file = "botocore-1.34.27-py3-none-any.whl", hash = "sha256:1c10f247136ad17b6ef1588c1e043e294dbaebdebe9ce84dc56713029f515c53"},
+    {file = "botocore-1.34.27.tar.gz", hash = "sha256:a0e68ba264275b358b8c1cca604161f4d9465cf7847d73e929543a9f30ff22d1"},
 ]
 
 [package.dependencies]
@@ -210,7 +270,7 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.19.17)"]
+crt = ["awscrt (==0.19.19)"]
 
 [[package]]
 name = "certifi"
@@ -333,6 +393,20 @@ files = [
     {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = "sha256:3e4d1f6587322d2788836a99c69062fbb091331ec940e02d12d179c1d53e25fc"},
 ]
 
+[[package]]
+name = "click"
+version = "8.1.7"
+description = "Composable command line interface toolkit"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"},
+    {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
 [[package]]
 name = "colorama"
 version = "0.4.6"
@@ -584,6 +658,37 @@ smb = ["smbprotocol"]
 ssh = ["paramiko"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "ghp-import"
+version = "2.1.0"
+description = "Copy your docs directly to the gh-pages branch."
+optional = false
+python-versions = "*"
+files = [
+    {file = "ghp-import-2.1.0.tar.gz", hash = "sha256:9c535c4c61193c2df8871222567d7fd7e5014d835f97dc7b7439069e2413d343"},
+    {file = "ghp_import-2.1.0-py3-none-any.whl", hash = "sha256:8337dd7b50877f163d4c0289bc1f1c7f127550241988d568c1db512c4324a619"},
+]
+
+[package.dependencies]
+python-dateutil = ">=2.8.1"
+
+[package.extras]
+dev = ["flake8", "markdown", "twine", "wheel"]
+
+[[package]]
+name = "griffe"
+version = "0.39.1"
+description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "griffe-0.39.1-py3-none-any.whl", hash = "sha256:6ce4ecffcf0d2f96362c5974b3f7df812da8f8d4cfcc5ebc8202ef72656fc087"},
+    {file = "griffe-0.39.1.tar.gz", hash = "sha256:ead8dfede6e6531cce6bf69090a4f3c6d36fdf923c43f8e85aa530552cef0c09"},
+]
+
+[package.dependencies]
+colorama = ">=0.4"
+
 [[package]]
 name = "identify"
 version = "2.5.33"
@@ -634,6 +739,23 @@ files = [
 [package.extras]
 colors = ["colorama (>=0.4.6)"]
 
+[[package]]
+name = "jinja2"
+version = "3.1.3"
+description = "A very fast and expressive template engine."
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"},
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+]
+
+[package.dependencies]
+MarkupSafe = ">=2.0"
+
+[package.extras]
+i18n = ["Babel (>=2.7)"]
+
 [[package]]
 name = "jmespath"
 version = "1.0.1"
@@ -647,13 +769,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.20.0"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -680,6 +802,21 @@ files = [
 [package.dependencies]
 referencing = ">=0.31.0"
 
+[[package]]
+name = "markdown"
+version = "3.5.2"
+description = "Python implementation of John Gruber's Markdown."
+optional = false
+python-versions = ">=3.8"
+files = [
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+
+[package.extras]
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+testing = ["coverage", "pyyaml"]
+
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -704,6 +841,75 @@ profiling = ["gprof2dot"]
 rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
 testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
+[[package]]
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+version = "2.1.4"
+description = "Safely add untrusted strings to HTML/XML markup."
+optional = false
+python-versions = ">=3.7"
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 [[package]]
 name = "mdurl"
 version = "0.1.2"
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+optional = false
+python-versions = ">=3.7"
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 [package.extras]
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+python-versions = ">=3.8"
+files = [
+    {file = "pymdown_extensions-10.7-py3-none-any.whl", hash = "sha256:6ca215bc57bc12bf32b414887a68b810637d039124ed9b2e5bd3325cbb2c050c"},
+    {file = "pymdown_extensions-10.7.tar.gz", hash = "sha256:c0d64d5cf62566f59e6b2b690a4095c931107c250a8c8e1351c1de5f6b036deb"},
+]
+
+[package.dependencies]
+markdown = ">=3.5"
+pyyaml = "*"
+
+[package.extras]
+extra = ["pygments (>=2.12)"]
+
 [[package]]
 name = "pytest"
 version = "7.4.4"
@@ -1221,6 +1604,22 @@ pytest = ">=4.6"
 [package.extras]
 testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
 
+[[package]]
+name = "pytest-examples"
+version = "0.0.9"
+description = "Pytest plugin for testing examples in docstrings and markdown files."
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+black = ">=23"
+pytest = ">=7"
+ruff = ">=0.0.258"
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.2"
@@ -1294,21 +1693,137 @@ files = [
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
+[[package]]
+name = "pyyaml-env-tag"
+version = "0.1"
+description = "A custom YAML tag for referencing environment variables in YAML files. "
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "pyyaml_env_tag-0.1.tar.gz", hash = "sha256:70092675bda14fdec33b31ba77e7543de9ddc88f2e5b99160396572d11525bdb"},
+]
+
+[package.dependencies]
+pyyaml = "*"
+
 [[package]]
 name = "referencing"
-version = "0.32.0"
+version = "0.32.1"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "referencing-0.32.0.tar.gz", hash = "sha256:689e64fe121843dcfd57b71933318ef1f91188ffb45367332700a86ac8fd6161"},
+    {file = "referencing-0.32.1-py3-none-any.whl", hash = "sha256:7e4dc12271d8e15612bfe35792f5ea1c40970dadf8624602e33db2758f7ee554"},
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 ]
 
 [package.dependencies]
 attrs = ">=22.2.0"
 rpds-py = ">=0.7.0"
 
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+version = "2023.12.25"
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+
 [[package]]
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 version = "1.16.0"
@@ -1768,4 +2348,4 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 [metadata]
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 python-versions = "^3.10"
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diff --git a/pyproject.toml b/pyproject.toml
index 0009a83..83e0643 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,7 @@ pydantic-zarr = "0.5.2"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
 rich = "^13.6.0"
+mkdocs-material = "^9.5.5"
 
 
 [tool.poetry.group.dev.dependencies]
@@ -24,6 +25,12 @@ mypy = "^1.0.1"
 requests = "^2.28.2"
 pytest-cov = "^4.0.0"
 
+
+[tool.poetry.group.docs.dependencies]
+mkdocs-material = "^9.5.5"
+mkdocstrings = {extras = ["python"], version = "^0.24.0"}
+pytest-examples = "^0.0.9"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

From 94e08dd97518356f9adb427ab9b42bec4dda9a11 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 14:04:20 +0100
Subject: [PATCH 27/69] merge branch "use_pydantic_zarr" from origin

---
 src/pydantic_ome_ngff/__about__.py          |  4 +
 src/pydantic_ome_ngff/base.py               |  5 --
 src/pydantic_ome_ngff/latest/base.py        |  8 +-
 src/pydantic_ome_ngff/latest/label.py       |  4 +-
 src/pydantic_ome_ngff/latest/multiscales.py |  2 +-
 src/pydantic_ome_ngff/latest/plate.py       |  4 +-
 src/pydantic_ome_ngff/latest/transforms.py  |  1 -
 src/pydantic_ome_ngff/latest/well.py        |  3 +-
 src/pydantic_ome_ngff/utils.py              |  4 +-
 src/pydantic_ome_ngff/v04/axis.py           | 17 +++--
 src/pydantic_ome_ngff/v04/multiscales.py    | 83 ++++++++++++---------
 src/pydantic_ome_ngff/v04/plate.py          |  7 +-
 src/pydantic_ome_ngff/v04/transforms.py     | 25 ++++---
 src/pydantic_ome_ngff/v04/well.py           |  8 +-
 tests/conftest.py                           |  6 +-
 tests/latest/test_multiscales.py            | 17 +++--
 tests/v04/test_multiscales.py               | 45 ++++++++---
 17 files changed, 143 insertions(+), 100 deletions(-)
 create mode 100644 src/pydantic_ome_ngff/__about__.py

diff --git a/src/pydantic_ome_ngff/__about__.py b/src/pydantic_ome_ngff/__about__.py
new file mode 100644
index 0000000..9068a16
--- /dev/null
+++ b/src/pydantic_ome_ngff/__about__.py
@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2023-present Davis Vann Bennett <davis.v.bennett@gmail.com>
+#
+# SPDX-License-Identifier: MIT
+__version__ = "0.3.0"
diff --git a/src/pydantic_ome_ngff/base.py b/src/pydantic_ome_ngff/base.py
index 4678c2d..acb4010 100644
--- a/src/pydantic_ome_ngff/base.py
+++ b/src/pydantic_ome_ngff/base.py
@@ -6,9 +6,6 @@ class StrictBase(BaseModel, extra="forbid"):
     A pydantic basemodel that refuses extra fields.
     """
 
-    class Config:
-        extra = Extra.forbid
-
 
 class VersionedBase(BaseModel):
     """
@@ -22,5 +19,3 @@ class StrictVersionedBase(VersionedBase, StrictBase):
     """
     An internally versioned pydantic basemodel that refuses extra fields.
     """
-
-    ...
diff --git a/src/pydantic_ome_ngff/latest/base.py b/src/pydantic_ome_ngff/latest/base.py
index 17d27e7..7998d64 100644
--- a/src/pydantic_ome_ngff/latest/base.py
+++ b/src/pydantic_ome_ngff/latest/base.py
@@ -1 +1,7 @@
-version = "0.5-dev"
+from __future__ import annotations
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Literal
+
+version: Literal["0.5-dev"] = "0.5-dev"
diff --git a/src/pydantic_ome_ngff/latest/label.py b/src/pydantic_ome_ngff/latest/label.py
index 18e6697..0f8212f 100644
--- a/src/pydantic_ome_ngff/latest/label.py
+++ b/src/pydantic_ome_ngff/latest/label.py
@@ -1,5 +1,7 @@
-from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
+from __future__ import annotations
+
 from pydantic_ome_ngff.latest.base import version
+from pydantic_ome_ngff.v04.label import ImageLabel as ImageLabelV04
 
 
 class ImageLabel(ImageLabelV04):
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscales.py
index 8f43d4d..733dfaf 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscales.py
@@ -1,5 +1,5 @@
+from __future__ import annotations
 from typing import Literal
-
 from pydantic_ome_ngff.latest.base import version
 import pydantic_ome_ngff.v04.multiscales as msv04
 
diff --git a/src/pydantic_ome_ngff/latest/plate.py b/src/pydantic_ome_ngff/latest/plate.py
index 75a6d6e..d6d85f5 100644
--- a/src/pydantic_ome_ngff/latest/plate.py
+++ b/src/pydantic_ome_ngff/latest/plate.py
@@ -1,6 +1,4 @@
 from __future__ import annotations
-from typing import Optional
-
 
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.v04.plate import PlateMetadata as PlateMetaV04
@@ -13,4 +11,4 @@ class PlateMeta(PlateMetaV04):
     """
 
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index 68c087f..7ca832a 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -1,5 +1,4 @@
 from __future__ import annotations
-import textwrap
 from typing import Union
 import pydantic_ome_ngff.v04.transforms as tx
 
diff --git a/src/pydantic_ome_ngff/latest/well.py b/src/pydantic_ome_ngff/latest/well.py
index 43a579e..6d81597 100644
--- a/src/pydantic_ome_ngff/latest/well.py
+++ b/src/pydantic_ome_ngff/latest/well.py
@@ -1,5 +1,4 @@
 from __future__ import annotations
-from typing import Optional
 from pydantic_ome_ngff.latest.base import version
 from pydantic_ome_ngff.v04.well import WellMetadata as WellMetaV04
 
@@ -13,4 +12,4 @@ class WellMeta(WellMetaV04):
     # we need to put the version here as a private class attribute because the version
     # is not required by the spec...
     _version = version
-    version: Optional[str] = version
+    version: str | None = version
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index b1b71bc..88b80de 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -1,8 +1,8 @@
 from collections import Counter
-from typing import Dict, Iterable, Hashable
+from collections.abc import Hashable, Iterable
 
 
-def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
+def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
     elements of the input that occurred at least once, and the values are the
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 8e6a511..e0fb97a 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,17 +1,18 @@
 from __future__ import annotations
+from enum import Enum
+import warnings
 
 from pydantic import model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
-import warnings
-from enum import Enum
 
 
 class AxisType(str, Enum):
     """
     String enum representing the three axis types (`space`, `time`, `channel`) defined in the specification.
     """
+
     space = "space"
     time = "time"
     channel = "channel"
@@ -83,19 +84,19 @@ def check_type_unit(model: Axis) -> Axis:
     unit = model.unit
 
     if typ == AxisType.space:
-         if unit not in [e.value for e in SpaceUnit]:
+        if unit not in [e.value for e in SpaceUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
-            warnings.warn(msg)
+            warnings.warn(msg, stacklevel=1)
     elif typ == AxisType.time:
         if unit not in [e.value for e in TimeUnit]:
             msg = (
                 f"Unit '{unit}' is not recognized as a standard unit "
                 f"for an axis with type '{typ}'."
             )
-            warnings.warn(msg)
+            warnings.warn(msg, stacklevel=1)
     elif typ == AxisType.channel:
         pass
     elif typ is None:
@@ -103,21 +104,21 @@ def check_type_unit(model: Axis) -> Axis:
             f"The `type` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the 'type' field of an axis should be set to a string."
         )
-        warnings.warn(msg, UserWarning)
+        warnings.warn(msg, stacklevel=1)
     else:
         msg = (
             f"Unknown axis type '{typ}'. Version {model._version} of the OME-NGFF "
             " spec states that the 'type' field of an axis should be one of "
             f"{AxisType._member_names_}."
         )
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=1)
 
     if unit is None:
         msg = (
             f"The `unit` field of this axis was set to `None`. Version {model._version} of the OME-NGFF spec states "
             "that the `unit` field of an axis should be set to a string."
         )
-        warnings.warn(msg)
+        warnings.warn(msg, stacklevel=1)
     return model
 
 
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 32f7bde..49542be 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -12,12 +12,14 @@
 import numpy.typing as npt
 
 VALID_NDIM = (2, 3, 4, 5)
+NUM_TX_MAX = 2
+
 
 def ensure_scale_translation(
     transforms: Sequence[Union[tx.VectorScale, tx.VectorTranslation]],
 ) -> Sequence[Union[tx.VectorScale, tx.VectorTranslation]]:
     """
-    Ensures that the first element is a scale transformation, the second element, 
+    Ensures that the first element is a scale transformation, the second element,
     if present, is a translation transform, and that there are only 1 or 2 transforms.
     """
 
@@ -32,7 +34,7 @@ def ensure_scale_translation(
             f"transform. Got {maybe_scale} instead."
         )
         raise ValueError(msg)
-    if len(transforms) == 2:
+    if len(transforms) == NUM_TX_MAX:
         maybe_trans = transforms[1]
         if (maybe_trans.type) != "translation":
             msg = (
@@ -56,7 +58,7 @@ def ensure_transforms_length(
 class Dataset(StrictBase):
     """
     A single entry in the `multiscales.datasets` list.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -100,13 +102,13 @@ def ensure_axis_names(axes: Sequence[Axis]) -> Sequence[Axis]:
 
 def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
-        Ensures that the following conditions are true:
+    Ensures that the following conditions are true:
 
-        - there are only 2 or 3 axes with type `space`
-        - the axes with type `space` are last in the list of axes
-        - there is only 1 axis with type `time`
-        - there is only 1 axis with type `channel`
-        - there is only 1 axis with a type that is not `space`, `time`, or `channel`
+    - there are only 2 or 3 axes with type `space`
+    - the axes with type `space` are last in the list of axes
+    - there is only 1 axis with type `time`
+    - there is only 1 axis with type `channel`
+    - there is only 1 axis with a type that is not `space`, `time`, or `channel`
     """
     axis_types = [ax.type for ax in axes]
     type_census = Counter(axis_types)
@@ -115,7 +117,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
         msg = f"Invalid number of space axes: {num_spaces}. Only 2 or 3 space axes are allowed."
         raise ValueError(msg)
 
-    elif not all(a == "space" for a in axis_types[-num_spaces:]):
+    if not all(a == "space" for a in axis_types[-num_spaces:]):
         msg = f"Space axes must come last. Got axes with order: {axis_types}."
         raise ValueError(msg)
 
@@ -137,7 +139,7 @@ def ensure_axis_types(axes: Sequence[Axis]) -> Sequence[Axis]:
 class MultiscaleMetadata(StrictVersionedBase):
     """
     Multiscale image metadata.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -154,7 +156,7 @@ class MultiscaleMetadata(StrictVersionedBase):
     axes: List[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
     coordinateTransformations: List[tx.Scale, tx.Translation]
-        Coordinate transformations that express a scaling and translation shared by all elements of 
+        Coordinate transformations that express a scaling and translation shared by all elements of
         `datasets`.
     """
 
@@ -165,7 +167,7 @@ class MultiscaleMetadata(StrictVersionedBase):
     metadata: Dict[str, Any] | None = None
     datasets: Annotated[List[Dataset], Field(..., min_length=1)]
     axes: Annotated[
-        List[Axis],
+        list[Axis],
         AfterValidator(ensure_axis_length),
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
@@ -176,13 +178,13 @@ class MultiscaleMetadata(StrictVersionedBase):
 class GroupAttrs(BaseModel):
     """
     A model of the required attributes of a Zarr group that implements OME-NGFF Multiscales metadata.
-    
-    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.    
-    
+
+    See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
+
     Attributes
     ----------
     multiscales: List[MultiscaleMetadata]
-        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image. 
+        A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image.
     """
 
     multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
@@ -191,7 +193,7 @@ class GroupAttrs(BaseModel):
 class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#multiscale-md](https://ngff.openmicroscopy.org/0.4/#multiscale-md) for the specification of this data structure.
 
     Attributes
@@ -203,31 +205,40 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """
+
     @classmethod
     def from_arrays(
-        cls, 
+        cls,
         arrays: npt.NDArray[Any],
         paths: Sequence[str],
         transforms: Sequence[Sequence[tx.Transform]],
         axes: Sequence[Axis],
-        *, 
-        name: str | None = None, 
-        type: str | None = None, 
+        *,
+        name: str | None = None,
+        type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        top_level_transforms: List[tx.Transform] | None = None, 
-        **kwargs):
-            """
-            Create a `Group` from a sequence of arrays + spatial metadata.
-            """
-            members = {key: ArraySpec.from_array(arr, **kwargs) for key, arr in zip(paths, arrays, strict=True)}
-            multimeta = MultiscaleMetadata(
-                name=name, 
-                type=type,
-                metadata=metadata,
-                axes=axes,
-                datasets=[Dataset(path=path, coordinateTransformations=txs) for path, txs in zip(paths, transforms, strict=True)],
-                coordinateTransformations=top_level_transforms)
-            return cls(members=members, attributes=multimeta)
+        top_level_transforms: List[tx.Transform] | None = None,
+        **kwargs,
+    ):
+        """
+        Create a `Group` from a sequence of arrays + spatial metadata.
+        """
+        members = {
+            key: ArraySpec.from_array(arr, **kwargs)
+            for key, arr in zip(paths, arrays, strict=True)
+        }
+        multimeta = MultiscaleMetadata(
+            name=name,
+            type=type,
+            metadata=metadata,
+            axes=axes,
+            datasets=[
+                Dataset(path=path, coordinateTransformations=txs)
+                for path, txs in zip(paths, transforms, strict=True)
+            ],
+            coordinateTransformations=top_level_transforms,
+        )
+        return cls(members=members, attributes=multimeta)
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index 659838f..b065c29 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,10 +1,11 @@
 from __future__ import annotations
-from typing import List, Optional
+from typing import List
 
 from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
+
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from typing import Union
 
 import pydantic_ome_ngff.v04.well as well
@@ -12,7 +13,7 @@
 
 class Acquisition(BaseModel):
     id: PositiveInt
-    name: Optional[str] = None
+    name: str | None = None
     maximumfieldcount: PositiveInt
 
 
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index adf5af1..3d192fc 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -1,13 +1,17 @@
 from __future__ import annotations
 
-from typing import Literal, Sequence, Tuple, Union
+from typing import TYPE_CHECKING, Literal
+
 from pydantic_ome_ngff.base import StrictBase
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 
 class Identity(StrictBase):
     """
     An identity transform. It has no parameters other than `type`, and no valid use according to the spec.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -26,7 +30,7 @@ class PathTranslation(StrictBase):
     A translation transformation with a `path` field. The spec states that `path` should resolve to "binary data".
 
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
-    
+
     Attributes
     ----------
 
@@ -43,7 +47,7 @@ class PathTranslation(StrictBase):
 class PathScale(StrictBase):
     """
     A scaling transformation with a `path` field. The spec states that `path` should resolve to "binary data".
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -61,7 +65,7 @@ class PathScale(StrictBase):
 class VectorTranslation(StrictBase):
     """
     A translation transformation defined by a sequence of numbers.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -79,7 +83,7 @@ class VectorTranslation(StrictBase):
 class VectorScale(StrictBase):
     """
     A scaling transformation defined by a sequence of numbers.
-    
+
     See [https://ngff.openmicroscopy.org/0.4/#trafo-md](https://ngff.openmicroscopy.org/0.4/#trafo-md) for the specification of this data structure.
 
     Attributes
@@ -95,7 +99,7 @@ class VectorScale(StrictBase):
 
 
 def ndim(
-    transform: Union[VectorScale, VectorTranslation],
+    transform: VectorScale | VectorTranslation,
 ) -> int:
     """
     Get the dimensionality of a `VectorScale` or `VectorTranslation`.
@@ -115,17 +119,17 @@ def ndim(
 
 def scale_translation(
     scale: Sequence[float], translation: Sequence[float]
-) -> Tuple[Scale, Translation]:
+) -> tuple[Scale, Translation]:
     """
     Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
     """
     len_scale = len(scale)
     len_translation = len(translation)
     if len_scale < 1:
-        msg = f"Not enough values in scale. Got 0, expected at least 1."
+        msg = "Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation < 1:
-        msg = f"Not enough values in `translation`. Got 0, expected at least 1."
+        msg = "Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
     if len_translation != len_scale:
         msg = (
@@ -141,6 +145,7 @@ def scale_translation(
 Translation = VectorTranslation | PathTranslation
 Transform = Scale | Translation
 
+
 def ensure_dimensionality(
     transforms: Sequence[VectorScale | VectorTranslation],
 ) -> Sequence[VectorScale | VectorTranslation]:
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index c9c6780..c900962 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,17 +1,17 @@
 from __future__ import annotations
-from typing import List, Optional, Union
+from typing import List, Union
 
 from pydantic import BaseModel, ValidationError, field_validator
-from pydantic_ome_ngff.base import VersionedBase
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
 
+from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
 import pydantic_ome_ngff.v04.multiscales as multiscales
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
 
 
 class Image(BaseModel):
     path: str
-    acquisition: Optional[int]
+    acquisition: int | None
 
 
 class WellMetadata(VersionedBase):
diff --git a/tests/conftest.py b/tests/conftest.py
index d39d3a5..c8c5565 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,11 +1,9 @@
-from typing import Tuple, Any, Optional, Union, List, Dict
-from pathlib import Path
-import json
+from typing import Any
 
 import requests
 
 
-def fetch_schemas(version: str, schema_name: str) -> Tuple[Any, Any]:
+def fetch_schemas(version: str, schema_name: str) -> tuple[Any, Any]:
     """
     Get the relaxed and strict schemas for a given version of the spec.
     """
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index c938301..213b9c3 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -4,6 +4,8 @@
 import pytest
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
+
+from pydantic_ome_ngff.latest.axis import Axis
 from pydantic_ome_ngff.latest.multiscales import (
     MultiscaleMetadata,
     GroupAttrs,
@@ -16,7 +18,6 @@
     VectorScale,
     VectorTranslation,
 )
-from pydantic_ome_ngff.latest.axis import Axis
 from tests.conftest import fetch_schemas
 
 
@@ -126,10 +127,10 @@ def test_multiscale_unique_axis_names() -> None:
 
 @pytest.mark.parametrize(
     "axis_types",
-    (
+    [
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-    ),
+    ],
 )
 def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     units_map = {"space": "meter", "time": "second"}
@@ -179,7 +180,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
         )
 
 
-@pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
+@pytest.mark.parametrize("num_axes", [0, 1, 6, 7])
 def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
@@ -232,7 +233,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorScale(scale=(1, 1, 1)),
             VectorTranslation(translation=(1, 1, 1)),
@@ -242,7 +243,7 @@ def test_coordinate_transforms_invalid_ndims() -> None:
             VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
@@ -253,7 +254,7 @@ def test_coordinate_transforms_invalid_length(
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorTranslation(translation=(1, 1, 1)),
         ]
@@ -262,7 +263,7 @@ def test_coordinate_transforms_invalid_length(
             VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index c1a0ce7..e2e9578 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import List, Optional, Tuple
+from typing import Tuple
 from pydantic import ValidationError
 import pytest
 import jsonschema as jsc
@@ -128,12 +128,12 @@ def test_multiscale_unique_axis_names() -> None:
 
 @pytest.mark.parametrize(
     "axis_types",
-    (
+    [
         ("space", "space", "channel"),
         ("space", "channel", "space", "channel"),
-    ),
+    ],
 )
-def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
+def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
     units_map = {"space": "meter", "time": "second"}
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
@@ -181,7 +181,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
         )
 
 
-@pytest.mark.parametrize("num_axes", (0, 1, 6, 7))
+@pytest.mark.parametrize("num_axes", [0, 1, 6, 7])
 def test_multiscale_axis_length(num_axes: int) -> None:
     rank = num_axes
     axes = [Axis(name=str(idx), type="space", unit="meter") for idx in range(num_axes)]
@@ -227,14 +227,14 @@ def test_coordinate_transforms_invalid_ndims() -> None:
     ]
     with pytest.raises(
         ValidationError,
-        match="The transforms have inconsistent dimensionality.",  # noqa
+        match="The transforms have inconsistent dimensionality.",
     ):
         Dataset(path="foo", coordinateTransformations=tforms)
 
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorScale(scale=(1, 1, 1)),
             VectorTranslation(translation=(1, 1, 1)),
@@ -244,10 +244,10 @@ def test_coordinate_transforms_invalid_ndims() -> None:
             VectorScale(scale=(1, 1, 1)),
         ]
         * 5,
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_length(
-    transforms: List[Transform],
+    transforms: list[Transform],
 ) -> None:
     with pytest.raises(ValidationError, match="expected 1 or 2"):
         Dataset(path="foo", coordinateTransformations=transforms)
@@ -255,7 +255,7 @@ def test_coordinate_transforms_invalid_length(
 
 @pytest.mark.parametrize(
     "transforms",
-    (
+    [
         [
             VectorTranslation(translation=(1, 1, 1)),
         ]
@@ -264,7 +264,7 @@ def test_coordinate_transforms_invalid_length(
             VectorTranslation(translation=(1, 1, 1)),
             VectorScale(scale=(1, 1, 1)),
         ],
-    ),
+    ],
 )
 def test_coordinate_transforms_invalid_first_element(
     transforms: Tuple[Transform, Transform],
@@ -307,6 +307,13 @@ def test_multiscale_group_datasets_exist(
     }
     Group(attributes=group_attrs, members=good_items)
 
+    bad_items = {
+        d.path + "x": ArraySpec(
+            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+        )
+        for d in default_multiscale.datasets
+    }
+
     with pytest.raises(
         ValidationError,
         match="array with that name was found in the items of that group.",
@@ -330,6 +337,17 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
     }
     Group(attributes=group_attrs, members=good_items)
 
+    # arrays with varying rank
+    bad_items = {
+        d.path: ArraySpec(
+            shape=(1,) * (idx + 1),
+            dtype="uint8",
+            chunks=(1,) * (idx + 1),
+            attributes={},
+        )
+        for idx, d in enumerate(default_multiscale.datasets)
+    }
+
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
@@ -345,6 +363,11 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
         }
         Group(attributes=group_attrs, members=bad_items)
 
+    # arrays with rank that doesn't match the transform
+    bad_items = {
+        d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
+        for d in default_multiscale.datasets
+    }
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {

From 5f7b90d5e5c453d81ed9821df22f7ca63160ed38 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 13:50:56 +0100
Subject: [PATCH 28/69] tighten some names and type annotations

---
 src/pydantic_ome_ngff/latest/transforms.py | 10 ++++++++++
 src/pydantic_ome_ngff/v04/transforms.py    |  5 +----
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transforms.py
index 7ca832a..c5e17d0 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transforms.py
@@ -9,6 +9,8 @@ class Identity(tx.Identity):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class PathScale(tx.PathScale):
     """ "
@@ -16,6 +18,8 @@ class PathScale(tx.PathScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class PathTranslation(tx.PathTranslation):
     """ "
@@ -23,6 +27,8 @@ class PathTranslation(tx.PathTranslation):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class VectorTranslation(tx.VectorTranslation):
     """
@@ -30,6 +36,8 @@ class VectorTranslation(tx.VectorTranslation):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 class VectorScale(tx.VectorScale):
     """
@@ -37,6 +45,8 @@ class VectorScale(tx.VectorScale):
     See https://ngff.openmicroscopy.org/latest/#trafo-md
     """
 
+    ...
+
 
 Scale = Union[VectorScale, PathScale]
 Translation = Union[VectorTranslation, PathTranslation]
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 3d192fc..df1a9f5 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -1,12 +1,9 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Literal
+from typing import Literal, Sequence
 
 from pydantic_ome_ngff.base import StrictBase
 
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-
 
 class Identity(StrictBase):
     """

From 5e2cbbe0cf6f254cdfcd65ee841c60df065c37b4 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Thu, 15 Feb 2024 19:41:43 +0100
Subject: [PATCH 29/69] start handling deeper arrays

---
 docs/index.md                            | 26 ++++---
 example.py                               |  5 ++
 src/pydantic_ome_ngff/utils.py           | 57 +++++++++++++-
 src/pydantic_ome_ngff/v04/axis.py        | 11 +--
 src/pydantic_ome_ngff/v04/label.py       |  7 +-
 src/pydantic_ome_ngff/v04/multiscales.py | 98 +++++++++++++++++++-----
 tests/latest/test_multiscales.py         |  2 +-
 tests/test_utils.py                      | 33 ++++++++
 tests/v04/test_axis.py                   | 18 -----
 tests/v04/test_label.py                  | 12 +--
 tests/v04/test_multiscales.py            | 60 ++++++++++++++-
 11 files changed, 256 insertions(+), 73 deletions(-)
 create mode 100644 example.py
 create mode 100644 tests/test_utils.py
 delete mode 100644 tests/v04/test_axis.py

diff --git a/docs/index.md b/docs/index.md
index 000ea34..ad01c67 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,17 +1,19 @@
-# Welcome to MkDocs
+# pydantic-ome-ngff
 
-For full documentation visit [mkdocs.org](https://www.mkdocs.org).
+[Pydantic](https://docs.pydantic.dev/latest/) models for [OME-NGFF](https://ngff.openmicroscopy.org/)
 
-## Commands
+# About
 
-* `mkdocs new [dir-name]` - Create a new project.
-* `mkdocs serve` - Start the live-reloading docs server.
-* `mkdocs build` - Build the documentation site.
-* `mkdocs -h` - Print help message and exit.
+This library aims to provide models for the the metadata objects and Zarr hierarchies described in the [OME-NGFF](https://ngff.openmicroscopy.org/) specifications.
 
-## Project layout
+# Reading Multiscale metadata
 
-    mkdocs.yml    # The configuration file.
-    docs/
-        index.md  # The documentation homepage.
-        ...       # Other markdown pages, images and other files.
+```python
+# example data on S3-compatible cloud storage
+from pydantic_ome_ngff.v04.multiscales import Group
+import zarr
+url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+zgroup = zarr.open(url)
+group = Group.from_zarr(zgroup)
+
+```
diff --git a/example.py b/example.py
new file mode 100644
index 0000000..ee18a04
--- /dev/null
+++ b/example.py
@@ -0,0 +1,5 @@
+from pydantic_ome_ngff.v04.multiscales import Group
+import zarr
+url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+zgroup = zarr.open(url)
+group = Group.from_zarr(zgroup)
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index 88b80de..7dd675c 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -1,8 +1,16 @@
+from __future__ import annotations
+from typing import TYPE_CHECKING, runtime_checkable
 from collections import Counter
-from collections.abc import Hashable, Iterable
+from typing import Protocol
+import numpy as np
 
+if TYPE_CHECKING:
+    from typing import Dict, Iterable, Hashable, Tuple
 
-def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
+from pydantic_zarr.v2 import GroupSpec, ArraySpec
+import os
+
+def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
     elements of the input that occurred at least once, and the values are the
@@ -10,3 +18,48 @@ def duplicates(values: Iterable[Hashable]) -> dict[Hashable, int]:
     """
     counts = Counter(values)
     return {k: v for k, v in counts.items() if v > 1}
+
+
+def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, ArraySpec | GroupSpec]:
+    """
+    Flatten a `GroupSpec` or `ArraySpec`.
+    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are 
+    `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
+    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute 
+    under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
+    to the name of each member.
+
+    Paramters
+    ---------
+    node: `GroupSpec` | `ArraySpec`
+        The node to flatten.
+    path: `str`, default is '/'
+        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be 
+        made relative to `path` when used as keys in the result dictionary.
+
+    Returns
+    -------
+    `Dict[str, GroupSpec | ArraySpec]`
+
+    """
+    result = {}
+    if isinstance(node, ArraySpec):
+        model_copy = node.model_copy(deep=True)
+
+    else:
+        model_copy = node.model_copy(update={"members": {}})
+        for name, value in node.members.items():
+            result.update(flatten_node(value, os.path.join(path, name)))
+
+    result[path] = model_copy
+        
+    return result
+
+@runtime_checkable
+class ArrayLike(Protocol):
+    shape: Tuple[int, ...]
+    dtype: np.dtype
+
+@runtime_checkable
+class ChunkedArrayLike(ArrayLike, Protocol):
+    chunks: Tuple[int, ...]
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index e0fb97a..043c7b4 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 from enum import Enum
+from typing import Optional
 import warnings
 
 from pydantic import model_validator
@@ -134,16 +135,12 @@ class Axis(StrictVersionedBase):
     name: str
         The name for this axis.
     type: str | None
-        The type for this axis, e.g. `space`.
+        The type for this axis, e.g. "space".
     unit: str | None
         The unit of measure associated with the interval defined by this axis.
     """
 
     _version = version
     name: str
-    type: str | None
-    unit: str | None
-
-    @model_validator(mode="after")
-    def check_type_unit(self):
-        return check_type_unit(self)
+    type: Optional[str] = None
+    unit: Optional[str] = None
\ No newline at end of file
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 95ef442..7ccc5ce 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -52,11 +52,12 @@ def parse_colors(colors: List[Color] | None) -> List[Color] | None:
 
 def parse_version(version: Literal["0.4"] | None) -> Literal["0.4"] | None:
     if version is None:
-        msg = (
+        _ = (
             f"The `version` attribute is `None`. Version {NGFF_VERSION} of "
-            f"the OME-NGFF spec states that `version` must either be unset or the string {NGFF_VERSION}"
+            f"the OME-NGFF spec states that `version` should either be unset or the string {NGFF_VERSION}"
         )
-        warnings.warn(msg, stacklevel=1)
+        # This goes against a recommendation from the spec, but emitting a warning is annoying. 
+        # leaving this here as a placeholder.
     return version
 
 
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 49542be..0a100b6 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,16 +1,15 @@
 from __future__ import annotations
 from collections import Counter
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
-
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-from pydantic_ome_ngff.utils import duplicates
+from pydantic_ome_ngff.utils import ArrayLike, ChunkedArrayLike, duplicates, flatten_node
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
-import numpy.typing as npt
-
+import zarr
+from zarr.errors import ArrayNotFoundError, ContainsGroupError
 VALID_NDIM = (2, 3, 4, 5)
 NUM_TX_MAX = 2
 
@@ -79,6 +78,18 @@ class Dataset(StrictBase):
     ]
 
 
+def create_dataset(
+        path: str, 
+        scale: Sequence[int | float], 
+        translation: Sequence[int | float]) -> Dataset:
+    """
+    Create a `Dataset` from a path, a scale, and a translation.
+    """
+    return Dataset(
+        path=path,
+        coordinateTransformations=[tx.VectorScale(scale=scale), tx.VectorTranslation(translation=translation)])
+
+
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
     """
     Ensures that there are between 2 and 5 axes (inclusive)
@@ -206,23 +217,67 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
 
     """
 
+    @classmethod
+    def from_zarr(cls, node: zarr.Group) -> Group:
+        guess = GroupSpec.from_zarr(node)
+        
+        try:
+            multi_meta_maybe = guess.attributes['multiscales']
+        except KeyError as e:
+            msg = (f"Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
+                  f"{node.store.path}/{node.path}")
+            raise ValueError(msg) from e
+        
+        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
+
+        for multiscale in multi_meta.multiscales:
+            for dataset in multiscale.datasets:
+                array_path = '/'.join([node.path, dataset.path])
+                try:
+                    array = zarr.open_array(
+                        store=node.store, 
+                        path=array_path,
+                        mode='r')
+                    array_spec = ArraySpec.from_zarr(array)
+                except ArrayNotFoundError as e:
+                    raise ValueError(f"Expected to find an array at {array_path}, but no array was found there.")
+                except ContainsGroupError as e:
+
+
+        return guess
+
     @classmethod
     def from_arrays(
         cls,
-        arrays: npt.NDArray[Any],
         paths: Sequence[str],
-        transforms: Sequence[Sequence[tx.Transform]],
         axes: Sequence[Axis],
+        arrays: Sequence[ArrayLike | ChunkedArrayLike],
+        scales: Sequence[int | float],
+        translations: Sequence[int | float],
         *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        top_level_transforms: List[tx.Transform] | None = None,
+        group_scale: tx.Scale | None = None,
+        group_translation: tx.Translation | None = None,
         **kwargs,
     ):
         """
-        Create a `Group` from a sequence of arrays + spatial metadata.
+        Create a `Group` from a sequence of arrays and spatial metadata.
+
+        Parameters
+        ----------
+        paths: Sequence[str]
+            The paths to the arrays.
         """
+        
+        group_transforms = list(filter(lambda v: v is not None, [group_scale, group_translation]))
+        for idx, value in enumerate(group_transforms):
+            if idx == 0:
+                group_transforms[idx] = tx.VectorScale(scale=value)
+            if idx == 1:
+                group_transforms[idx] = tx.VectorTranslation(translation=value) 
+
         members = {
             key: ArraySpec.from_array(arr, **kwargs)
             for key, arr in zip(paths, arrays, strict=True)
@@ -233,12 +288,12 @@ def from_arrays(
             metadata=metadata,
             axes=axes,
             datasets=[
-                Dataset(path=path, coordinateTransformations=txs)
-                for path, txs in zip(paths, transforms, strict=True)
+                create_dataset(path=path, scale=scale, translation=translation)
+                for path, scale, translation in zip(paths, scales, translations, strict=True)
             ],
-            coordinateTransformations=top_level_transforms,
+            coordinateTransformations=group_transforms,
         )
-        return cls(members=members, attributes=multimeta)
+        return cls(members=members, attributes=GroupAttrs(multiscales=[multimeta]))
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
@@ -249,17 +304,20 @@ def check_arrays_exist(self) -> "Group":
         allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
-        array_items: dict[str, dict[str, ArraySpec]] = {
-            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
-        }
-
+        flattened = flatten_node(self)
+        
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                if (dpath := dataset.path) not in array_items:
+                dpath = '/' + dataset.path
+                if dpath in flattened:
+                    if not isinstance(flattened[dpath], ArraySpec):
+                        msg = f'The node at {dpath} should be an array, found {type(flattened[dpath])} instead'
+                        raise ValueError(msg)
+                else:
                     msg = (
-                        f"Dataset {dpath} was specified in multiscale metadata, but no "
-                        "array with that name was found in the items of that group. "
-                        "All arrays referenced in multiscale metadata must be items of the group."
+                        f"Dataset {dataset.path} was specified in multiscale metadata, but no "
+                        "array with that name was found in the hierarchy. "
+                        "All arrays referenced in multiscale metadata must be contained in the group."
                     )
                     raise ValueError(msg)
         return self
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 213b9c3..e3b2212 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -308,7 +308,7 @@ def test_multiscale_group_datasets_exist(
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the items of that group.",
+        match="array with that name was found in the hierarchy.",
     ):
         bad_items = {
             d.path + "x": ArraySpec(
diff --git a/tests/test_utils.py b/tests/test_utils.py
new file mode 100644
index 0000000..df62bb7
--- /dev/null
+++ b/tests/test_utils.py
@@ -0,0 +1,33 @@
+from __future__ import annotations
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from typing import Any, List
+
+from pydantic_ome_ngff.utils import duplicates, flatten_node
+from pydantic_zarr.v2 import ArraySpec, GroupSpec
+import numpy as np
+import pytest
+
+def test_flatten_node() -> None:
+    a = ArraySpec.from_array(np.arange(10))
+    flattened = flatten_node(a)
+    assert flattened == {'/': a}
+
+    b = GroupSpec(attributes={'foo': 10}, members={'name': a})
+    flattened_b = flatten_node(b)
+    assert flattened_b['/'] == b.model_copy(update={"members": {}})
+    assert flattened_b['/name'] == a
+
+    c = GroupSpec(attributes={}, members={'b': b, 'a': a})
+    flattened_c = flatten_node(c, path='c')
+    assert flattened_c['c'] == c.model_copy(update={"members": {}})
+    assert flattened_c["c/b"] == b.model_copy(update={"members": {}})
+    assert flattened_c["c/a"] == a
+    assert flattened_c["c/b/name"] == a
+
+@pytest.mark.parametrize('data', [[0], [0,1,1,1,2], ['a','a','b','b','c','c','d']])
+def test_duplicates(data: List[Any]) -> None:
+    dupes = duplicates(data)
+    for key, value in dupes.items():
+        assert data.count(key) == value
+        assert value > 1
\ No newline at end of file
diff --git a/tests/v04/test_axis.py b/tests/v04/test_axis.py
deleted file mode 100644
index 968c507..0000000
--- a/tests/v04/test_axis.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import pytest
-
-from pydantic_ome_ngff.v04.axis import Axis
-
-
-@pytest.mark.parametrize(
-    "axis_type, unit",
-    [
-        ("space", "second"),
-        ("time", "meter"),
-        ("space", None),
-        (None, None),
-        ("foo", None),
-    ],
-)
-def test_axis_type_unit_match_warning(axis_type: str, unit: str) -> None:
-    with pytest.warns(UserWarning):
-        Axis(name="axis", type=axis_type, unit=unit)
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index e2c4523..f94365d 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -29,14 +29,10 @@ def test_properties_colors_match():
         ImageLabel(colors=[color], properties=[prop])
 
 
-@pytest.mark.parametrize("version", ("0.5", None))
-def test_imagelabel_version(version: str | None) -> None:
-    if version is None:
-        with pytest.warns(UserWarning):
-            _ = ImageLabel(version=version)
-    else:
-        with pytest.raises(ValidationError, match="Input should be '0.4'"):
-            _ = ImageLabel(version=version)
+@pytest.mark.parametrize("version", ("0.5", "0.3"))
+def test_imagelabel_version(version: str) -> None:
+    with pytest.raises(ValidationError, match="Input should be '0.4'"):
+        _ = ImageLabel(version=version)
 
 
 @pytest.mark.parametrize(
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index e2e9578..eeb3934 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import Tuple
+from typing import Dict, Tuple
 from pydantic import ValidationError
 import pytest
 import jsonschema as jsc
@@ -316,7 +316,7 @@ def test_multiscale_group_datasets_exist(
 
     with pytest.raises(
         ValidationError,
-        match="array with that name was found in the items of that group.",
+        match="array with that name was found in the hierarchy",
     ):
         bad_items = {
             d.path + "x": ArraySpec(
@@ -375,3 +375,59 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
             for d in default_multiscale.datasets
         }
         Group(attributes=group_attrs, members=bad_items)
+
+
+import numpy as np
+from itertools import accumulate
+import operator
+@pytest.mark.parametrize('name', [None, "foo"])
+@pytest.mark.parametrize('type', [None, "foo"])
+@pytest.mark.parametrize('path_pattern', ['{0}', 's{0}'])
+@pytest.mark.parametrize('metadata', [None, {'foo': 10}])
+@pytest.mark.parametrize('ndim', [2,3,4,5])
+def test_from_arrays(
+    name: str | None, 
+    type: str | None, 
+    path_pattern: str,
+    metadata: Dict[str, int] | str | None, 
+    ndim: int):
+    arrays = [np.arange(x ** ndim).reshape((x,) * ndim) for  x in [3,2,1]]
+    paths = [path_pattern.format(idx) for idx in range(len(arrays))]
+    scales = [(2 ** idx, ) * ndim for idx in range(len(arrays))]
+    translations = [(t,) * ndim for t in accumulate([(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add)]
+    
+    group_scale = (1,) * ndim
+    group_translation = (0,) * ndim
+
+
+    all_axes = [Axis(name="x", type="space",), Axis(name="y", type="space"), Axis(name="z", type="space"), Axis(name="t", type="time"), Axis(name="c", type="barf")]
+    # spatial axes have to come last
+    if ndim in (2, 3):
+        axes = all_axes[:ndim]
+    else:
+        axes = [*all_axes[4:], *all_axes[:3]]
+    
+    group = Group.from_arrays(
+        paths=paths,
+        axes=axes,
+        arrays=arrays,
+        scales=scales,
+        translations=translations,
+        name=name,
+        type=type,
+        metadata=metadata, 
+        group_scale=group_scale,
+        group_translation=group_translation
+    )
+
+    assert group.attributes.multiscales[0].name == name
+    assert group.attributes.multiscales[0].type == type
+    assert group.attributes.multiscales[0].metadata == metadata
+    assert group.attributes.multiscales[0].coordinateTransformations == [VectorScale(scale=group_scale), VectorTranslation(translation=group_translation)]
+    assert group.attributes.multiscales[0].axes == axes
+    for idx, array in enumerate(arrays):
+        assert array.shape == group.members[paths[idx]].shape
+        assert array.dtype == group.members[paths[idx]].dtype
+        assert group.attributes.multiscales[0].datasets[idx].coordinateTransformations == [VectorScale(scale=scales[idx]), VectorTranslation(translation=translations[idx])]
+
+

From 5296cce707a3509a8fad8689f6ea02dadfda04e1 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Tue, 20 Feb 2024 13:18:20 +0100
Subject: [PATCH 30/69] flattening and unflattening routines for GroupSpec

---
 src/pydantic_ome_ngff/utils.py           | 56 ++++++++++++++---
 src/pydantic_ome_ngff/v04/multiscales.py | 79 +++++++++++++++++-------
 2 files changed, 102 insertions(+), 33 deletions(-)

diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index 7dd675c..f9e4b4a 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -5,11 +5,12 @@
 import numpy as np
 
 if TYPE_CHECKING:
-    from typing import Dict, Iterable, Hashable, Tuple
+    from typing import Dict, Iterable, Hashable, Tuple, Any
 
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 import os
 
+
 def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
     Takes a sequence of hashable elements and returns a dict where the keys are the
@@ -20,12 +21,14 @@ def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     return {k: v for k, v in counts.items() if v > 1}
 
 
-def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, ArraySpec | GroupSpec]:
+def flatten_node(
+    node: ArraySpec | GroupSpec, path: str = "/"
+) -> Dict[str, ArraySpec | GroupSpec]:
     """
     Flatten a `GroupSpec` or `ArraySpec`.
-    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are 
+    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are
     `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
-    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute 
+    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute
     under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
     to the name of each member.
 
@@ -33,8 +36,8 @@ def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, Arra
     ---------
     node: `GroupSpec` | `ArraySpec`
         The node to flatten.
-    path: `str`, default is '/'
-        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be 
+    path: `str`, default is 'root'
+        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be
         made relative to `path` when used as keys in the result dictionary.
 
     Returns
@@ -52,14 +55,49 @@ def flatten_node(node: ArraySpec | GroupSpec, path: str = '/') -> Dict[str, Arra
             result.update(flatten_node(value, os.path.join(path, name)))
 
     result[path] = model_copy
-        
+
     return result
 
+
+ArraySpec.model_dump
+
+
+def unflatten_node(
+    tree: Dict[str, ArraySpec | GroupSpec], attributes: Dict[str, Any] = {}
+) -> ArraySpec | GroupSpec:
+    member_lobby = {}
+    tree_mut: Dict[str, Dict[str, ArraySpec | GroupSpec]] = {}
+    for key, value in tree.items():
+        key_parts = key.split("/")
+        if key_parts[0] != "":
+            raise ValueError(f'Invalid path: {key} does not start with "/".')
+        if len(key_parts) == 2:
+            member_lobby[key_parts[1]] = value
+        else:
+            subparent = key_parts[1]
+            if subparent not in tree_mut:
+                tree_mut[subparent] = {}
+            tree_mut[subparent]["/".join(["", *key_parts[2:]])] = value
+    for subparent, subchildren in tree_mut.items():
+        if subparent in member_lobby:
+            if isinstance(member_lobby[subparent], ArraySpec):
+                msg = f"Invalid tree: the node named {subparent} is declared both as ArraySpec and GroupSpec"
+                raise ValueError(msg)
+            else:
+                member_lobby[subparent] = unflatten_node(
+                    subchildren, attributes=member_lobby[subparent].attributes
+                )
+        else:
+            member_lobby[subparent] = unflatten_node(subchildren)
+    return GroupSpec(members=member_lobby, attributes=attributes)
+
+
 @runtime_checkable
 class ArrayLike(Protocol):
     shape: Tuple[int, ...]
-    dtype: np.dtype
+    dtype: np.dtype[Any]
+
 
 @runtime_checkable
 class ChunkedArrayLike(ArrayLike, Protocol):
-    chunks: Tuple[int, ...]
\ No newline at end of file
+    chunks: Tuple[int, ...]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 0a100b6..9775570 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -3,13 +3,20 @@
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
-from pydantic_ome_ngff.utils import ArrayLike, ChunkedArrayLike, duplicates, flatten_node
+from pydantic_ome_ngff.utils import (
+    ArrayLike,
+    ChunkedArrayLike,
+    duplicates,
+    flatten_node,
+    resolve_groups,
+)
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transforms as tx
 import zarr
 from zarr.errors import ArrayNotFoundError, ContainsGroupError
+
 VALID_NDIM = (2, 3, 4, 5)
 NUM_TX_MAX = 2
 
@@ -79,15 +86,18 @@ class Dataset(StrictBase):
 
 
 def create_dataset(
-        path: str, 
-        scale: Sequence[int | float], 
-        translation: Sequence[int | float]) -> Dataset:
+    path: str, scale: Sequence[int | float], translation: Sequence[int | float]
+) -> Dataset:
     """
     Create a `Dataset` from a path, a scale, and a translation.
     """
     return Dataset(
         path=path,
-        coordinateTransformations=[tx.VectorScale(scale=scale), tx.VectorTranslation(translation=translation)])
+        coordinateTransformations=[
+            tx.VectorScale(scale=scale),
+            tx.VectorTranslation(translation=translation),
+        ],
+    )
 
 
 def ensure_axis_length(axes: Sequence[Axis]) -> Sequence[Axis]:
@@ -220,29 +230,46 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     @classmethod
     def from_zarr(cls, node: zarr.Group) -> Group:
         guess = GroupSpec.from_zarr(node)
-        
+
         try:
-            multi_meta_maybe = guess.attributes['multiscales']
+            multi_meta_maybe = guess.attributes["multiscales"]
         except KeyError as e:
-            msg = (f"Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
-                  f"{node.store.path}/{node.path}")
+            msg = (
+                "Failed to find mandatory `multiscales` key in the attributes of the zarr group at ",
+                f"{node.store.path}/{node.path}",
+            )
             raise ValueError(msg) from e
-        
-        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
 
+        multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
         for multiscale in multi_meta.multiscales:
+            members = {}
             for dataset in multiscale.datasets:
-                array_path = '/'.join([node.path, dataset.path])
+                array_path = "/".join([node.path, dataset.path])
                 try:
-                    array = zarr.open_array(
-                        store=node.store, 
-                        path=array_path,
-                        mode='r')
+                    array = zarr.open_array(store=node.store, path=array_path, mode="r")
                     array_spec = ArraySpec.from_zarr(array)
                 except ArrayNotFoundError as e:
-                    raise ValueError(f"Expected to find an array at {array_path}, but no array was found there.")
+                    msg = (
+                        f"Expected to find an array at {array_path}, ",
+                        "but no array was found there.",
+                    )
+                    raise ArrayNotFoundError(msg) from e
                 except ContainsGroupError as e:
+                    msg = (
+                        f"Expected to find an array at {array_path}, ",
+                        "but a group was found there instead.",
+                    )
+                    raise ContainsGroupError(msg) from e
+                dataset_path_parts = dataset.path.split("/")
+                if len(dataset_path_parts) == 1:
+                    members[dataset.path] = array_spec
+                else:
+                    # this will not be correct for multiple arrays in the same deep group
+                    members[dataset.path] = resolve_groups(
+                        "/".join(dataset_path_parts[1:]), array_spec
+                    )
 
+            guess = guess.model_copy(update={**guess.members, **members})
 
         return guess
 
@@ -270,13 +297,15 @@ def from_arrays(
         paths: Sequence[str]
             The paths to the arrays.
         """
-        
-        group_transforms = list(filter(lambda v: v is not None, [group_scale, group_translation]))
+
+        group_transforms = list(
+            filter(lambda v: v is not None, [group_scale, group_translation])
+        )
         for idx, value in enumerate(group_transforms):
             if idx == 0:
                 group_transforms[idx] = tx.VectorScale(scale=value)
             if idx == 1:
-                group_transforms[idx] = tx.VectorTranslation(translation=value) 
+                group_transforms[idx] = tx.VectorTranslation(translation=value)
 
         members = {
             key: ArraySpec.from_array(arr, **kwargs)
@@ -289,7 +318,9 @@ def from_arrays(
             axes=axes,
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
-                for path, scale, translation in zip(paths, scales, translations, strict=True)
+                for path, scale, translation in zip(
+                    paths, scales, translations, strict=True
+                )
             ],
             coordinateTransformations=group_transforms,
         )
@@ -305,13 +336,13 @@ def check_arrays_exist(self) -> "Group":
         """
         attrs = self.attributes
         flattened = flatten_node(self)
-        
+
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                dpath = '/' + dataset.path
+                dpath = "/" + dataset.path
                 if dpath in flattened:
                     if not isinstance(flattened[dpath], ArraySpec):
-                        msg = f'The node at {dpath} should be an array, found {type(flattened[dpath])} instead'
+                        msg = f"The node at {dpath} should be an array, found {type(flattened[dpath])} instead"
                         raise ValueError(msg)
                 else:
                     msg = (

From 9a226ab8b6f75430fd25e5162724a1a39098245e Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:09:24 +0100
Subject: [PATCH 31/69] fix: use tuple instead of list for transforms; defer to
 pydantic-zarr for flattening / unflattening; handle arrays in subgroups when
 validating multiscale metadata

---
 poetry.lock                              | 1299 +++++++++++-----------
 pyproject.toml                           |    2 +-
 src/pydantic_ome_ngff/utils.py           |   74 --
 src/pydantic_ome_ngff/v04/multiscales.py |  125 ++-
 src/pydantic_ome_ngff/v04/transforms.py  |   20 +-
 tests/latest/test_multiscales.py         |   52 +-
 tests/test_utils.py                      |   27 +-
 tests/v04/test_multiscales.py            |  130 ++-
 8 files changed, 844 insertions(+), 885 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 132606d..9c3ff82 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,109 +1,109 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
-version = "2.11.1"
+version = "2.12.0"
 description = "Async client for aws services using botocore and aiohttp"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiobotocore-2.11.1-py3-none-any.whl", hash = "sha256:904a7ad7cc8671d662cfd596906dafe839118ea2a66332c37908e3dcfdee1e45"},
-    {file = "aiobotocore-2.11.1.tar.gz", hash = "sha256:0b095af50da2d6f94e93ca959e2a4876f0f0d84d534b61b21d8e050832d04ab6"},
+    {file = "aiobotocore-2.12.0-py3-none-any.whl", hash = "sha256:e121503dca049cf361dea19730e335aff2e7508f7f8b24db2e6a43a6fb70299e"},
+    {file = "aiobotocore-2.12.0.tar.gz", hash = "sha256:bc841cef234afcb781f2d600680c9e49d01b9a2e8169790a32579bb0df51777f"},
 ]
 
 [package.dependencies]
 aiohttp = ">=3.7.4.post0,<4.0.0"
 aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.33.2,<1.34.28"
+botocore = ">=1.34.41,<1.34.52"
 wrapt = ">=1.10.10,<2.0.0"
 
 [package.extras]
-awscli = ["awscli (>=1.31.2,<1.32.28)"]
-boto3 = ["boto3 (>=1.33.2,<1.34.28)"]
+awscli = ["awscli (>=1.32.41,<1.32.52)"]
+boto3 = ["boto3 (>=1.34.41,<1.34.52)"]
 
 [[package]]
 name = "aiohttp"
-version = "3.9.1"
+version = "3.9.3"
 description = "Async http client/server framework (asyncio)"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:e1f80197f8b0b846a8d5cf7b7ec6084493950d0882cc5537fb7b96a69e3c8590"},
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c72444d17777865734aa1a4d167794c34b63e5883abb90356a0364a28904e6c0"},
-    {file = "aiohttp-3.9.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9b05d5cbe9dafcdc733262c3a99ccf63d2f7ce02543620d2bd8db4d4f7a22f83"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5c4fa235d534b3547184831c624c0b7c1e262cd1de847d95085ec94c16fddcd5"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:289ba9ae8e88d0ba16062ecf02dd730b34186ea3b1e7489046fc338bdc3361c4"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:bff7e2811814fa2271be95ab6e84c9436d027a0e59665de60edf44e529a42c1f"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:81b77f868814346662c96ab36b875d7814ebf82340d3284a31681085c051320f"},
-    {file = "aiohttp-3.9.1-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3b9c7426923bb7bd66d409da46c41e3fb40f5caf679da624439b9eba92043fa6"},
-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:8d44e7bf06b0c0a70a20f9100af9fcfd7f6d9d3913e37754c12d424179b4e48f"},
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-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:ca7ca5abfbfe8d39e653870fbe8d7710be7a857f8a8386fc9de1aae2e02ce7e4"},
-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_s390x.whl", hash = "sha256:8d7f98fde213f74561be1d6d3fa353656197f75d4edfbb3d94c9eb9b0fc47f5d"},
-    {file = "aiohttp-3.9.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:5216b6082c624b55cfe79af5d538e499cd5f5b976820eac31951fb4325974501"},
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 [package.dependencies]
@@ -209,33 +209,33 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "black"
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 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -255,13 +255,13 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.27"
+version = "1.34.51"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.8"
 files = [
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 [package.dependencies]
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 [package.dependencies]
@@ -677,13 +677,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.39.1"
+version = "0.41.2"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
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 [[package]]
 name = "identify"
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+version = "2.5.35"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
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 [[package]]
@@ -964,28 +964,29 @@ min-versions = ["babel (==2.9.0)", "click (==7.0)", "colorama (==0.4)", "ghp-imp
 
 [[package]]
 name = "mkdocs-autorefs"
-version = "0.5.0"
+version = "1.0.1"
 description = "Automatically link across pages in MkDocs."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 Markdown = ">=3.3"
+markupsafe = ">=2.0.1"
 mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.5"
+version = "9.5.12"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1002,7 +1003,7 @@ regex = ">=2022.4"
 requests = ">=2.26,<3.0"
 
 [package.extras]
-git = ["mkdocs-git-committers-plugin-2 (>=1.1,<2.0)", "mkdocs-git-revision-date-localized-plugin (>=1.2,<2.0)"]
+git = ["mkdocs-git-committers-plugin-2 (>=1.1,<2.0)", "mkdocs-git-revision-date-localized-plugin (>=1.2.4,<2.0)"]
 imaging = ["cairosvg (>=2.6,<3.0)", "pillow (>=10.2,<11.0)"]
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@@ -1019,13 +1020,13 @@ files = [
 
 [[package]]
 name = "mkdocstrings"
-version = "0.24.0"
+version = "0.24.1"
 description = "Automatic documentation from sources, for MkDocs."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1061,85 +1062,101 @@ mkdocstrings = ">=0.20"
 
 [[package]]
 name = "multidict"
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+version = "6.0.5"
 description = "multidict implementation"
 optional = false
 python-versions = ">=3.7"
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 [[package]]
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 [[package]]
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 [[package]]
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@@ -2057,13 +2048,13 @@ files = [
 
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 [[package]]
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 [[package]]
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 [package.dependencies]
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 [[package]]
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-    {file = "watchdog-3.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:0e06ab8858a76e1219e68c7573dfeba9dd1c0219476c5a44d5333b01d7e1743a"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:d00e6be486affb5781468457b21a6cbe848c33ef43f9ea4a73b4882e5f188a44"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:c07253088265c363d1ddf4b3cdb808d59a0468ecd017770ed716991620b8f77a"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:5113334cf8cf0ac8cd45e1f8309a603291b614191c9add34d33075727a967709"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:51f90f73b4697bac9c9a78394c3acbbd331ccd3655c11be1a15ae6fe289a8c83"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:ba07e92756c97e3aca0912b5cbc4e5ad802f4557212788e72a72a47ff376950d"},
-    {file = "watchdog-3.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:d429c2430c93b7903914e4db9a966c7f2b068dd2ebdd2fa9b9ce094c7d459f33"},
-    {file = "watchdog-3.0.0-py3-none-win32.whl", hash = "sha256:3ed7c71a9dccfe838c2f0b6314ed0d9b22e77d268c67e015450a29036a81f60f"},
-    {file = "watchdog-3.0.0-py3-none-win_amd64.whl", hash = "sha256:4c9956d27be0bb08fc5f30d9d0179a855436e655f046d288e2bcc11adfae893c"},
-    {file = "watchdog-3.0.0-py3-none-win_ia64.whl", hash = "sha256:5d9f3a10e02d7371cd929b5d8f11e87d4bad890212ed3901f9b4d68767bee759"},
-    {file = "watchdog-3.0.0.tar.gz", hash = "sha256:4d98a320595da7a7c5a18fc48cb633c2e73cda78f93cac2ef42d42bf609a33f9"},
+    {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:39cb34b1f1afbf23e9562501673e7146777efe95da24fab5707b88f7fb11649b"},
+    {file = "watchdog-4.0.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:c522392acc5e962bcac3b22b9592493ffd06d1fc5d755954e6be9f4990de932b"},
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+    {file = "watchdog-4.0.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:8350d4055505412a426b6ad8c521bc7d367d1637a762c70fdd93a3a0d595990b"},
+    {file = "watchdog-4.0.0-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:c17d98799f32e3f55f181f19dd2021d762eb38fdd381b4a748b9f5a36738e935"},
+    {file = "watchdog-4.0.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:4986db5e8880b0e6b7cd52ba36255d4793bf5cdc95bd6264806c233173b1ec0b"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:11e12fafb13372e18ca1bbf12d50f593e7280646687463dd47730fd4f4d5d257"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:5369136a6474678e02426bd984466343924d1df8e2fd94a9b443cb7e3aa20d19"},
+    {file = "watchdog-4.0.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:76ad8484379695f3fe46228962017a7e1337e9acadafed67eb20aabb175df98b"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_10_9_universal2.whl", hash = "sha256:45cc09cc4c3b43fb10b59ef4d07318d9a3ecdbff03abd2e36e77b6dd9f9a5c85"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:eed82cdf79cd7f0232e2fdc1ad05b06a5e102a43e331f7d041e5f0e0a34a51c4"},
+    {file = "watchdog-4.0.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:ba30a896166f0fee83183cec913298151b73164160d965af2e93a20bbd2ab605"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:d18d7f18a47de6863cd480734613502904611730f8def45fc52a5d97503e5101"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:2895bf0518361a9728773083908801a376743bcc37dfa252b801af8fd281b1ca"},
+    {file = "watchdog-4.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:87e9df830022488e235dd601478c15ad73a0389628588ba0b028cb74eb72fed8"},
+    {file = "watchdog-4.0.0-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6e949a8a94186bced05b6508faa61b7adacc911115664ccb1923b9ad1f1ccf7b"},
+    {file = "watchdog-4.0.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6a4db54edea37d1058b08947c789a2354ee02972ed5d1e0dca9b0b820f4c7f92"},
+    {file = "watchdog-4.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:d31481ccf4694a8416b681544c23bd271f5a123162ab603c7d7d2dd7dd901a07"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_aarch64.whl", hash = "sha256:8fec441f5adcf81dd240a5fe78e3d83767999771630b5ddfc5867827a34fa3d3"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:6a9c71a0b02985b4b0b6d14b875a6c86ddea2fdbebd0c9a720a806a8bbffc69f"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:557ba04c816d23ce98a06e70af6abaa0485f6d94994ec78a42b05d1c03dcbd50"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:d0f9bd1fd919134d459d8abf954f63886745f4660ef66480b9d753a7c9d40927"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:f9b2fdca47dc855516b2d66eef3c39f2672cbf7e7a42e7e67ad2cbfcd6ba107d"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:73c7a935e62033bd5e8f0da33a4dcb763da2361921a69a5a95aaf6c93aa03a87"},
+    {file = "watchdog-4.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:6a80d5cae8c265842c7419c560b9961561556c4361b297b4c431903f8c33b269"},
+    {file = "watchdog-4.0.0-py3-none-win32.whl", hash = "sha256:8f9a542c979df62098ae9c58b19e03ad3df1c9d8c6895d96c0d51da17b243b1c"},
+    {file = "watchdog-4.0.0-py3-none-win_amd64.whl", hash = "sha256:f970663fa4f7e80401a7b0cbeec00fa801bf0287d93d48368fc3e6fa32716245"},
+    {file = "watchdog-4.0.0-py3-none-win_ia64.whl", hash = "sha256:9a03e16e55465177d416699331b0f3564138f1807ecc5f2de9d55d8f188d08c7"},
+    {file = "watchdog-4.0.0.tar.gz", hash = "sha256:e3e7065cbdabe6183ab82199d7a4f6b3ba0a438c5a512a68559846ccb76a78ec"},
 ]
 
 [package.extras]
@@ -2326,26 +2319,26 @@ multidict = ">=4.0"
 
 [[package]]
 name = "zarr"
-version = "2.16.1"
+version = "2.17.0"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
-    {file = "zarr-2.16.1.tar.gz", hash = "sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286"},
+    {file = "zarr-2.17.0-py3-none-any.whl", hash = "sha256:d287cb61019c4a0a0f386f76eeaa7f0b1160b1cb90cf96173a4b6cbc135df6e1"},
+    {file = "zarr-2.17.0.tar.gz", hash = "sha256:6390a2b8af31babaab4c963efc45bf1da7f9500c9aafac193f84cf019a7c66b0"},
 ]
 
 [package.dependencies]
 asciitree = "*"
-fasteners = "*"
+fasteners = {version = "*", markers = "sys_platform != \"emscripten\""}
 numcodecs = ">=0.10.0"
-numpy = ">=1.20,<1.21.0 || >1.21.0"
+numpy = ">=1.21.1"
 
 [package.extras]
-docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "f5afbf936caecbd37768b0fbdbbd193014831dfdf71897f94aaad8e20798b31a"
+content-hash = "9fcbaf31547db3838421ab6496d8081ee87f365ddadc7790d16c605d5e258444"
diff --git a/pyproject.toml b/pyproject.toml
index 83e0643..8cd2c22 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-pydantic-zarr = "0.5.2"
+pydantic-zarr = "0.6.1"
 fsspec = "^2023.10.0"
 s3fs = "^2023.10.0"
 rich = "^13.6.0"
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index f9e4b4a..a1cf0c4 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -7,9 +7,6 @@
 if TYPE_CHECKING:
     from typing import Dict, Iterable, Hashable, Tuple, Any
 
-from pydantic_zarr.v2 import GroupSpec, ArraySpec
-import os
-
 
 def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     """
@@ -21,77 +18,6 @@ def duplicates(values: Iterable[Hashable]) -> Dict[Hashable, int]:
     return {k: v for k, v in counts.items() if v > 1}
 
 
-def flatten_node(
-    node: ArraySpec | GroupSpec, path: str = "/"
-) -> Dict[str, ArraySpec | GroupSpec]:
-    """
-    Flatten a `GroupSpec` or `ArraySpec`.
-    Takes a `GroupSpec` or `ArraySpec` and a string, and returns dictionary with string keys and values that are
-    `GroupSpec` or `ArraySpec`. If the input is an `ArraySpec`, then this function just returns the dict `{path: node}`.
-    If the input is a `GroupSpec`, then the resulting dictionary will contain a copy of the input with an empty `members` attribute
-    under the key `path`, as well as copies of the result of calling `flatten_node` on each member of the input, each under a key created by joining `path` with a '/` character
-    to the name of each member.
-
-    Paramters
-    ---------
-    node: `GroupSpec` | `ArraySpec`
-        The node to flatten.
-    path: `str`, default is 'root'
-        The root path. If the input is a `GroupSpec`, then the keys in `GroupSpec.members` will be
-        made relative to `path` when used as keys in the result dictionary.
-
-    Returns
-    -------
-    `Dict[str, GroupSpec | ArraySpec]`
-
-    """
-    result = {}
-    if isinstance(node, ArraySpec):
-        model_copy = node.model_copy(deep=True)
-
-    else:
-        model_copy = node.model_copy(update={"members": {}})
-        for name, value in node.members.items():
-            result.update(flatten_node(value, os.path.join(path, name)))
-
-    result[path] = model_copy
-
-    return result
-
-
-ArraySpec.model_dump
-
-
-def unflatten_node(
-    tree: Dict[str, ArraySpec | GroupSpec], attributes: Dict[str, Any] = {}
-) -> ArraySpec | GroupSpec:
-    member_lobby = {}
-    tree_mut: Dict[str, Dict[str, ArraySpec | GroupSpec]] = {}
-    for key, value in tree.items():
-        key_parts = key.split("/")
-        if key_parts[0] != "":
-            raise ValueError(f'Invalid path: {key} does not start with "/".')
-        if len(key_parts) == 2:
-            member_lobby[key_parts[1]] = value
-        else:
-            subparent = key_parts[1]
-            if subparent not in tree_mut:
-                tree_mut[subparent] = {}
-            tree_mut[subparent]["/".join(["", *key_parts[2:]])] = value
-    for subparent, subchildren in tree_mut.items():
-        if subparent in member_lobby:
-            if isinstance(member_lobby[subparent], ArraySpec):
-                msg = f"Invalid tree: the node named {subparent} is declared both as ArraySpec and GroupSpec"
-                raise ValueError(msg)
-            else:
-                member_lobby[subparent] = unflatten_node(
-                    subchildren, attributes=member_lobby[subparent].attributes
-                )
-        else:
-            member_lobby[subparent] = unflatten_node(subchildren)
-    return GroupSpec(members=member_lobby, attributes=attributes)
-
-
 @runtime_checkable
 class ArrayLike(Protocol):
     shape: Tuple[int, ...]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 9775570..327a116 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,14 +1,12 @@
 from __future__ import annotations
 from collections import Counter
-from typing import Annotated, Any, Dict, List, Sequence, Union, cast
+from typing import Annotated, Any, Dict, List, Self, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import (
     ArrayLike,
     ChunkedArrayLike,
     duplicates,
-    flatten_node,
-    resolve_groups,
 )
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -78,8 +76,7 @@ class Dataset(StrictBase):
 
     path: str
     coordinateTransformations: Annotated[
-        List[tx.Scale | tx.Translation],
-        AfterValidator(ensure_transforms_length),
+        tuple[tx.Scale] | tuple[tx.Scale, tx.Translation],
         AfterValidator(ensure_scale_translation),
         AfterValidator(tx.ensure_dimensionality),
     ]
@@ -193,7 +190,9 @@ class MultiscaleMetadata(StrictVersionedBase):
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
     ]
-    coordinateTransformations: List[tx.Scale | tx.Translation] | None = None
+    coordinateTransformations: tuple[tx.Scale] | tuple[
+        tx.Scale, tx.Translation
+    ] | None = None
 
 
 class GroupAttrs(BaseModel):
@@ -229,6 +228,22 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
 
     @classmethod
     def from_zarr(cls, node: zarr.Group) -> Group:
+        """
+        Create an instance of `Group` from a `node`, a `zarr.Group`. This method infers the
+        discovers Zarr arrays in the hierarchy rooted at `node` by inspecting the OME-NGFF
+        multiscales metadata.
+
+        Paramters
+        ---------
+        node: zarr.Group
+            A Zarr group that has valid OME-NGFF multiscale metadata.
+
+        Returns
+        -------
+        Group
+            A model of the zarr Group.
+        """
+        # on unlistable storage backends, the members of this group will be {}
         guess = GroupSpec.from_zarr(node)
 
         try:
@@ -241,37 +256,32 @@ def from_zarr(cls, node: zarr.Group) -> Group:
             raise ValueError(msg) from e
 
         multi_meta = GroupAttrs(multiscales=multi_meta_maybe)
+        members_tree_flat = {}
         for multiscale in multi_meta.multiscales:
-            members = {}
             for dataset in multiscale.datasets:
                 array_path = "/".join([node.path, dataset.path])
                 try:
                     array = zarr.open_array(store=node.store, path=array_path, mode="r")
                     array_spec = ArraySpec.from_zarr(array)
-                except ArrayNotFoundError as e:
+                except ArrayNotFoundError:
                     msg = (
                         f"Expected to find an array at {array_path}, ",
                         "but no array was found there.",
                     )
-                    raise ArrayNotFoundError(msg) from e
-                except ContainsGroupError as e:
+                    raise ArrayNotFoundError(msg)
+                except ContainsGroupError:
                     msg = (
                         f"Expected to find an array at {array_path}, ",
                         "but a group was found there instead.",
                     )
-                    raise ContainsGroupError(msg) from e
-                dataset_path_parts = dataset.path.split("/")
-                if len(dataset_path_parts) == 1:
-                    members[dataset.path] = array_spec
-                else:
-                    # this will not be correct for multiple arrays in the same deep group
-                    members[dataset.path] = resolve_groups(
-                        "/".join(dataset_path_parts[1:]), array_spec
-                    )
-
-            guess = guess.model_copy(update={**guess.members, **members})
+                    raise ContainsGroupError(msg)
+                members_tree_flat["/" + dataset.path] = array_spec
+        members_normalized = GroupSpec.from_flat(members_tree_flat)
 
-        return guess
+        guess_inferred_members = guess.model_copy(
+            update={"members": {**guess.members, **members_normalized.members}}
+        )
+        return guess_inferred_members
 
     @classmethod
     def from_arrays(
@@ -279,16 +289,16 @@ def from_arrays(
         paths: Sequence[str],
         axes: Sequence[Axis],
         arrays: Sequence[ArrayLike | ChunkedArrayLike],
-        scales: Sequence[int | float],
-        translations: Sequence[int | float],
+        scales: Sequence[Sequence[int | float]],
+        translations: Sequence[Sequence[int | float]],
         *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        group_scale: tx.Scale | None = None,
-        group_translation: tx.Translation | None = None,
-        **kwargs,
-    ):
+        group_scale: Sequence[int | float] | None = None,
+        group_translation: Sequence[int | float] | None = None,
+        **kwargs: Any,
+    ) -> Self:
         """
         Create a `Group` from a sequence of arrays and spatial metadata.
 
@@ -297,25 +307,20 @@ def from_arrays(
         paths: Sequence[str]
             The paths to the arrays.
         """
+        group_transforms = None
+        if group_scale is not None:
+            group_transforms = tx.scale_translation(group_scale, group_translation)
 
-        group_transforms = list(
-            filter(lambda v: v is not None, [group_scale, group_translation])
-        )
-        for idx, value in enumerate(group_transforms):
-            if idx == 0:
-                group_transforms[idx] = tx.VectorScale(scale=value)
-            if idx == 1:
-                group_transforms[idx] = tx.VectorTranslation(translation=value)
-
-        members = {
-            key: ArraySpec.from_array(arr, **kwargs)
+        members_flat = {
+            "/" + key.lstrip("/"): ArraySpec.from_array(arr, **kwargs)
             for key, arr in zip(paths, arrays, strict=True)
         }
+
         multimeta = MultiscaleMetadata(
             name=name,
             type=type,
             metadata=metadata,
-            axes=axes,
+            axes=list(axes),
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
                 for path, scale, translation in zip(
@@ -324,7 +329,10 @@ def from_arrays(
             ],
             coordinateTransformations=group_transforms,
         )
-        return cls(members=members, attributes=GroupAttrs(multiscales=[multimeta]))
+        return cls(
+            members=GroupSpec.from_flat(members_flat).members,
+            attributes=GroupAttrs(multiscales=[multimeta]),
+        )
 
     @model_validator(mode="after")
     def check_arrays_exist(self) -> "Group":
@@ -335,14 +343,17 @@ def check_arrays_exist(self) -> "Group":
         allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
-        flattened = flatten_node(self)
+        flattened = self.to_flat()
 
         for multiscale in attrs.multiscales:
             for dataset in multiscale.datasets:
-                dpath = "/" + dataset.path
+                dpath = "/" + dataset.path.lstrip("/")
                 if dpath in flattened:
                     if not isinstance(flattened[dpath], ArraySpec):
-                        msg = f"The node at {dpath} should be an array, found {type(flattened[dpath])} instead"
+                        msg = (
+                            f"The node at {dpath} should be an array, "
+                            f"found {type(flattened[dpath])} instead"
+                        )
                         raise ValueError(msg)
                 else:
                     msg = (
@@ -357,14 +368,26 @@ def check_arrays_exist(self) -> "Group":
     def check_array_ndim(self) -> "Group":
         """
         Check that all the arrays referenced by the `multiscales` metadata have the same
-        dimensionality, and that this dimensionality is consistent with the `coordinateTransformations` metadata.
+        dimensionality, and that this dimensionality is consistent with the
+        `coordinateTransformations` metadata.
         """
-        attrs = self.attributes
-        array_items: dict[str, ArraySpec] = {
-            k: v for k, v in self.members.items() if isinstance(v, ArraySpec)
-        }
+        multimeta = self.attributes.multiscales
+
+        flat_self = self.to_flat()
+        ndims = []
+        # get shapes from all the arrays referenced in `multiscales`
+        for multiscale in multimeta:
+            for dataset in multiscale.datasets:
+                node = flat_self["/" + dataset.path.lstrip("/")]
+                if isinstance(node, ArraySpec):
+                    ndims.append(len(flat_self["/" + dataset.path.lstrip("/")].shape))
+                else:
+                    msg = (
+                        f"Expected an instance of ArraySpec at {dataset.path}, "
+                        f"got {type(node)} instead"
+                    )
+                    raise TypeError(msg)
 
-        ndims = tuple(len(a.shape) for a in array_items.values())
         if len(set(ndims)) > 1:
             msg = (
                 "All arrays must have the same dimensionality. "
@@ -373,7 +396,7 @@ def check_array_ndim(self) -> "Group":
             raise ValueError(msg)
 
         # check that each transform has compatible rank
-        for multiscale in attrs.multiscales:
+        for multiscale in multimeta:
             tforms = []
             if multiscale.coordinateTransformations is not None:
                 tforms.extend(multiscale.coordinateTransformations)
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index df1a9f5..67dc998 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -115,16 +115,24 @@ def ndim(
 
 
 def scale_translation(
-    scale: Sequence[float], translation: Sequence[float]
-) -> tuple[Scale, Translation]:
+    scale: Sequence[float], translation: Sequence[float] | None
+) -> tuple[Scale] | tuple[Scale, Translation]:
     """
-    Create a `VectorScale` and a `VectorTranslation` from a scale and a translation parameter.
+    Create a `VectorScale` and, optionally, a `VectorTranslation` from a scale and a translation
+    parameter.
     """
     len_scale = len(scale)
-    len_translation = len(translation)
+
     if len_scale < 1:
         msg = "Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
+
+    vec_scale = VectorScale(scale=scale)
+
+    if translation is None:
+        return (vec_scale,)
+
+    len_translation = len(translation)
     if len_translation < 1:
         msg = "Not enough values in `translation`. Got 0, expected at least 1."
         raise ValueError(msg)
@@ -135,7 +143,9 @@ def scale_translation(
         )
         raise ValueError(msg)
 
-    return (VectorScale(scale=scale), VectorTranslation(translation=translation))
+    vec_trans = VectorTranslation(translation=translation)
+
+    return (vec_scale, vec_trans)
 
 
 Scale = VectorScale | PathScale
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index e3b2212..b920dc9 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -33,7 +33,7 @@ def default_multiscale() -> MultiscaleMetadata:
     datasets = [
         Dataset(
             path=f"path{idx}",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -46,7 +46,7 @@ def default_multiscale() -> MultiscaleMetadata:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
         for idx in range(num_datasets)
     ]
@@ -55,21 +55,23 @@ def default_multiscale() -> MultiscaleMetadata:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
+        coordinateTransformations=(
             VectorScale(
                 scale=[
                     1,
                 ]
                 * rank
             ),
-        ],
+        ),
     )
     return multi
 
 
 def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     _, strict_schema = fetch_schemas("latest", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
+    jsc.validate(
+        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
+    )
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -83,10 +85,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -94,9 +96,7 @@ def test_multiscale_unique_axis_names() -> None:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
-            VectorScale(scale=[1, 1, 1]),
-        ],
+        coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
     )
 
     # make axis names collide
@@ -107,10 +107,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -119,9 +119,7 @@ def test_multiscale_unique_axis_names() -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
-                VectorScale(scale=[1, 1, 1]),
-            ],
+            coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
         )
 
 
@@ -147,7 +145,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -160,7 +158,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     # TODO: make some axis-specifc exceptions
@@ -169,14 +167,14 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -187,7 +185,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -200,7 +198,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
@@ -208,14 +206,14 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -248,7 +246,9 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 def test_coordinate_transforms_invalid_length(
     transforms: List[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="expected 1 or 2"):
+    with pytest.raises(
+        ValidationError, match=f"after validation, not {len(transforms)}"
+    ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -270,7 +270,7 @@ def test_coordinate_transforms_invalid_first_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The first element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorScale",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -289,7 +289,7 @@ def test_coordinate_transforms_invalid_second_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The second element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorTranslation",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
diff --git a/tests/test_utils.py b/tests/test_utils.py
index df62bb7..4672071 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,33 +1,18 @@
 from __future__ import annotations
 from typing import TYPE_CHECKING
+
 if TYPE_CHECKING:
     from typing import Any, List
 
-from pydantic_ome_ngff.utils import duplicates, flatten_node
-from pydantic_zarr.v2 import ArraySpec, GroupSpec
-import numpy as np
+from pydantic_ome_ngff.utils import duplicates
 import pytest
 
-def test_flatten_node() -> None:
-    a = ArraySpec.from_array(np.arange(10))
-    flattened = flatten_node(a)
-    assert flattened == {'/': a}
-
-    b = GroupSpec(attributes={'foo': 10}, members={'name': a})
-    flattened_b = flatten_node(b)
-    assert flattened_b['/'] == b.model_copy(update={"members": {}})
-    assert flattened_b['/name'] == a
-
-    c = GroupSpec(attributes={}, members={'b': b, 'a': a})
-    flattened_c = flatten_node(c, path='c')
-    assert flattened_c['c'] == c.model_copy(update={"members": {}})
-    assert flattened_c["c/b"] == b.model_copy(update={"members": {}})
-    assert flattened_c["c/a"] == a
-    assert flattened_c["c/b/name"] == a
 
-@pytest.mark.parametrize('data', [[0], [0,1,1,1,2], ['a','a','b','b','c','c','d']])
+@pytest.mark.parametrize(
+    "data", [[0], [0, 1, 1, 1, 2], ["a", "a", "b", "b", "c", "c", "d"]]
+)
 def test_duplicates(data: List[Any]) -> None:
     dupes = duplicates(data)
     for key, value in dupes.items():
         assert data.count(key) == value
-        assert value > 1
\ No newline at end of file
+        assert value > 1
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index eeb3934..d9a1824 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -18,6 +18,9 @@
 )
 from pydantic_ome_ngff.v04.axis import Axis
 from tests.conftest import fetch_schemas
+import numpy as np
+from itertools import accumulate
+import operator
 
 loader = JsonLoader("v04")
 
@@ -34,7 +37,7 @@ def default_multiscale() -> MultiscaleMetadata:
     datasets = [
         Dataset(
             path=f"path{idx}",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -47,7 +50,7 @@ def default_multiscale() -> MultiscaleMetadata:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
         for idx in range(num_datasets)
     ]
@@ -56,21 +59,23 @@ def default_multiscale() -> MultiscaleMetadata:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
+        coordinateTransformations=(
             VectorScale(
                 scale=[
                     1,
                 ]
                 * rank
             ),
-        ],
+        ),
     )
     return multi
 
 
 def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
-    jsc.validate({"multiscales": [default_multiscale.model_dump()]}, strict_schema)
+    jsc.validate(
+        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
+    )
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -84,10 +89,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -95,9 +100,7 @@ def test_multiscale_unique_axis_names() -> None:
         name="foo",
         axes=axes,
         datasets=datasets,
-        coordinateTransformations=[
-            VectorScale(scale=[1, 1, 1]),
-        ],
+        coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
     )
 
     # make axis names collide
@@ -108,10 +111,10 @@ def test_multiscale_unique_axis_names() -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(scale=[1, 1, 1]),
                 VectorTranslation(translation=[0, 0, 0]),
-            ],
+            ),
         )
     ]
 
@@ -120,9 +123,7 @@ def test_multiscale_unique_axis_names() -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
-                VectorScale(scale=[1, 1, 1]),
-            ],
+            coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
         )
 
 
@@ -148,7 +149,7 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -161,7 +162,7 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     # TODO: make some axis-specifc exceptions
@@ -170,14 +171,14 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -188,7 +189,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
     datasets = [
         Dataset(
             path="path",
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
@@ -201,7 +202,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
     ]
     with pytest.raises(ValidationError, match="Incorrect number of axes provided"):
@@ -209,14 +210,14 @@ def test_multiscale_axis_length(num_axes: int) -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=[
+            coordinateTransformations=(
                 VectorScale(
                     scale=[
                         1,
                     ]
                     * rank
                 ),
-            ],
+            ),
         )
 
 
@@ -249,7 +250,9 @@ def test_coordinate_transforms_invalid_ndims() -> None:
 def test_coordinate_transforms_invalid_length(
     transforms: list[Transform],
 ) -> None:
-    with pytest.raises(ValidationError, match="expected 1 or 2"):
+    with pytest.raises(
+        ValidationError, match=f"after validation, not {len(transforms)}"
+    ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
 
@@ -271,7 +274,7 @@ def test_coordinate_transforms_invalid_first_element(
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The first element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorScale",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -286,11 +289,11 @@ def test_coordinate_transforms_invalid_first_element(
     ),
 )
 def test_coordinate_transforms_invalid_second_element(
-    transforms: Tuple[Transform, Transform],
+    transforms: Tuple[VectorScale, VectorScale],
 ) -> None:
     with pytest.raises(
         ValidationError,
-        match="The second element of `coordinateTransformations` must be a",
+        match="Input should be a valid dictionary or instance of VectorTranslation",
     ):
         Dataset(path="foo", coordinateTransformations=transforms)
 
@@ -377,36 +380,47 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
         Group(attributes=group_attrs, members=bad_items)
 
 
-import numpy as np
-from itertools import accumulate
-import operator
-@pytest.mark.parametrize('name', [None, "foo"])
-@pytest.mark.parametrize('type', [None, "foo"])
-@pytest.mark.parametrize('path_pattern', ['{0}', 's{0}'])
-@pytest.mark.parametrize('metadata', [None, {'foo': 10}])
-@pytest.mark.parametrize('ndim', [2,3,4,5])
+@pytest.mark.parametrize("name", [None, "foo"])
+@pytest.mark.parametrize("type", [None, "foo"])
+@pytest.mark.parametrize("path_pattern", ["{0}", "s{0}", "foo/{0}"])
+@pytest.mark.parametrize("metadata", [None, {"foo": 10}])
+@pytest.mark.parametrize("ndim", [2, 3, 4, 5])
 def test_from_arrays(
-    name: str | None, 
-    type: str | None, 
+    name: str | None,
+    type: str | None,
     path_pattern: str,
-    metadata: Dict[str, int] | str | None, 
-    ndim: int):
-    arrays = [np.arange(x ** ndim).reshape((x,) * ndim) for  x in [3,2,1]]
+    metadata: Dict[str, int] | None,
+    ndim: int,
+) -> None:
+    arrays = [np.arange(x**ndim).reshape((x,) * ndim) for x in [3, 2, 1]]
     paths = [path_pattern.format(idx) for idx in range(len(arrays))]
-    scales = [(2 ** idx, ) * ndim for idx in range(len(arrays))]
-    translations = [(t,) * ndim for t in accumulate([(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add)]
-    
+    scales = [(2**idx,) * ndim for idx in range(len(arrays))]
+    translations = [
+        (t,) * ndim
+        for t in accumulate(
+            [(2 ** (idx - 1)) for idx in range(len(arrays))], operator.add
+        )
+    ]
+
     group_scale = (1,) * ndim
     group_translation = (0,) * ndim
 
-
-    all_axes = [Axis(name="x", type="space",), Axis(name="y", type="space"), Axis(name="z", type="space"), Axis(name="t", type="time"), Axis(name="c", type="barf")]
+    all_axes = [
+        Axis(
+            name="x",
+            type="space",
+        ),
+        Axis(name="y", type="space"),
+        Axis(name="z", type="space"),
+        Axis(name="t", type="time"),
+        Axis(name="c", type="barf"),
+    ]
     # spatial axes have to come last
     if ndim in (2, 3):
         axes = all_axes[:ndim]
     else:
         axes = [*all_axes[4:], *all_axes[:3]]
-    
+
     group = Group.from_arrays(
         paths=paths,
         axes=axes,
@@ -415,19 +429,27 @@ def test_from_arrays(
         translations=translations,
         name=name,
         type=type,
-        metadata=metadata, 
+        metadata=metadata,
         group_scale=group_scale,
-        group_translation=group_translation
+        group_translation=group_translation,
     )
 
+    group_flat = group.to_flat()
+
     assert group.attributes.multiscales[0].name == name
     assert group.attributes.multiscales[0].type == type
     assert group.attributes.multiscales[0].metadata == metadata
-    assert group.attributes.multiscales[0].coordinateTransformations == [VectorScale(scale=group_scale), VectorTranslation(translation=group_translation)]
+    assert group.attributes.multiscales[0].coordinateTransformations == (
+        VectorScale(scale=group_scale),
+        VectorTranslation(translation=group_translation),
+    )
     assert group.attributes.multiscales[0].axes == axes
     for idx, array in enumerate(arrays):
-        assert array.shape == group.members[paths[idx]].shape
-        assert array.dtype == group.members[paths[idx]].dtype
-        assert group.attributes.multiscales[0].datasets[idx].coordinateTransformations == [VectorScale(scale=scales[idx]), VectorTranslation(translation=translations[idx])]
-
-
+        assert array.shape == group_flat["/" + paths[idx]].shape
+        assert array.dtype == group_flat["/" + paths[idx]].dtype
+        assert group.attributes.multiscales[0].datasets[
+            idx
+        ].coordinateTransformations == (
+            VectorScale(scale=scales[idx]),
+            VectorTranslation(translation=translations[idx]),
+        )

From 0887e4a2e231849e1b0605e6b6964265f7853cfa Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:10:33 +0100
Subject: [PATCH 32/69] chore: add gha

---
 .github/workflows/test.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..04d4084
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,24 @@
+name: Linux Testing
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10', '3.11', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install dependencies
+      shell: "bash -l {0}"
+      run: |
+        pip install poetry
+        poetry install
+    - name: Test
+      run: |
+        poetry run pytest
\ No newline at end of file

From 81afac6056c4c6c96d319d41a7875f5060566ca1 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:43:01 +0100
Subject: [PATCH 33/69] chore: fix broken tests

---
 tests/conftest.py                |  5 ++-
 tests/latest/test_multiscales.py | 65 +++++++++++++++--------------
 tests/v04/test_multiscales.py    | 71 ++++++++++----------------------
 3 files changed, 58 insertions(+), 83 deletions(-)

diff --git a/tests/conftest.py b/tests/conftest.py
index c8c5565..8f612a4 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,6 @@
-from typing import Any
-
+import json
+from typing import Any, Dict, List, Optional, Union
+from pathlib import Path
 import requests
 
 
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index b920dc9..7f02452 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -22,7 +22,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> MultiscaleMetadata:
+def multi_meta() -> MultiscaleMetadata:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -67,11 +67,9 @@ def default_multiscale() -> MultiscaleMetadata:
     return multi
 
 
-def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
+def test_multiscale(multi_meta: MultiscaleMetadata) -> None:
     _, strict_schema = fetch_schemas("latest", schema_name="image")
-    jsc.validate(
-        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
-    )
+    jsc.validate({"multiscales": [multi_meta.model_dump(mode="json")]}, strict_schema)
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -135,8 +133,7 @@ def test_multiscale_space_axes_last(axis_types: List[Optional[str]]) -> None:
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
         if t is None or t == "channel":
-            with pytest.warns(UserWarning, match="Null"):
-                ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
+            ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
         else:
             ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
         axes.append(ax)
@@ -295,59 +292,63 @@ def test_coordinate_transforms_invalid_second_element(
 
 
 def test_multiscale_group_datasets_exist(
-    default_multiscale: MultiscaleMetadata,
+    multi_meta: MultiscaleMetadata,
 ) -> None:
-    group_attrs = GroupAttrs(multiscales=[default_multiscale])
+    meta_ndim = len(multi_meta.axes)
+    group_attrs = GroupAttrs(multiscales=[multi_meta])
     good_items = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1,) * meta_ndim, dtype="uint8", chunks=(1,) * meta_ndim
         )
-        for d in default_multiscale.datasets
+        for d in multi_meta.datasets
     }
     Group(attributes=group_attrs, members=good_items)
 
+    bad_items = {
+        d.path + "x": ArraySpec(
+            shape=(1,) * meta_ndim, dtype="uint8", chunks=(1,) * meta_ndim
+        )
+        for d in multi_meta.datasets
+    }
+
     with pytest.raises(
         ValidationError,
         match="array with that name was found in the hierarchy.",
     ):
-        bad_items = {
-            d.path + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
-            )
-            for d in default_multiscale.datasets
-        }
         Group(attributes=group_attrs, members=bad_items)
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
-    group_attrs = GroupAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(multi_meta: MultiscaleMetadata) -> None:
+    meta_ndim = len(multi_meta.axes)
+    group_attrs = GroupAttrs(multiscales=[multi_meta])
     good_items = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1,) * meta_ndim, dtype="uint8", chunks=(1,) * meta_ndim
         )
-        for d in default_multiscale.datasets
+        for d in multi_meta.datasets
     }
     Group(attributes=group_attrs, members=good_items)
 
+    # arrays with varying rank
+    bad_items = {
+        d.path: ArraySpec(
+            shape=(1,) * (idx + 1),
+            dtype="uint8",
+            chunks=(1,) * (idx + 1),
+            attributes={},
+        )
+        for idx, d in enumerate(multi_meta.datasets)
+    }
+
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
-        # arrays with varying rank
-        bad_items = {
-            d.path: ArraySpec(
-                shape=(1,) * (idx + 1),
-                dtype="uint8",
-                chunks=(1,) * (idx + 1),
-                attributes={},
-            )
-            for idx, d in enumerate(default_multiscale.datasets)
-        }
         Group(attributes=group_attrs, members=bad_items)
 
     with pytest.raises(ValidationError, match="Transform dimensionality"):
         # arrays with rank that doesn't match the transform
         bad_items = {
             d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
-            for d in default_multiscale.datasets
+            for d in multi_meta.datasets
         }
         Group(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index d9a1824..4a6f066 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -17,7 +17,7 @@
     VectorTranslation,
 )
 from pydantic_ome_ngff.v04.axis import Axis
-from tests.conftest import fetch_schemas
+from tests.conftest import JsonLoader, fetch_schemas
 import numpy as np
 from itertools import accumulate
 import operator
@@ -26,7 +26,7 @@
 
 
 @pytest.fixture
-def default_multiscale() -> MultiscaleMetadata:
+def multi_meta() -> MultiscaleMetadata:
     axes = [
         Axis(name="z", type="space", unit="meter"),
         Axis(name="x", type="space", unit="meter"),
@@ -71,11 +71,9 @@ def default_multiscale() -> MultiscaleMetadata:
     return multi
 
 
-def test_multiscale(default_multiscale: MultiscaleMetadata) -> None:
+def test_multiscale(multi_meta: MultiscaleMetadata) -> None:
     base_schema, strict_schema = fetch_schemas("0.4", schema_name="image")
-    jsc.validate(
-        {"multiscales": [default_multiscale.model_dump(mode="json")]}, strict_schema
-    )
+    jsc.validate({"multiscales": [multi_meta.model_dump(mode="json")]}, strict_schema)
 
 
 def test_multiscale_unique_axis_names() -> None:
@@ -139,8 +137,7 @@ def test_multiscale_space_axes_last(axis_types: list[str | None]) -> None:
     axes: list[Axis] = []
     for idx, t in enumerate(axis_types):
         if t is None or t == "channel":
-            with pytest.warns(UserWarning, match="Null"):
-                ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
+            ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
         else:
             ax = Axis(name=str(idx), type=t, unit=units_map.get(t, None))
         axes.append(ax)
@@ -299,44 +296,35 @@ def test_coordinate_transforms_invalid_second_element(
 
 
 def test_multiscale_group_datasets_exist(
-    default_multiscale: MultiscaleMetadata,
+    multi_meta: MultiscaleMetadata,
 ) -> None:
-    group_attrs = GroupAttrs(multiscales=[default_multiscale])
-    good_items = {
+    meta_ndim = len(multi_meta.axes)
+    group_attrs = GroupAttrs(multiscales=[multi_meta])
+    good_members = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
-        )
-        for d in default_multiscale.datasets
-    }
-    Group(attributes=group_attrs, members=good_items)
-
-    bad_items = {
-        d.path + "x": ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1,) * meta_ndim,
+            dtype="uint8",
+            chunks=(1,) * meta_ndim,
         )
-        for d in default_multiscale.datasets
+        for d in multi_meta.datasets
     }
+    Group(attributes=group_attrs, members=good_members)
 
     with pytest.raises(
         ValidationError,
         match="array with that name was found in the hierarchy",
     ):
-        bad_items = {
-            d.path + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
-            )
-            for d in default_multiscale.datasets
-        }
-        Group(attributes=group_attrs, members=bad_items)
+        Group(attributes=group_attrs, members=dict(tuple(good_members.items())[1:]))
 
 
-def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata) -> None:
-    group_attrs = GroupAttrs(multiscales=[default_multiscale])
+def test_multiscale_group_datasets_rank(multi_meta: MultiscaleMetadata) -> None:
+    meta_ndim = len(multi_meta.axes)
+    group_attrs = GroupAttrs(multiscales=[multi_meta])
     good_items = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1,) * meta_ndim, dtype="uint8", chunks=(1,) * meta_ndim
         )
-        for d in default_multiscale.datasets
+        for d in multi_meta.datasets
     }
     Group(attributes=group_attrs, members=good_items)
 
@@ -348,35 +336,20 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
             chunks=(1,) * (idx + 1),
             attributes={},
         )
-        for idx, d in enumerate(default_multiscale.datasets)
+        for idx, d in enumerate(multi_meta.datasets)
     }
 
     with pytest.raises(
         ValidationError, match="All arrays must have the same dimensionality."
     ):
-        # arrays with varying rank
-        bad_items = {
-            d.path: ArraySpec(
-                shape=(1,) * (idx + 1),
-                dtype="uint8",
-                chunks=(1,) * (idx + 1),
-                attributes={},
-            )
-            for idx, d in enumerate(default_multiscale.datasets)
-        }
         Group(attributes=group_attrs, members=bad_items)
 
     # arrays with rank that doesn't match the transform
     bad_items = {
         d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
-        for d in default_multiscale.datasets
+        for d in multi_meta.datasets
     }
     with pytest.raises(ValidationError, match="Transform dimensionality"):
-        # arrays with rank that doesn't match the transform
-        bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
-            for d in default_multiscale.datasets
-        }
         Group(attributes=group_attrs, members=bad_items)
 
 

From a365bfafbb1e9028ac86faadc8857e6192b11a1b Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 00:55:11 +0100
Subject: [PATCH 34/69] remove redundant ci

---
 .github/workflows/test.yml | 24 ------------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 04d4084..0000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-name: Linux Testing
-
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.10', '3.11', '3.12']
-    steps:
-    - uses: actions/checkout@v4
-    - name: Install dependencies
-      shell: "bash -l {0}"
-      run: |
-        pip install poetry
-        poetry install
-    - name: Test
-      run: |
-        poetry run pytest
\ No newline at end of file

From 00870425d59c09a6633fa09a9d7c864c9d606f25 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 01:04:38 +0100
Subject: [PATCH 35/69] lint

---
 src/pydantic_ome_ngff/v04/axis.py  | 3 +--
 src/pydantic_ome_ngff/v04/label.py | 2 +-
 src/pydantic_ome_ngff/v04/plate.py | 8 +++++++-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/axis.py b/src/pydantic_ome_ngff/v04/axis.py
index 043c7b4..f74bc44 100644
--- a/src/pydantic_ome_ngff/v04/axis.py
+++ b/src/pydantic_ome_ngff/v04/axis.py
@@ -3,7 +3,6 @@
 from typing import Optional
 import warnings
 
-from pydantic import model_validator
 
 from pydantic_ome_ngff.base import StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
@@ -143,4 +142,4 @@ class Axis(StrictVersionedBase):
     _version = version
     name: str
     type: Optional[str] = None
-    unit: Optional[str] = None
\ No newline at end of file
+    unit: Optional[str] = None
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 7ccc5ce..0615bd5 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -56,7 +56,7 @@ def parse_version(version: Literal["0.4"] | None) -> Literal["0.4"] | None:
             f"The `version` attribute is `None`. Version {NGFF_VERSION} of "
             f"the OME-NGFF spec states that `version` should either be unset or the string {NGFF_VERSION}"
         )
-        # This goes against a recommendation from the spec, but emitting a warning is annoying. 
+        # This goes against a recommendation from the spec, but emitting a warning is annoying.
         # leaving this here as a placeholder.
     return version
 
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index b065c29..e5d7e0f 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,7 +1,13 @@
 from __future__ import annotations
 from typing import List
 
-from pydantic import BaseModel, PositiveInt, ValidationError, field_validator
+from pydantic import (
+    BaseModel,
+    NonNegativeInt,
+    PositiveInt,
+    ValidationError,
+    field_validator,
+)
 from pydantic_zarr.v2 import ArraySpec, GroupSpec
 
 from pydantic_ome_ngff.base import VersionedBase

From 007438b620a0014cdd5ba4f13ef6fe6c45cf611a Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 01:07:05 +0100
Subject: [PATCH 36/69] ci: increment the python version used for linting

---
 .github/workflows/ci.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 7056dd0..01a3c42 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - uses: abatilo/actions-poetry@v2
       - run: poetry install
       - run: poetry run pre-commit run --all-files
@@ -20,9 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.9"
           - "3.10"
-          - "3.11"
+          - "3.10"
+          - "3.12"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3

From 8b871f789388eb34b9c46e4656aa736caddfbffb Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 01:11:48 +0100
Subject: [PATCH 37/69] chore: use typing_extensions for self import

---
 src/pydantic_ome_ngff/v04/multiscales.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 97ab4b7..ae13b43 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -1,7 +1,11 @@
 from __future__ import annotations
-
+from typing import TYPE_CHECKING
 from collections import Counter
-from typing import Annotated, Any, Dict, List, Self, Sequence, Union, cast
+
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
+from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import (
@@ -91,10 +95,10 @@ def create_dataset(
     """
     return Dataset(
         path=path,
-        coordinateTransformations=[
+        coordinateTransformations=(
             tx.VectorScale(scale=scale),
             tx.VectorTranslation(translation=translation),
-        ],
+        ),
     )
 
 

From 475ecca22685321f2e32cc32829bc4ce22f2c09f Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 01:12:09 +0100
Subject: [PATCH 38/69] remove extra script

---
 example.py | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 example.py

diff --git a/example.py b/example.py
deleted file mode 100644
index ee18a04..0000000
--- a/example.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from pydantic_ome_ngff.v04.multiscales import Group
-import zarr
-url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
-zgroup = zarr.open(url)
-group = Group.from_zarr(zgroup)

From bb349cc842a22a752a2a84779c7f87e67dad1505 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 4 Mar 2024 01:40:31 +0100
Subject: [PATCH 39/69] fix: remove support for group_scale and
 group_translation in Group.from_arrays()

---
 src/pydantic_ome_ngff/v04/multiscales.py | 25 ++++++++++++++++--------
 tests/v04/test_multiscales.py            | 10 +---------
 2 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index ae13b43..03d30e7 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -300,22 +300,31 @@ def from_arrays(
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
-        group_scale: Sequence[int | float] | None = None,
-        group_translation: Sequence[int | float] | None = None,
         **kwargs: Any,
     ) -> Self:
         """
-        Create a `Group` from a sequence of arrays and spatial metadata.
+        Create a `Group` from a sequence of multiscale arrays and spatial metadata.
 
         Parameters
         ----------
         paths: Sequence[str]
             The paths to the arrays.
+        axes: Sequence[Axis]
+            `Axis` objects describing the dimensions of the arrays.
+        arrays: Sequence[ArrayLike] | Sequence[ChunkedArrayLike]
+            A sequence of array-like objects that collectively represent the same image
+            at multiple levels of detail.
+        scales: Sequence[Sequence[int | float]]
+            A scale value for each axis of the array, for each array in `arrays`.
+        translations: Sequence[Sequence[int | float]]
+            A translation value for each axis the array, for each array in `arrays`.
+        name: str | None, default = None
+            A name for the multiscale collection. Optional.
+        type: str | None, default = None
+            A description of the type of multiscale image represented by this group. Optional.
+        metadata: Dict[str, Any] | None, default = None
+            Arbitrary metadata associated with this multiscale collection. Optional.
         """
-        group_transforms = None
-        if group_scale is not None:
-            group_transforms = tx.scale_translation(group_scale, group_translation)
-
         members_flat = {
             "/" + key.lstrip("/"): ArraySpec.from_array(arr, **kwargs)
             for key, arr in zip(paths, arrays, strict=True)
@@ -332,7 +341,7 @@ def from_arrays(
                     paths, scales, translations, strict=True
                 )
             ],
-            coordinateTransformations=group_transforms,
+            coordinateTransformations=None,
         )
         return cls(
             members=GroupSpec.from_flat(members_flat).members,
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index ad3a2ed..21978c7 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -396,9 +396,6 @@ def test_from_arrays(
         )
     ]
 
-    group_scale = (1,) * ndim
-    group_translation = (0,) * ndim
-
     all_axes = [
         Axis(
             name="x",
@@ -424,8 +421,6 @@ def test_from_arrays(
         name=name,
         type=type,
         metadata=metadata,
-        group_scale=group_scale,
-        group_translation=group_translation,
     )
 
     group_flat = group.to_flat()
@@ -433,10 +428,7 @@ def test_from_arrays(
     assert group.attributes.multiscales[0].name == name
     assert group.attributes.multiscales[0].type == type
     assert group.attributes.multiscales[0].metadata == metadata
-    assert group.attributes.multiscales[0].coordinateTransformations == (
-        VectorScale(scale=group_scale),
-        VectorTranslation(translation=group_translation),
-    )
+    assert group.attributes.multiscales[0].coordinateTransformations is None
     assert group.attributes.multiscales[0].axes == axes
     for idx, array in enumerate(arrays):
         assert array.shape == group_flat["/" + paths[idx]].shape

From c2a68319d11351b4d80edc068ef38edc52f3e00a Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 6 Mar 2024 10:04:09 +0100
Subject: [PATCH 40/69] Update pyproject.toml

---
 pyproject.toml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8cd2c22..9a90c1a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,11 +10,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 [tool.poetry.dependencies]
 python = "^3.10"
 pydantic-zarr = "0.6.1"
-fsspec = "^2023.10.0"
-s3fs = "^2023.10.0"
 rich = "^13.6.0"
-mkdocs-material = "^9.5.5"
-
 
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^3.0.4"
@@ -82,4 +78,4 @@ source = [
 ]
 
 [tool.coverage.html]
-directory = "htmlcov"
\ No newline at end of file
+directory = "htmlcov"

From 474e541dfcac9c8f7adb32a02a30f5f1a22867d0 Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Wed, 6 Mar 2024 10:07:44 +0100
Subject: [PATCH 41/69] Update poetry.lock

---
 poetry.lock | 635 ++--------------------------------------------------
 1 file changed, 15 insertions(+), 620 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 7663d52..9b0176b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,147 +1,5 @@
 # This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
 
-[[package]]
-name = "aiobotocore"
-version = "2.12.0"
-description = "Async client for aws services using botocore and aiohttp"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "aiobotocore-2.12.0-py3-none-any.whl", hash = "sha256:e121503dca049cf361dea19730e335aff2e7508f7f8b24db2e6a43a6fb70299e"},
-    {file = "aiobotocore-2.12.0.tar.gz", hash = "sha256:bc841cef234afcb781f2d600680c9e49d01b9a2e8169790a32579bb0df51777f"},
-]
-
-[package.dependencies]
-aiohttp = ">=3.7.4.post0,<4.0.0"
-aioitertools = ">=0.5.1,<1.0.0"
-botocore = ">=1.34.41,<1.34.52"
-wrapt = ">=1.10.10,<2.0.0"
-
-[package.extras]
-awscli = ["awscli (>=1.32.41,<1.32.52)"]
-boto3 = ["boto3 (>=1.34.41,<1.34.52)"]
-
-[[package]]
-name = "aiohttp"
-version = "3.9.3"
-description = "Async http client/server framework (asyncio)"
-optional = false
-python-versions = ">=3.8"
-files = [
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 testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
 typing = ["typing-extensions (>=4.8)"]
 
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-[package.extras]
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-adl = ["adlfs"]
-arrow = ["pyarrow (>=1)"]
-dask = ["dask", "distributed"]
-devel = ["pytest", "pytest-cov"]
-dropbox = ["dropbox", "dropboxdrivefs", "requests"]
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-fuse = ["fusepy"]
-gcs = ["gcsfs"]
-git = ["pygit2"]
-github = ["requests"]
-gs = ["gcsfs"]
-gui = ["panel"]
-hdfs = ["pyarrow (>=1)"]
-http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
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-oci = ["ocifs"]
-s3 = ["s3fs"]
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-smb = ["smbprotocol"]
-ssh = ["paramiko"]
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-
 [[package]]
 name = "ghp-import"
 version = "2.1.0"
@@ -677,13 +384,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.41.2"
+version = "0.41.3"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
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 ]
 
 [package.dependencies]
@@ -756,17 +463,6 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
-[[package]]
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-version = "1.0.1"
-description = "JSON Matching Expressions"
-optional = false
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 [[package]]
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 [[package]]
 name = "mkdocs-material"
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+version = "9.5.13"
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-    {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
-    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
-]
-
-[package.dependencies]
-idna = ">=2.0"
-multidict = ">=4.0"
-
 [[package]]
 name = "zarr"
 version = "2.17.0"
@@ -2341,4 +1736,4 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "9fcbaf31547db3838421ab6496d8081ee87f365ddadc7790d16c605d5e258444"
+content-hash = "cd94d9fe75239599e158a667d0eacf333067a873d3b8ef5666530199a9be3ac8"

From ce03791650acba3ad140b60950e2f134cc4b337e Mon Sep 17 00:00:00 2001
From: Davis Vann Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 12:56:23 +0100
Subject: [PATCH 42/69] add doctests, set minimum python version to 3.9

---
 docs/index.md                            |  68 ++-
 poetry.lock                              | 595 +++++++++++++++++++++--
 pyproject.toml                           |   3 +-
 src/pydantic_ome_ngff/v04/multiscales.py |   3 +-
 tests/test_docs.py                       |   7 +
 5 files changed, 618 insertions(+), 58 deletions(-)
 create mode 100644 tests/test_docs.py

diff --git a/docs/index.md b/docs/index.md
index ad01c67..fa6c8a2 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,11 +9,75 @@ This library aims to provide models for the the metadata objects and Zarr hierar
 # Reading Multiscale metadata
 
 ```python
-# example data on S3-compatible cloud storage
+# example data served over http
 from pydantic_ome_ngff.v04.multiscales import Group
 import zarr
 url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
 zgroup = zarr.open(url)
+# this is a Pydantic model of a Zarr group
 group = Group.from_zarr(zgroup)
-
+# it has an `attributes` attribute, which in turn has a `multiscales` attribute 
+# which models the OME-NGFF multiscales metadata
+print(group.attributes.multiscales)
+"""
+[
+    MultiscaleMetadata(
+        version='0.4',
+        name=None,
+        type=None,
+        metadata=None,
+        datasets=[
+            Dataset(
+                path='0',
+                coordinateTransformations=(
+                    VectorScale(
+                        type='scale',
+                        scale=[
+                            1.0,
+                            0.5002025531914894,
+                            0.3603981534640209,
+                            0.3603981534640209,
+                        ],
+                    ),
+                ),
+            ),
+            Dataset(
+                path='1',
+                coordinateTransformations=(
+                    VectorScale(
+                        type='scale',
+                        scale=[
+                            1.0,
+                            0.5002025531914894,
+                            0.7207963069280418,
+                            0.7207963069280418,
+                        ],
+                    ),
+                ),
+            ),
+            Dataset(
+                path='2',
+                coordinateTransformations=(
+                    VectorScale(
+                        type='scale',
+                        scale=[
+                            1.0,
+                            0.5002025531914894,
+                            1.4415926138560835,
+                            1.4415926138560835,
+                        ],
+                    ),
+                ),
+            ),
+        ],
+        axes=[
+            Axis(name='c', type='channel', unit=None),
+            Axis(name='z', type='space', unit='micrometer'),
+            Axis(name='y', type='space', unit='micrometer'),
+            Axis(name='x', type='space', unit='micrometer'),
+        ],
+        coordinateTransformations=None,
+    )
+]
+"""
 ```
diff --git a/poetry.lock b/poetry.lock
index 9b0176b..dfb1fab 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,115 @@
 # This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
 
+[[package]]
+name = "aiohttp"
+version = "3.9.3"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.8"
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+attrs = ">=17.3.0"
+frozenlist = ">=1.1.1"
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+yarl = ">=1.0,<2.0"
+
+[package.extras]
+speedups = ["Brotli", "aiodns", "brotlicffi"]
+
+[[package]]
+name = "aiosignal"
+version = "1.3.1"
+description = "aiosignal: a list of registered asynchronous callbacks"
+optional = false
+python-versions = ">=3.7"
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+
 [[package]]
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 version = "0.6.0"
@@ -21,6 +131,17 @@ files = [
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+optional = false
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 version = "23.2.0"
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 typing = ["typing-extensions (>=4.8)"]
 
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+description = "File-system specification"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "fsspec-2024.2.0-py3-none-any.whl", hash = "sha256:817f969556fa5916bc682e02ca2045f96ff7f586d45110fcb76022063ad2c7d8"},
+    {file = "fsspec-2024.2.0.tar.gz", hash = "sha256:b6ad1a679f760dda52b1168c859d01b7b80648ea6f7f7c7f5a8a91dc3f3ecb84"},
+]
+
+[package.dependencies]
+aiohttp = {version = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1", optional = true, markers = "extra == \"http\""}
+
+[package.extras]
+abfs = ["adlfs"]
+adl = ["adlfs"]
+arrow = ["pyarrow (>=1)"]
+dask = ["dask", "distributed"]
+devel = ["pytest", "pytest-cov"]
+dropbox = ["dropbox", "dropboxdrivefs", "requests"]
+full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "dask", "distributed", "dropbox", "dropboxdrivefs", "fusepy", "gcsfs", "libarchive-c", "ocifs", "panel", "paramiko", "pyarrow (>=1)", "pygit2", "requests", "s3fs", "smbprotocol", "tqdm"]
+fuse = ["fusepy"]
+gcs = ["gcsfs"]
+git = ["pygit2"]
+github = ["requests"]
+gs = ["gcsfs"]
+gui = ["panel"]
+hdfs = ["pyarrow (>=1)"]
+http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)"]
+libarchive = ["libarchive-c"]
+oci = ["ocifs"]
+s3 = ["s3fs"]
+sftp = ["paramiko"]
+smb = ["smbprotocol"]
+ssh = ["paramiko"]
+tqdm = ["tqdm"]
+
 [[package]]
 name = "ghp-import"
 version = "2.1.0"
@@ -421,6 +666,25 @@ files = [
     {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
+[[package]]
+name = "importlib-metadata"
+version = "7.0.2"
+description = "Read metadata from Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "importlib_metadata-7.0.2-py3-none-any.whl", hash = "sha256:f4bc4c0c070c490abf4ce96d715f68e95923320370efb66143df00199bb6c100"},
+    {file = "importlib_metadata-7.0.2.tar.gz", hash = "sha256:198f568f3230878cb1b44fbd7975f87906c22336dba2e4a7f05278c281fbd792"},
+]
+
+[package.dependencies]
+zipp = ">=0.5"
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+perf = ["ipython"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+
 [[package]]
 name = "iniconfig"
 version = "2.0.0"
@@ -509,6 +773,9 @@ files = [
     {file = "Markdown-3.5.2.tar.gz", hash = "sha256:e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8"},
 ]
 
+[package.dependencies]
+importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
+
 [package.extras]
 docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
 testing = ["coverage", "pyyaml"]
@@ -643,6 +910,7 @@ files = [
 click = ">=7.0"
 colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
 ghp-import = ">=1.0"
+importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
 jinja2 = ">=2.11.1"
 markdown = ">=3.2.1"
 markupsafe = ">=2.0.1"
@@ -727,6 +995,7 @@ files = [
 
 [package.dependencies]
 click = ">=7.0"
+importlib-metadata = {version = ">=4.6", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.11.1"
 Markdown = ">=3.3"
 MarkupSafe = ">=1.1"
@@ -735,6 +1004,7 @@ mkdocs-autorefs = ">=0.3.1"
 mkdocstrings-python = {version = ">=0.5.2", optional = true, markers = "extra == \"python\""}
 platformdirs = ">=2.2.0"
 pymdown-extensions = ">=6.3"
+typing-extensions = {version = ">=4.1", markers = "python_version < \"3.10\""}
 
 [package.extras]
 crystal = ["mkdocstrings-crystal (>=0.3.4)"]
@@ -756,40 +1026,139 @@ files = [
 griffe = ">=0.37"
 mkdocstrings = ">=0.20"
 
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+    {file = "yarl-1.9.4-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:604f31d97fa493083ea21bd9b92c419012531c4e17ea6da0f65cacdcf5d0bd27"},
+    {file = "yarl-1.9.4-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:8a854227cf581330ffa2c4824d96e52ee621dd571078a252c25e3a3b3d94a1b1"},
+    {file = "yarl-1.9.4-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:ba6f52cbc7809cd8d74604cce9c14868306ae4aa0282016b641c661f981a6e91"},
+    {file = "yarl-1.9.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a6327976c7c2f4ee6816eff196e25385ccc02cb81427952414a64811037bbc8b"},
+    {file = "yarl-1.9.4-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:8397a3817d7dcdd14bb266283cd1d6fc7264a48c186b986f32e86d86d35fbac5"},
+    {file = "yarl-1.9.4-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:e0381b4ce23ff92f8170080c97678040fc5b08da85e9e292292aba67fdac6c34"},
+    {file = "yarl-1.9.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:23d32a2594cb5d565d358a92e151315d1b2268bc10f4610d098f96b147370136"},
+    {file = "yarl-1.9.4-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:ddb2a5c08a4eaaba605340fdee8fc08e406c56617566d9643ad8bf6852778fc7"},
+    {file = "yarl-1.9.4-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:26a1dc6285e03f3cc9e839a2da83bcbf31dcb0d004c72d0730e755b33466c30e"},
+    {file = "yarl-1.9.4-cp39-cp39-musllinux_1_1_i686.whl", hash = "sha256:18580f672e44ce1238b82f7fb87d727c4a131f3a9d33a5e0e82b793362bf18b4"},
+    {file = "yarl-1.9.4-cp39-cp39-musllinux_1_1_ppc64le.whl", hash = "sha256:29e0f83f37610f173eb7e7b5562dd71467993495e568e708d99e9d1944f561ec"},
+    {file = "yarl-1.9.4-cp39-cp39-musllinux_1_1_s390x.whl", hash = "sha256:1f23e4fe1e8794f74b6027d7cf19dc25f8b63af1483d91d595d4a07eca1fb26c"},
+    {file = "yarl-1.9.4-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:db8e58b9d79200c76956cefd14d5c90af54416ff5353c5bfd7cbe58818e26ef0"},
+    {file = "yarl-1.9.4-cp39-cp39-win32.whl", hash = "sha256:c7224cab95645c7ab53791022ae77a4509472613e839dab722a72abe5a684575"},
+    {file = "yarl-1.9.4-cp39-cp39-win_amd64.whl", hash = "sha256:824d6c50492add5da9374875ce72db7a0733b29c2394890aef23d533106e2b15"},
+    {file = "yarl-1.9.4-py3-none-any.whl", hash = "sha256:928cecb0ef9d5a7946eb6ff58417ad2fe9375762382f1bf5c55e61645f2c43ad"},
+    {file = "yarl-1.9.4.tar.gz", hash = "sha256:566db86717cf8080b99b58b083b773a908ae40f06681e87e589a976faf8246bf"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+
 [[package]]
 name = "zarr"
-version = "2.17.0"
+version = "2.17.1"
 description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "zarr-2.17.0-py3-none-any.whl", hash = "sha256:d287cb61019c4a0a0f386f76eeaa7f0b1160b1cb90cf96173a4b6cbc135df6e1"},
-    {file = "zarr-2.17.0.tar.gz", hash = "sha256:6390a2b8af31babaab4c963efc45bf1da7f9500c9aafac193f84cf019a7c66b0"},
+    {file = "zarr-2.17.1-py3-none-any.whl", hash = "sha256:e25df2741a6e92645f3890f30f3136d5b57a0f8f831094b024bbcab5f2797bc7"},
+    {file = "zarr-2.17.1.tar.gz", hash = "sha256:564b3aa072122546fe69a0fa21736f466b20fad41754334b62619f088ce46261"},
 ]
 
 [package.dependencies]
@@ -1733,7 +2205,22 @@ numpy = ">=1.21.1"
 docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-automodapi", "sphinx-copybutton", "sphinx-design", "sphinx-issues"]
 jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
+    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.10"
-content-hash = "cd94d9fe75239599e158a667d0eacf333067a873d3b8ef5666530199a9be3ac8"
+python-versions = "^3.9"
+content-hash = "8339793aab56453a96e746e6928015ed41de0f0e73e6c2ef7061f8db12a7a33d"
diff --git a/pyproject.toml b/pyproject.toml
index 9a90c1a..8b3d0ad 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ readme = "README.md"
 packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
-python = "^3.10"
+python = "^3.9"
 pydantic-zarr = "0.6.1"
 rich = "^13.6.0"
 
@@ -20,6 +20,7 @@ pytest = "^7.2.1"
 mypy = "^1.0.1"
 requests = "^2.28.2"
 pytest-cov = "^4.0.0"
+fsspec = {version = "^2024.2.0", extras=["http"]}
 
 
 [tool.poetry.group.docs.dependencies]
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 03d30e7..6b1d8b5 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -286,7 +286,8 @@ def from_zarr(cls, node: zarr.Group) -> Group:
         guess_inferred_members = guess.model_copy(
             update={"members": {**guess.members, **members_normalized.members}}
         )
-        return guess_inferred_members
+        result = cls(**guess_inferred_members.model_dump())
+        return result
 
     @classmethod
     def from_arrays(
diff --git a/tests/test_docs.py b/tests/test_docs.py
new file mode 100644
index 0000000..9429392
--- /dev/null
+++ b/tests/test_docs.py
@@ -0,0 +1,7 @@
+import pytest
+from pytest_examples import find_examples, CodeExample, EvalExample
+
+
+@pytest.mark.parametrize("example", find_examples("docs"), ids=str)
+def test_docstrings(example: CodeExample, eval_example: EvalExample):
+    eval_example.run_print_check(example)

From c7d0f3a23ae8251285aa2e1472474af3eba6978a Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 14:19:10 +0100
Subject: [PATCH 43/69] handle numpy arrays as arguments to  and  transforms

---
 src/pydantic_ome_ngff/v04/transforms.py | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transforms.py
index 67dc998..cf8bc10 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transforms.py
@@ -1,8 +1,11 @@
 from __future__ import annotations
 
-from typing import Literal, Sequence
+from typing import Annotated, Any, Literal, Sequence
+
+from pydantic import BeforeValidator
 
 from pydantic_ome_ngff.base import StrictBase
+import numpy as np
 
 
 class Identity(StrictBase):
@@ -74,7 +77,7 @@ class VectorTranslation(StrictBase):
     """
 
     type: Literal["translation"] = "translation"
-    translation: Sequence[float | int]
+    translation: Annotated[Sequence[float | int], BeforeValidator(listify_numpy)]
 
 
 class VectorScale(StrictBase):
@@ -92,7 +95,7 @@ class VectorScale(StrictBase):
     """
 
     type: Literal["scale"] = "scale"
-    scale: Sequence[float | int]
+    scale: Annotated[Sequence[float | int], BeforeValidator(listify_numpy)]
 
 
 def ndim(
@@ -168,3 +171,13 @@ def ensure_dimensionality(
         )
         raise ValueError(msg)
     return transforms
+
+
+def listify_numpy(data: Any) -> Any:
+    """
+    If the input is a numpy array, turn it into a list and return it.
+    Otherwise return the input unchanged.
+    """
+    if isinstance(data, np.ndarray):
+        return data.tolist()
+    return data

From 2af58d7ccef709f96d09c961ada1fc07edf47170 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 14:23:59 +0100
Subject: [PATCH 44/69] dont cast to list

---
 src/pydantic_ome_ngff/v04/multiscales.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscales.py
index 6b1d8b5..f6b8761 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscales.py
@@ -335,7 +335,7 @@ def from_arrays(
             name=name,
             type=type,
             metadata=metadata,
-            axes=list(axes),
+            axes=axes,
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
                 for path, scale, translation in zip(

From 516d35daff1f524d39396826b2ad48654bb85f35 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 14:24:15 +0100
Subject: [PATCH 45/69] add multiscale creation example

---
 docs/index.md | 213 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 208 insertions(+), 5 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index fa6c8a2..16dffc6 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -6,19 +6,28 @@
 
 This library aims to provide models for the the metadata objects and Zarr hierarchies described in the [OME-NGFF](https://ngff.openmicroscopy.org/) specifications.
 
-# Reading Multiscale metadata
+# Examples
+
+## Reading Multiscale metadata
+
+This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscales` to model a multiscale group.
 
 ```python
-# example data served over http
 from pydantic_ome_ngff.v04.multiscales import Group
 import zarr
+# example data served over http
 url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+
+# open the Zarr group
 zgroup = zarr.open(url)
-# this is a Pydantic model of a Zarr group
-group = Group.from_zarr(zgroup)
+
+# group_model is a `GroupSpec`, i.e. a Pydantic model of a Zarr group
+group_model = Group.from_zarr(zgroup)
+
 # it has an `attributes` attribute, which in turn has a `multiscales` attribute 
 # which models the OME-NGFF multiscales metadata
-print(group.attributes.multiscales)
+multi_meta = group_model.attributes.multiscales
+print(multi_meta)
 """
 [
     MultiscaleMetadata(
@@ -80,4 +89,198 @@ print(group.attributes.multiscales)
     )
 ]
 """
+
+# to get the Zarr arrays referenced by the multiscale metadata, we access them by name from the Zarr group.
+arrays = [zgroup[d.path] for d in multi_meta[0].datasets]
+print(arrays)
+"""
+[<zarr.core.Array '/0' (2, 236, 275, 271) uint16>, <zarr.core.Array '/1' (2, 236, 137, 135) uint16>, <zarr.core.Array '/2' (2, 236, 68, 67) uint16>]
+"""
 ```
+
+## Creating multiscale metadata
+
+`pydantic-ome-ngff` provides simple way to create multiscale metadata from a collection of arrays accompanied by spatial metadata.
+
+```python
+from pydantic_ome_ngff.v04.multiscales import Group
+from pydantic_ome_ngff.v04.axis import Axis
+import numpy as np
+import zarr
+
+# define the axes
+axes = [
+    Axis(name='t', unit='second', type='time'),
+    Axis(name='z', unit='nanometer', type='space'),
+    Axis(name='y', unit='nanometer', type='space'),
+    Axis(name='x', unit='nanometer', type='space')
+]
+
+ndim = len(axes)
+
+# simulate a multiscale pyramid
+shapes = (10,) * ndim, (5,) * ndim
+arrays = []
+scales = []
+translations = []
+paths = []
+
+# define the base scaling and translation
+scale_base = [1.0, 2.0, 2.0, 2.0]
+trans_base = [0.0, 0.0, 0.0, 0.0]
+
+for idx, s in enumerate(shapes):
+    arrays.append(np.zeros(s))
+    # power of 2 downsampling per-axis for each image
+    scales.append(np.multiply(2 ** idx, scale_base))
+    # downsampling-induced translation per-axis for each image
+    translations.append(
+        np.multiply(scale_base, 2 ** (idx - 1)),
+    )
+
+    if idx > 0:
+        translations[-1] += np.sum(translations[:-1], axis=0)
+
+    # name the arrays s0, s1, s2
+    paths.append(f's{idx}')
+
+# this is now a complete model of the Zarr group
+group_model = Group.from_arrays(
+    axes=axes,
+    paths=paths,
+    arrays=arrays,
+    scales=scales,
+    translations=translations
+    )
+
+print(group_model.model_dump())
+"""
+{
+    'zarr_version': 2,
+    'attributes': {
+        'multiscales': [
+            {
+                'version': '0.4',
+                'name': None,
+                'type': None,
+                'metadata': None,
+                'datasets': [
+                    {
+                        'path': 's0',
+                        'coordinateTransformations': (
+                            {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
+                            {
+                                'type': 'translation',
+                                'translation': [0.5, 1.0, 1.0, 1.0],
+                            },
+                        ),
+                    },
+                    {
+                        'path': 's1',
+                        'coordinateTransformations': (
+                            {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
+                            {
+                                'type': 'translation',
+                                'translation': [1.5, 3.0, 3.0, 3.0],
+                            },
+                        ),
+                    },
+                ],
+                'axes': [
+                    {'name': 't', 'type': 'time', 'unit': 'second'},
+                    {'name': 'z', 'type': 'space', 'unit': 'nanometer'},
+                    {'name': 'y', 'type': 'space', 'unit': 'nanometer'},
+                    {'name': 'x', 'type': 'space', 'unit': 'nanometer'},
+                ],
+                'coordinateTransformations': None,
+            }
+        ]
+    },
+    'members': {
+        's0': {
+            'zarr_version': 2,
+            'attributes': {},
+            'shape': (10, 10, 10, 10),
+            'chunks': (10, 10, 10, 10),
+            'dtype': '<f8',
+            'fill_value': 0,
+            'order': 'C',
+            'filters': None,
+            'dimension_separator': '/',
+            'compressor': None,
+        },
+        's1': {
+            'zarr_version': 2,
+            'attributes': {},
+            'shape': (5, 5, 5, 5),
+            'chunks': (5, 5, 5, 5),
+            'dtype': '<f8',
+            'fill_value': 0,
+            'order': 'C',
+            'filters': None,
+            'dimension_separator': '/',
+            'compressor': None,
+        },
+    },
+}
+"""
+
+# to actually do something useful with this model, we have to serialize it to storage
+
+# make an in-memory zarr store for demo purposes
+# with real data, you would use DirectoryStore or FSStore
+store = zarr.MemoryStore()
+path = 'foo'
+stored_group = group_model.to_zarr(store, path='foo')
+
+
+# check that the expected arrays are present
+# no data has been written to these arrays, you must do that separately.
+print(stored_group.tree())
+"""
+foo
+ ├── s0 (10, 10, 10, 10) float64
+ └── s1 (5, 5, 5, 5) float64
+"""
+
+# check that the expected attributes are present
+print(stored_group.attrs.asdict())
+"""
+{
+    'multiscales': [
+        {
+            'version': '0.4',
+            'name': None,
+            'type': None,
+            'metadata': None,
+            'datasets': [
+                {
+                    'path': 's0',
+                    'coordinateTransformations': (
+                        {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
+                        {'type': 'translation', 'translation': [0.5, 1.0, 1.0, 1.0]},
+                    ),
+                },
+                {
+                    'path': 's1',
+                    'coordinateTransformations': (
+                        {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
+                        {'type': 'translation', 'translation': [1.5, 3.0, 3.0, 3.0]},
+                    ),
+                },
+            ],
+            'axes': [
+                {'name': 't', 'type': 'time', 'unit': 'second'},
+                {'name': 'z', 'type': 'space', 'unit': 'nanometer'},
+                {'name': 'y', 'type': 'space', 'unit': 'nanometer'},
+                {'name': 'x', 'type': 'space', 'unit': 'nanometer'},
+            ],
+            'coordinateTransformations': None,
+        }
+    ]
+}
+"""
+
+
+
+```
\ No newline at end of file

From c4c1cd74f9614733e4ba2bedbcb5c65c22984580 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 14:30:39 +0100
Subject: [PATCH 46/69] add chunking to group creation example

---
 docs/index.md | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index 16dffc6..1f23272 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -118,6 +118,9 @@ axes = [
 
 ndim = len(axes)
 
+# the chunk size we want to use for our Zarr arrays
+store_chunks = (1, 2, 2, 2)
+
 # simulate a multiscale pyramid
 shapes = (10,) * ndim, (5,) * ndim
 arrays = []
@@ -150,8 +153,8 @@ group_model = Group.from_arrays(
     paths=paths,
     arrays=arrays,
     scales=scales,
-    translations=translations
-    )
+    translations=translations,
+    chunks=store_chunks)
 
 print(group_model.model_dump())
 """
@@ -201,7 +204,7 @@ print(group_model.model_dump())
             'zarr_version': 2,
             'attributes': {},
             'shape': (10, 10, 10, 10),
-            'chunks': (10, 10, 10, 10),
+            'chunks': (1, 2, 2, 2),
             'dtype': '<f8',
             'fill_value': 0,
             'order': 'C',
@@ -213,7 +216,7 @@ print(group_model.model_dump())
             'zarr_version': 2,
             'attributes': {},
             'shape': (5, 5, 5, 5),
-            'chunks': (5, 5, 5, 5),
+            'chunks': (1, 2, 2, 2),
             'dtype': '<f8',
             'fill_value': 0,
             'order': 'C',
@@ -228,14 +231,14 @@ print(group_model.model_dump())
 # to actually do something useful with this model, we have to serialize it to storage
 
 # make an in-memory zarr store for demo purposes
-# with real data, you would use DirectoryStore or FSStore
+# with real data, you would use `zarr.storage.DirectoryStore` or `zarr.storage.FSStore`
 store = zarr.MemoryStore()
 path = 'foo'
 stored_group = group_model.to_zarr(store, path='foo')
 
-
 # check that the expected arrays are present
 # no data has been written to these arrays, you must do that separately.
+# e.g., stored_group[s0] = arrays[0]
 print(stored_group.tree())
 """
 foo

From a63fef507ae5c5eadb6cc0445d4e632ecd5add9f Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Mon, 11 Mar 2024 18:32:15 +0100
Subject: [PATCH 47/69] simplify array creation in example, and remove
 incorrect translation

---
 docs/index.md | 41 +++++++++++++++++------------------------
 1 file changed, 17 insertions(+), 24 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index 1f23272..3fa5a08 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -123,29 +123,22 @@ store_chunks = (1, 2, 2, 2)
 
 # simulate a multiscale pyramid
 shapes = (10,) * ndim, (5,) * ndim
-arrays = []
-scales = []
-translations = []
-paths = []
+arrays = [np.zeros(s) for s in shapes]
 
-# define the base scaling and translation
-scale_base = [1.0, 2.0, 2.0, 2.0]
-trans_base = [0.0, 0.0, 0.0, 0.0]
+# arrays will be named s0, s1, etc
+paths = [f's{idx}' for idx in range(len(shapes))]
 
-for idx, s in enumerate(shapes):
-    arrays.append(np.zeros(s))
-    # power of 2 downsampling per-axis for each image
-    scales.append(np.multiply(2 ** idx, scale_base))
-    # downsampling-induced translation per-axis for each image
-    translations.append(
-        np.multiply(scale_base, 2 ** (idx - 1)),
-    )
-
-    if idx > 0:
-        translations[-1] += np.sum(translations[:-1], axis=0)
+# regular 2x downsampling
+scales = [
+    [1.0, 2.0, 2.0, 2.0],
+    [2.0, 4.0, 4.0, 4.0],
+]
 
-    # name the arrays s0, s1, s2
-    paths.append(f's{idx}')
+# translation introduced by 2x downsampling
+translations = [
+    [0.0, 0.0, 0.0, 0.0],
+    [0.5, 1.0, 1.0, 1.0]
+]
 
 # this is now a complete model of the Zarr group
 group_model = Group.from_arrays(
@@ -174,7 +167,7 @@ print(group_model.model_dump())
                             {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
                             {
                                 'type': 'translation',
-                                'translation': [0.5, 1.0, 1.0, 1.0],
+                                'translation': [0.0, 0.0, 0.0, 0.0],
                             },
                         ),
                     },
@@ -184,7 +177,7 @@ print(group_model.model_dump())
                             {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
                             {
                                 'type': 'translation',
-                                'translation': [1.5, 3.0, 3.0, 3.0],
+                                'translation': [0.5, 1.0, 1.0, 1.0],
                             },
                         ),
                     },
@@ -261,14 +254,14 @@ print(stored_group.attrs.asdict())
                     'path': 's0',
                     'coordinateTransformations': (
                         {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
-                        {'type': 'translation', 'translation': [0.5, 1.0, 1.0, 1.0]},
+                        {'type': 'translation', 'translation': [0.0, 0.0, 0.0, 0.0]},
                     ),
                 },
                 {
                     'path': 's1',
                     'coordinateTransformations': (
                         {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
-                        {'type': 'translation', 'translation': [1.5, 3.0, 3.0, 3.0]},
+                        {'type': 'translation', 'translation': [0.5, 1.0, 1.0, 1.0]},
                     ),
                 },
             ],

From a40f2bca77cf9a9f3ef1e4036211c2c9e165508d Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 12 Mar 2024 11:59:13 +0100
Subject: [PATCH 48/69] chore: depluralize module names

---
 src/pydantic_ome_ngff/latest/__init__.py      |  2 +-
 .../latest/{multiscales.py => multiscale.py}  |  2 +-
 .../latest/{transforms.py => transform.py}    |  2 +-
 src/pydantic_ome_ngff/utils.py                | 10 +++
 src/pydantic_ome_ngff/v04/__init__.py         |  4 +-
 src/pydantic_ome_ngff/v04/label.py            |  6 +-
 .../v04/{multiscales.py => multiscale.py}     |  3 +-
 .../v04/{transforms.py => transform.py}       | 44 ++++---------
 src/pydantic_ome_ngff/v04/well.py             |  6 +-
 tests/latest/test_multiscales.py              |  4 +-
 tests/test_utils.py                           | 13 +++-
 tests/v04/test_multiscales.py                 |  4 +-
 tests/v04/test_transform.py                   | 64 +++++++++++++++++++
 13 files changed, 116 insertions(+), 48 deletions(-)
 rename src/pydantic_ome_ngff/latest/{multiscales.py => multiscale.py} (96%)
 rename src/pydantic_ome_ngff/latest/{transforms.py => transform.py} (96%)
 rename src/pydantic_ome_ngff/v04/{multiscales.py => multiscale.py} (99%)
 rename src/pydantic_ome_ngff/v04/{transforms.py => transform.py} (83%)
 create mode 100644 tests/v04/test_transform.py

diff --git a/src/pydantic_ome_ngff/latest/__init__.py b/src/pydantic_ome_ngff/latest/__init__.py
index 1bccf6f..1fe6284 100644
--- a/src/pydantic_ome_ngff/latest/__init__.py
+++ b/src/pydantic_ome_ngff/latest/__init__.py
@@ -1,5 +1,5 @@
 from pydantic_ome_ngff.latest.axis import Axis  # noqa
-from pydantic_ome_ngff.latest.multiscales import MultiscaleMetadata  # noqa
+from pydantic_ome_ngff.latest.multiscale import MultiscaleMetadata  # noqa
 from pydantic_ome_ngff.latest.label import ImageLabel  # noqa
 from pydantic_ome_ngff.latest.well import WellMeta  # noqa
 from pydantic_ome_ngff.latest.plate import PlateMeta  # noqa
diff --git a/src/pydantic_ome_ngff/latest/multiscales.py b/src/pydantic_ome_ngff/latest/multiscale.py
similarity index 96%
rename from src/pydantic_ome_ngff/latest/multiscales.py
rename to src/pydantic_ome_ngff/latest/multiscale.py
index 733dfaf..109c031 100644
--- a/src/pydantic_ome_ngff/latest/multiscales.py
+++ b/src/pydantic_ome_ngff/latest/multiscale.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 from typing import Literal
 from pydantic_ome_ngff.latest.base import version
-import pydantic_ome_ngff.v04.multiscales as msv04
+import pydantic_ome_ngff.v04.multiscale as msv04
 
 
 class Dataset(msv04.Dataset):
diff --git a/src/pydantic_ome_ngff/latest/transforms.py b/src/pydantic_ome_ngff/latest/transform.py
similarity index 96%
rename from src/pydantic_ome_ngff/latest/transforms.py
rename to src/pydantic_ome_ngff/latest/transform.py
index c5e17d0..ec0de32 100644
--- a/src/pydantic_ome_ngff/latest/transforms.py
+++ b/src/pydantic_ome_ngff/latest/transform.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 from typing import Union
-import pydantic_ome_ngff.v04.transforms as tx
+import pydantic_ome_ngff.v04.transform as tx
 
 
 class Identity(tx.Identity):
diff --git a/src/pydantic_ome_ngff/utils.py b/src/pydantic_ome_ngff/utils.py
index a1cf0c4..310385a 100644
--- a/src/pydantic_ome_ngff/utils.py
+++ b/src/pydantic_ome_ngff/utils.py
@@ -27,3 +27,13 @@ class ArrayLike(Protocol):
 @runtime_checkable
 class ChunkedArrayLike(ArrayLike, Protocol):
     chunks: Tuple[int, ...]
+
+
+def listify_numpy(data: Any) -> Any:
+    """
+    If the input is a numpy array, turn it into a list and return it.
+    Otherwise return the input unchanged.
+    """
+    if isinstance(data, np.ndarray):
+        return data.tolist()
+    return data
diff --git a/src/pydantic_ome_ngff/v04/__init__.py b/src/pydantic_ome_ngff/v04/__init__.py
index f63d655..c702016 100644
--- a/src/pydantic_ome_ngff/v04/__init__.py
+++ b/src/pydantic_ome_ngff/v04/__init__.py
@@ -1,6 +1,6 @@
 from pydantic_ome_ngff.v04.axis import Axis
-from pydantic_ome_ngff.v04.transforms import Transform
-from pydantic_ome_ngff.v04.multiscales import MultiscaleMetadata
+from pydantic_ome_ngff.v04.transform import Transform
+from pydantic_ome_ngff.v04.multiscale import MultiscaleMetadata
 from pydantic_ome_ngff.v04.label import ImageLabel
 from pydantic_ome_ngff.v04.well import WellMetadata
 from pydantic_ome_ngff.v04.plate import PlateMetadata
diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 0615bd5..59295de 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -7,7 +7,7 @@
 from pydantic_ome_ngff.utils import duplicates
 from pydantic_ome_ngff.v04.base import version as NGFF_VERSION
 
-import pydantic_ome_ngff.v04.multiscales as multiscales
+import pydantic_ome_ngff.v04.multiscale as multiscale
 
 ConInt = Annotated[int, Field(strict=True, ge=0, le=255)]
 RGBA = Tuple[ConInt, ConInt, ConInt, ConInt]
@@ -101,7 +101,7 @@ def parse_model(self):
         return parse_imagelabel(self)
 
 
-class GroupAttrs(multiscales.GroupAttrs):
+class GroupAttrs(multiscale.GroupAttrs):
     """
     Attributes for a Zarr group that contains `image-label` metadata.
     Inherits from `v04.multiscales.MultiscaleAttrs`.
@@ -119,5 +119,5 @@ class GroupAttrs(multiscales.GroupAttrs):
     image_label: Annotated[ImageLabel, Field(..., serialization_alias="image-label")]
 
 
-class Group(multiscales.Group):
+class Group(multiscale.Group):
     attributes: GroupAttrs
diff --git a/src/pydantic_ome_ngff/v04/multiscales.py b/src/pydantic_ome_ngff/v04/multiscale.py
similarity index 99%
rename from src/pydantic_ome_ngff/v04/multiscales.py
rename to src/pydantic_ome_ngff/v04/multiscale.py
index f6b8761..f6bead9 100644
--- a/src/pydantic_ome_ngff/v04/multiscales.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -16,7 +16,7 @@
 from pydantic_ome_ngff.base import StrictBase, StrictVersionedBase
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
-import pydantic_ome_ngff.v04.transforms as tx
+import pydantic_ome_ngff.v04.transform as tx
 import zarr
 from zarr.errors import ArrayNotFoundError, ContainsGroupError
 
@@ -76,7 +76,6 @@ class Dataset(StrictBase):
         The path to the Zarr array that stores the image described by this metadata. This path should be relative to the group that contains this metadata.
     coordinateTransformations: ctx.ScaleTransform | ctx.TranslationTransform
         The coordinate transformations for this image.
-
     """
 
     path: str
diff --git a/src/pydantic_ome_ngff/v04/transforms.py b/src/pydantic_ome_ngff/v04/transform.py
similarity index 83%
rename from src/pydantic_ome_ngff/v04/transforms.py
rename to src/pydantic_ome_ngff/v04/transform.py
index cf8bc10..5a0858b 100644
--- a/src/pydantic_ome_ngff/v04/transforms.py
+++ b/src/pydantic_ome_ngff/v04/transform.py
@@ -1,11 +1,12 @@
 from __future__ import annotations
 
-from typing import Annotated, Any, Literal, Sequence
+from typing import Annotated, Literal, Sequence
 
 from pydantic import BeforeValidator
 
 from pydantic_ome_ngff.base import StrictBase
-import numpy as np
+
+from pydantic_ome_ngff.utils import listify_numpy
 
 
 class Identity(StrictBase):
@@ -107,39 +108,32 @@ def ndim(
     if hasattr(transform, "scale"):
         return len(transform.scale)
 
-    if hasattr(transform, "translation"):
+    else:
         return len(transform.translation)
 
-    msg = (
-        "Transform must be either `VectorScaleTransform` or `VectorTranslationTransform`."
-        f"Got {type(transform)} instead."
-    )
-    raise ValueError(msg)
-
 
 def scale_translation(
-    scale: Sequence[float], translation: Sequence[float] | None
-) -> tuple[Scale] | tuple[Scale, Translation]:
+    scale: Sequence[float], translation: Sequence[float]
+) -> tuple[Scale, Translation]:
     """
-    Create a `VectorScale` and, optionally, a `VectorTranslation` from a scale and a translation
+    Create a `VectorScale` and a `VectorTranslation` from a scale and a translation
     parameter.
     """
+
     len_scale = len(scale)
+    len_translation = len(translation)
 
     if len_scale < 1:
         msg = "Not enough values in scale. Got 0, expected at least 1."
         raise ValueError(msg)
 
-    vec_scale = VectorScale(scale=scale)
-
-    if translation is None:
-        return (vec_scale,)
-
-    len_translation = len(translation)
     if len_translation < 1:
-        msg = "Not enough values in `translation`. Got 0, expected at least 1."
+        msg = "Not enough values in translation. Got 0, expected at least 1."
         raise ValueError(msg)
-    if len_translation != len_scale:
+
+    vec_scale = VectorScale(scale=scale)
+
+    if len(translation) != len_scale:
         msg = (
             f"Length of `scale` and `translation` do not match. `scale` has length = {len_scale}"
             f"but `translation` has length = {len_translation}"
@@ -171,13 +165,3 @@ def ensure_dimensionality(
         )
         raise ValueError(msg)
     return transforms
-
-
-def listify_numpy(data: Any) -> Any:
-    """
-    If the input is a numpy array, turn it into a list and return it.
-    Otherwise return the input unchanged.
-    """
-    if isinstance(data, np.ndarray):
-        return data.tolist()
-    return data
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index c900962..7605ddf 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -6,7 +6,7 @@
 
 from pydantic_ome_ngff.base import VersionedBase
 from pydantic_ome_ngff.v04.base import version
-import pydantic_ome_ngff.v04.multiscales as multiscales
+import pydantic_ome_ngff.v04.multiscale as multiscale
 
 
 class Image(BaseModel):
@@ -29,7 +29,7 @@ class GroupAttrs(BaseModel):
     well: WellMetadata
 
 
-class Group(GroupSpec[GroupAttrs, Union[multiscales.Group, GroupSpec, ArraySpec]]):
+class Group(GroupSpec[GroupAttrs, Union[multiscale.Group, GroupSpec, ArraySpec]]):
     @field_validator("members", mode="after")
     @classmethod
     def contains_multiscale_group(
@@ -38,6 +38,6 @@ def contains_multiscale_group(
         """
         Check that .members contains a MultiscaleGroup
         """
-        if not any(map(lambda v: isinstance(v, multiscales.Group), members.values())):
+        if not any(map(lambda v: isinstance(v, multiscale.Group), members.values())):
             raise ValidationError
         return members
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index 212b25d..ea40d95 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -6,14 +6,14 @@
 from pydantic_zarr.v2 import ArraySpec
 
 from pydantic_ome_ngff.latest.axis import Axis
-from pydantic_ome_ngff.latest.multiscales import (
+from pydantic_ome_ngff.latest.multiscale import (
     MultiscaleMetadata,
     GroupAttrs,
     Dataset,
     Group,
 )
 
-from pydantic_ome_ngff.latest.transforms import (
+from pydantic_ome_ngff.latest.transform import (
     Transform,
     VectorScale,
     VectorTranslation,
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 4672071..8ae66fd 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,10 +1,12 @@
 from __future__ import annotations
 from typing import TYPE_CHECKING
 
+import numpy as np
+
 if TYPE_CHECKING:
     from typing import Any, List
 
-from pydantic_ome_ngff.utils import duplicates
+from pydantic_ome_ngff.utils import duplicates, listify_numpy
 import pytest
 
 
@@ -16,3 +18,12 @@ def test_duplicates(data: List[Any]) -> None:
     for key, value in dupes.items():
         assert data.count(key) == value
         assert value > 1
+
+
+@pytest.mark.parametrize("data", [np.arange(100), "100", np.dtype("int"), (0, 1, 2, 3)])
+def test_listify_numpy(data) -> None:
+    observed = listify_numpy(data)
+    if isinstance(data, np.ndarray):
+        assert observed == data.tolist()
+    else:
+        assert observed == data
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 21978c7..6a0beb8 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -4,14 +4,14 @@
 import pytest
 import jsonschema as jsc
 from pydantic_zarr.v2 import ArraySpec
-from pydantic_ome_ngff.v04.multiscales import (
+from pydantic_ome_ngff.v04.multiscale import (
     MultiscaleMetadata,
     GroupAttrs,
     Dataset,
     Group,
 )
 
-from pydantic_ome_ngff.v04.transforms import (
+from pydantic_ome_ngff.v04.transform import (
     Transform,
     VectorScale,
     VectorTranslation,
diff --git a/tests/v04/test_transform.py b/tests/v04/test_transform.py
new file mode 100644
index 0000000..95619ab
--- /dev/null
+++ b/tests/v04/test_transform.py
@@ -0,0 +1,64 @@
+from typing import Sequence, Tuple
+import pytest
+from pydantic_ome_ngff.v04.transform import (
+    VectorScale,
+    VectorTranslation,
+    ensure_dimensionality,
+    ndim,
+    scale_translation,
+)
+
+
+@pytest.mark.parametrize(
+    "scale, translation",
+    (
+        [(0,), (0,)],
+        [(1, 1), (0, 0)],
+        [(1,), (0, 0)],
+        [(), (10,)],
+        [(10,), ()],
+    ),
+)
+def test_scale_translation(
+    scale: Tuple[int, ...], translation: Tuple[int, ...]
+) -> None:
+    if len(scale) == len(translation):
+        result = scale_translation(scale=scale, translation=translation)
+        assert isinstance(result[0], VectorScale)
+        assert isinstance(result[1], VectorTranslation)
+        assert result[0].scale == scale
+        assert result[1].translation == translation
+    else:
+        if len(scale) == 0:
+            match = "Not enough values in scale. Got 0, expected at least 1."
+        elif len(translation) == 0:
+            match = "Not enough values in translation. Got 0, expected at least 1."
+        else:
+            match = (
+                f"Length of `scale` and `translation` do not match. `scale` has length = {len(scale)}"
+                f"but `translation` has length = {len(translation)}"
+            )
+        with pytest.raises(ValueError, match=match):
+            scale_translation(scale, translation)
+
+
+@pytest.mark.parametrize(
+    "data",
+    [
+        (VectorScale(scale=(10, 10)), VectorTranslation(translation=(1,))),
+        (VectorScale(scale=(10,)), VectorTranslation(translation=(1, 1))),
+    ],
+)
+def test_ensure_dimensionality(data: Sequence[VectorScale | VectorTranslation]) -> None:
+    with pytest.raises(
+        ValueError, match="The transforms have inconsistent dimensionality."
+    ):
+        ensure_dimensionality(data)
+
+
+def test_ndim() -> None:
+    tx = VectorScale(scale=(1, 1, 1))
+    assert ndim(tx) == 3
+
+    tx = VectorTranslation(translation=(1, 1, 1))
+    assert ndim(tx) == 3

From 7a28df76b8e24bd8537b04002a2ae4f3396447ac Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 12 Mar 2024 12:12:55 +0100
Subject: [PATCH 49/69] docs: update docs

---
 docs/api/v04/transform.md  | 1 +
 docs/api/v04/transforms.md | 1 -
 docs/index.md              | 9 +++------
 mkdocs.yml                 | 2 +-
 4 files changed, 5 insertions(+), 8 deletions(-)
 create mode 100644 docs/api/v04/transform.md
 delete mode 100644 docs/api/v04/transforms.md

diff --git a/docs/api/v04/transform.md b/docs/api/v04/transform.md
new file mode 100644
index 0000000..5aa4b1e
--- /dev/null
+++ b/docs/api/v04/transform.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.transform
\ No newline at end of file
diff --git a/docs/api/v04/transforms.md b/docs/api/v04/transforms.md
deleted file mode 100644
index 8a9a01f..0000000
--- a/docs/api/v04/transforms.md
+++ /dev/null
@@ -1 +0,0 @@
-::: pydantic_ome_ngff.v04.transforms
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 3fa5a08..47fb187 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -10,10 +10,10 @@ This library aims to provide models for the the metadata objects and Zarr hierar
 
 ## Reading Multiscale metadata
 
-This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscales` to model a multiscale group.
+This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscale` to model a multiscale group.
 
 ```python
-from pydantic_ome_ngff.v04.multiscales import Group
+from pydantic_ome_ngff.v04.multiscale import Group
 import zarr
 # example data served over http
 url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
@@ -103,7 +103,7 @@ print(arrays)
 `pydantic-ome-ngff` provides simple way to create multiscale metadata from a collection of arrays accompanied by spatial metadata.
 
 ```python
-from pydantic_ome_ngff.v04.multiscales import Group
+from pydantic_ome_ngff.v04.multiscale import Group
 from pydantic_ome_ngff.v04.axis import Axis
 import numpy as np
 import zarr
@@ -276,7 +276,4 @@ print(stored_group.attrs.asdict())
     ]
 }
 """
-
-
-
 ```
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index a358917..acf3ac5 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -34,7 +34,7 @@ nav:
       - v04:
         - api/v04/multiscales.md
         - api/v04/axis.md
-        - api/v04/transforms.md
+        - api/v04/transform.md
 
 plugins:
 - mkdocstrings:

From 0214f6562a1634c3ce6eae7bbc566e596ce08414 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 12 Mar 2024 14:22:27 +0100
Subject: [PATCH 50/69] docs: more docs

---
 README.md                   |  3 ---
 docs/api/v04/multiscale.md  |  1 +
 docs/api/v04/multiscales.md |  1 -
 docs/index.md               | 51 ++++++++++++++++++++++++++++---------
 mkdocs.yml                  |  8 +++---
 5 files changed, 45 insertions(+), 19 deletions(-)
 create mode 100644 docs/api/v04/multiscale.md
 delete mode 100644 docs/api/v04/multiscales.md

diff --git a/README.md b/README.md
index 7b01b8f..f103641 100644
--- a/README.md
+++ b/README.md
@@ -14,9 +14,6 @@ supported metadata models:
 `omero` and `bioformats2raw` are not currently supported, but contributions adding
 support for those models would be welcome.
 
-Support for container-level validation (i.e., checking that multiscale or coordinate 
-transformation metadata is compatible with a hierarchical array / group layout) is being added incrementally. 
-
 ## installation
 
 ```bash
diff --git a/docs/api/v04/multiscale.md b/docs/api/v04/multiscale.md
new file mode 100644
index 0000000..f8bf791
--- /dev/null
+++ b/docs/api/v04/multiscale.md
@@ -0,0 +1 @@
+::: pydantic_ome_ngff.v04.multiscale
\ No newline at end of file
diff --git a/docs/api/v04/multiscales.md b/docs/api/v04/multiscales.md
deleted file mode 100644
index f520758..0000000
--- a/docs/api/v04/multiscales.md
+++ /dev/null
@@ -1 +0,0 @@
-::: pydantic_ome_ngff.v04.multiscales
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 47fb187..f7f4c4e 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -4,13 +4,33 @@
 
 # About
 
-This library aims to provide models for the the metadata objects and Zarr hierarchies described in the [OME-NGFF](https://ngff.openmicroscopy.org/) specifications.
+This library aims to model the metadata objects and Zarr hierarchies described in the [OME-NGFF](https://ngff.openmicroscopy.org/) specifications, with an emphasis on the core multiscale metadata. 
+
+You can use this library to:
+
+- Read existing OME-NGFF data
+- Create your own OME-NGFF data  
+
+See the [reading](#reading-a-multiscale-group) and [writing](#creating-a-multiscale-group) examples for basic usage. 
+
+The base Pydantic models for Zarr groups and arrays used in this library are defined in [`pydantic-zarr`](https://janelia-cellmap.github.io/pydantic-zarr/)
+
+## Limitations
+
+### Supported versions
+
+Version 0.4 of OME-NGFF has pretty extensive support, although my focus has been on getting the `Multiscales` metadata right; I don't use `well` or `plate` metadata, so it's likely that I have missed something there. I have not put a lot of effort into supporting `0.5-dev`, as it's not clear when that version will be released, or even what will be in it, but contributions to rectify this are welcome. 
+
+### Array data
+
+This library only models the *structure* of a Zarr hierarchy, i.e. the layout of Zarr groups and arrays, and their metadata; it provides no functionality for efficiently reading or writing large Zarr arrays. Consider [`tensorstore`](https://google.github.io/tensorstore/) or [`dask`](https://www.dask.org/) for this purpose.
+
 
 # Examples
 
-## Reading Multiscale metadata
+## Reading a Multiscale group
 
-This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscale` to model a multiscale group.
+This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscale` to model an existing multiscale group.
 
 ```python
 from pydantic_ome_ngff.v04.multiscale import Group
@@ -98,9 +118,15 @@ print(arrays)
 """
 ```
 
-## Creating multiscale metadata
+## Creating a multiscale group
+
+`pydantic-ome-ngff` provides simple way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. 
+
+The basic workflow is as follows:
 
-`pydantic-ome-ngff` provides simple way to create multiscale metadata from a collection of arrays accompanied by spatial metadata.
+ 1. Use in-memory numpy or dask arrays and spatial metadata to instantiate a model of the OME-NGFF multiscale Zarr group we want to create. This model contains attributes and models of Zarr arrays, but no array data (which keeps the model lightweight). 
+ 2. Serialize the model to a storage backend, which will create the Zarr groups and arrays defined by the model, along with their metadata. 
+3. Write array data to the newly created Zarr arrays, using a method that suits your application. 
 
 ```python
 from pydantic_ome_ngff.v04.multiscale import Group
@@ -128,13 +154,13 @@ arrays = [np.zeros(s) for s in shapes]
 # arrays will be named s0, s1, etc
 paths = [f's{idx}' for idx in range(len(shapes))]
 
-# regular 2x downsampling
+# downsampling by 2 in each axis
 scales = [
     [1.0, 2.0, 2.0, 2.0],
     [2.0, 4.0, 4.0, 4.0],
 ]
 
-# translation introduced by 2x downsampling
+# s0 is at the origin; s1 is at the offset induced by downsampling
 translations = [
     [0.0, 0.0, 0.0, 0.0],
     [0.5, 1.0, 1.0, 1.0]
@@ -221,17 +247,14 @@ print(group_model.model_dump())
 }
 """
 
-# to actually do something useful with this model, we have to serialize it to storage
-
-# make an in-memory zarr store for demo purposes
+# to do something useful with this model, we have to serialize it to storage
+# we make an in-memory zarr store for demo purposes
 # with real data, you would use `zarr.storage.DirectoryStore` or `zarr.storage.FSStore`
 store = zarr.MemoryStore()
 path = 'foo'
 stored_group = group_model.to_zarr(store, path='foo')
 
 # check that the expected arrays are present
-# no data has been written to these arrays, you must do that separately.
-# e.g., stored_group[s0] = arrays[0]
 print(stored_group.tree())
 """
 foo
@@ -239,6 +262,10 @@ foo
  └── s1 (5, 5, 5, 5) float64
 """
 
+# NOTE:
+# no data has been written to these arrays, you must do that separately.
+# e.g., stored_group[s0] = arrays[0]
+
 # check that the expected attributes are present
 print(stored_group.attrs.asdict())
 """
diff --git a/mkdocs.yml b/mkdocs.yml
index acf3ac5..3b3dd04 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -5,8 +5,8 @@ site_description: >-
   Pydantic models for the OME-NGFF file format.
 
 # Repository
-repo_name: janeliascicomp/pydantic-ome-ngff
-repo_url: https://github.com/janeliascicomp/pydantic-zarr
+repo_name: janelia-cellmap/pydantic-ome-ngff
+repo_url: https://github.com/janeliascicomp/pydantic-ome-ngff
 
 # Copyright
 copyright: Copyright &copy; 2016 - 2023 HHMI / Janelia
@@ -32,9 +32,11 @@ nav:
     - About: index.md
     - API:
       - v04:
-        - api/v04/multiscales.md
+        - api/v04/multiscale.md
         - api/v04/axis.md
         - api/v04/transform.md
+        - api/v04/label.md
+        - api/v04/plate.md
 
 plugins:
 - mkdocstrings:

From 8d0e640f9557251fbdf9b1cd5b112835c7f098f0 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Tue, 12 Mar 2024 14:29:31 +0100
Subject: [PATCH 51/69] test: remove unnecessary transform validation logic

---
 src/pydantic_ome_ngff/v04/multiscale.py | 104 ++++++++++++------------
 src/pydantic_ome_ngff/v04/transform.py  |  14 +++-
 tests/latest/test_multiscales.py        |  14 ++--
 tests/v04/test_multiscales.py           |  30 ++++---
 4 files changed, 89 insertions(+), 73 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index f6bead9..fc6fbad 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -86,17 +86,32 @@ class Dataset(StrictBase):
     ]
 
 
+# consider making this a classmethod of `Dataset`
 def create_dataset(
     path: str, scale: Sequence[int | float], translation: Sequence[int | float]
 ) -> Dataset:
     """
-    Create a `Dataset` from a path, a scale, and a translation.
+    Create a `Dataset` from a path, a scale, and a translation. This metadata models a Zarr array that partially comprises a multiscale group.
+
+    Parameters
+    ----------
+
+    path: str
+        The path, relative to the multiscale group, of the Zarr array.
+    scale: Sequence[int | float]:
+        The scale parameter for data stored in the Zarr array. This should define the spacing between elements of the coordinate grid of the data.
+    translate: Sequence[int | float]:
+        The translation parameter for data stored in the Zarr array. This should define the origin of the coordinate grid of the data.
+
+    Returns
+    -------
+
+    `Dataset`
     """
     return Dataset(
         path=path,
         coordinateTransformations=(
-            tx.VectorScale(scale=scale),
-            tx.VectorTranslation(translation=translation),
+            tx.scale_translation(scale=scale, translation=translation)
         ),
     )
 
@@ -173,7 +188,7 @@ class MultiscaleMetadata(StrictVersionedBase):
         The type of the multiscale image. Optional. Defaults to `None`.
     metadata: Dict[str, Any] | None
         Metadata for this multiscale image. Optional. Defaults to `None`.
-    datasets: List[MultiscaleDataset]
+    datasets: List[Dataset]
         A collection of descriptions of arrays that collectively comprise this multiscale image.
     axes: List[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
@@ -223,8 +238,8 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     Attributes
     ----------
 
-    attributes: MultiscaleAttrs
-        The attributes of this Zarr group, which should contain valid `MultiscaleAttrs`.
+    attributes: GroupAttrs
+        The attributes of this Zarr group, which should contain valid `GroupAttrs`.
     members Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
@@ -233,11 +248,10 @@ class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
     @classmethod
     def from_zarr(cls, node: zarr.Group) -> Group:
         """
-        Create an instance of `Group` from a `node`, a `zarr.Group`. This method infers the
-        discovers Zarr arrays in the hierarchy rooted at `node` by inspecting the OME-NGFF
+        Create an instance of `Group` from a `node`, a `zarr.Group`. This method discovers Zarr arrays in the hierarchy rooted at `node` by inspecting the OME-NGFF
         multiscales metadata.
 
-        Paramters
+        Parameters
         ---------
         node: zarr.Group
             A Zarr group that has valid OME-NGFF multiscale metadata.
@@ -245,7 +259,7 @@ def from_zarr(cls, node: zarr.Group) -> Group:
         Returns
         -------
         Group
-            A model of the zarr Group.
+            A model of the Zarr group.
         """
         # on unlistable storage backends, the members of this group will be {}
         guess = GroupSpec.from_zarr(node)
@@ -305,6 +319,8 @@ def from_arrays(
         """
         Create a `Group` from a sequence of multiscale arrays and spatial metadata.
 
+        The arrays are used as templates for corresponding `ArraySpec` instances, which model the Zarr arrays that would be created if the `Group` was stored.
+
         Parameters
         ----------
         paths: Sequence[str]
@@ -313,7 +329,8 @@ def from_arrays(
             `Axis` objects describing the dimensions of the arrays.
         arrays: Sequence[ArrayLike] | Sequence[ChunkedArrayLike]
             A sequence of array-like objects that collectively represent the same image
-            at multiple levels of detail.
+            at multiple levels of detail. The attributes of these arrays are used to create `ArraySpec` objects
+            that model Zarr arrays stored in the Zarr group.
         scales: Sequence[Sequence[int | float]]
             A scale value for each axis of the array, for each array in `arrays`.
         translations: Sequence[Sequence[int | float]]
@@ -352,9 +369,6 @@ def from_arrays(
     def check_arrays_exist(self) -> "Group":
         """
         Check that the arrays referenced in the `multiscales` metadata are actually contained in this group.
-
-        Note that this is currently too strict, since it will not check for arrays in subgroups, but this is
-        allowed by the spec. Adding tree-flattening here or in pydantic-zarr can fix this.
         """
         attrs = self.attributes
         flattened = self.to_flat()
@@ -381,53 +395,37 @@ def check_arrays_exist(self) -> "Group":
     @model_validator(mode="after")
     def check_array_ndim(self) -> "Group":
         """
-        Check that all the arrays referenced by the `multiscales` metadata have the same
-        dimensionality, and that this dimensionality is consistent with the
+        Check that all the arrays referenced by the `multiscales` metadata have dimensionality consistent with the
         `coordinateTransformations` metadata.
         """
         multimeta = self.attributes.multiscales
 
         flat_self = self.to_flat()
-        ndims = []
-        # get shapes from all the arrays referenced in `multiscales`
-        for multiscale in multimeta:
-            for dataset in multiscale.datasets:
-                node = flat_self["/" + dataset.path.lstrip("/")]
-                if isinstance(node, ArraySpec):
-                    ndims.append(len(flat_self["/" + dataset.path.lstrip("/")].shape))
-                else:
-                    msg = (
-                        f"Expected an instance of ArraySpec at {dataset.path}, "
-                        f"got {type(node)} instead"
-                    )
-                    raise TypeError(msg)
-
-        if len(set(ndims)) > 1:
-            msg = (
-                "All arrays must have the same dimensionality. "
-                f"Got arrays with dimensionality {ndims}."
-            )
-            raise ValueError(msg)
 
         # check that each transform has compatible rank
         for multiscale in multimeta:
-            tforms = []
-            if multiscale.coordinateTransformations is not None:
-                tforms.extend(multiscale.coordinateTransformations)
             for dataset in multiscale.datasets:
-                tforms.extend(dataset.coordinateTransformations)
-            for tform in tforms:
-                if hasattr(tform, "scale") or hasattr(tform, "translation"):
-                    tform = cast(
-                        Union[tx.VectorScale, tx.VectorTranslation],
-                        tform,
-                    )
-                    if (tform_dims := tx.ndim(tform)) not in set(ndims):
-                        msg = (
-                            f"Transform {tform} has dimensionality {tform_dims} "
-                            "which does not match the dimensionality of the arrays "
-                            f"in this group ({ndims}). Transform dimensionality "
-                            "must match array dimensionality."
+                arr: ArraySpec = flat_self["/" + dataset.path.lstrip("/")]
+                arr_ndim = len(arr.shape)
+                tforms = dataset.coordinateTransformations
+
+                if multiscale.coordinateTransformations is not None:
+                    tforms += multiscale.coordinateTransformations
+
+                for tform in tforms:
+                    if hasattr(tform, "scale") or hasattr(tform, "translation"):
+                        tform = cast(
+                            Union[tx.VectorScale, tx.VectorTranslation],
+                            tform,
                         )
-                        raise ValueError(msg)
+                        if (tform_ndim := tx.ndim(tform)) != arr_ndim:
+                            msg = (
+                                f"Transform {tform} has dimensionality {tform_ndim}, "
+                                "which does not match the dimensionality of the array "
+                                f"found in this group at {dataset.path} ({arr_ndim}). "
+                                "Transform dimensionality must match array dimensionality."
+                            )
+
+                            raise ValueError(msg)
+
         return self
diff --git a/src/pydantic_ome_ngff/v04/transform.py b/src/pydantic_ome_ngff/v04/transform.py
index 5a0858b..f07d807 100644
--- a/src/pydantic_ome_ngff/v04/transform.py
+++ b/src/pydantic_ome_ngff/v04/transform.py
@@ -6,7 +6,7 @@
 
 from pydantic_ome_ngff.base import StrictBase
 
-from pydantic_ome_ngff.utils import listify_numpy
+from pydantic_ome_ngff.utils import ArrayLike, listify_numpy
 
 
 class Identity(StrictBase):
@@ -165,3 +165,15 @@ def ensure_dimensionality(
         )
         raise ValueError(msg)
     return transforms
+
+
+def array_transform_consistency(
+    array: ArrayLike, transforms: Sequence[VectorScale, VectorTranslation]
+) -> bool:
+    """
+    Check if an array is consistent, in terms of dimensionality, with a collection of transforms.
+    """
+    # check that the transforms are themselves consistent
+    transforms_checked = ensure_dimensionality(transforms=transforms)
+    # we only need to compare the array to the first transform
+    return len(array.shape) == ndim(transforms_checked[0])
diff --git a/tests/latest/test_multiscales.py b/tests/latest/test_multiscales.py
index ea40d95..2d9ad04 100644
--- a/tests/latest/test_multiscales.py
+++ b/tests/latest/test_multiscales.py
@@ -329,26 +329,28 @@ def test_multiscale_group_datasets_rank(multi_meta: MultiscaleMetadata) -> None:
     }
     Group(attributes=group_attrs, members=good_items)
 
+    match = "Transform dimensionality must match array dimensionality."
     # arrays with varying rank
     bad_items = {
         d.path: ArraySpec(
             shape=(1,) * (idx + 1),
             dtype="uint8",
             chunks=(1,) * (idx + 1),
-            attributes={},
         )
         for idx, d in enumerate(multi_meta.datasets)
     }
 
-    with pytest.raises(
-        ValidationError, match="All arrays must have the same dimensionality."
-    ):
+    with pytest.raises(ValidationError, match=match):
         Group(attributes=group_attrs, members=bad_items)
 
-    with pytest.raises(ValidationError, match="Transform dimensionality"):
+    with pytest.raises(ValidationError, match=match):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
+            d.path: ArraySpec(
+                shape=(1,),
+                dtype="uint8",
+                chunks=(1,),
+            )
             for d in multi_meta.datasets
         }
         Group(attributes=group_attrs, members=bad_items)
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 6a0beb8..d7239b4 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -298,7 +298,9 @@ def test_multiscale_group_datasets_exist(
     group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1, 1, 1, 1),
+            dtype="uint8",
+            chunks=(1, 1, 1, 1),
         )
         for d in default_multiscale.datasets
     }
@@ -306,7 +308,9 @@ def test_multiscale_group_datasets_exist(
 
     bad_items = {
         d.path + "x": ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1, 1, 1, 1),
+            dtype="uint8",
+            chunks=(1, 1, 1, 1),
         )
         for d in default_multiscale.datasets
     }
@@ -317,7 +321,9 @@ def test_multiscale_group_datasets_exist(
     ):
         bad_items = {
             d.path + "x": ArraySpec(
-                shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+                shape=(1, 1, 1, 1),
+                dtype="uint8",
+                chunks=(1, 1, 1, 1),
             )
             for d in default_multiscale.datasets
         }
@@ -328,7 +334,9 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
     group_attrs = GroupAttrs(multiscales=[default_multiscale])
     good_items = {
         d.path: ArraySpec(
-            shape=(1, 1, 1, 1), dtype="uint8", chunks=(1, 1, 1, 1), attributes={}
+            shape=(1, 1, 1, 1),
+            dtype="uint8",
+            chunks=(1, 1, 1, 1),
         )
         for d in default_multiscale.datasets
     }
@@ -340,21 +348,17 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
             shape=(1,) * (idx + 1),
             dtype="uint8",
             chunks=(1,) * (idx + 1),
-            attributes={},
         )
         for idx, d in enumerate(default_multiscale.datasets)
     }
-
-    with pytest.raises(
-        ValidationError, match="All arrays must have the same dimensionality."
-    ):
+    match = "Transform dimensionality must match array dimensionality."
+    with pytest.raises(ValidationError, match=match):
         # arrays with varying rank
         bad_items = {
             d.path: ArraySpec(
                 shape=(1,) * (idx + 1),
                 dtype="uint8",
                 chunks=(1,) * (idx + 1),
-                attributes={},
             )
             for idx, d in enumerate(default_multiscale.datasets)
         }
@@ -362,13 +366,13 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
 
     # arrays with rank that doesn't match the transform
     bad_items = {
-        d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
+        d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,))
         for d in default_multiscale.datasets
     }
-    with pytest.raises(ValidationError, match="Transform dimensionality"):
+    with pytest.raises(ValidationError, match=match):
         # arrays with rank that doesn't match the transform
         bad_items = {
-            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,), attributes={})
+            d.path: ArraySpec(shape=(1,), dtype="uint8", chunks=(1,))
             for d in default_multiscale.datasets
         }
         Group(attributes=group_attrs, members=bad_items)

From cb86c5d66f75d8f82aaa83777679884d246ce46f Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:28:56 +0100
Subject: [PATCH 52/69] docs: add links, remove unused var from examples

---
 docs/index.md | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index f7f4c4e..82a1229 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -19,18 +19,17 @@ The base Pydantic models for Zarr groups and arrays used in this library are def
 
 ### Supported versions
 
-Version 0.4 of OME-NGFF has pretty extensive support, although my focus has been on getting the `Multiscales` metadata right; I don't use `well` or `plate` metadata, so it's likely that I have missed something there. I have not put a lot of effort into supporting `0.5-dev`, as it's not clear when that version will be released, or even what will be in it, but contributions to rectify this are welcome. 
+Version 0.4 of OME-NGFF has pretty extensive support, although my focus has been on getting the `Multiscales` metadata right; I don't use `well` or `plate` metadata, so it's highly likely that I have missed something there. I have not put a lot of effort into supporting `0.5-dev`, as it's not clear when that version will be released, or even what will be in it, but contributions to rectify this are welcome. If you find something that I didn't implement correctly, please [open an issue](https://github.com/JaneliaSciComp/pydantic-ome-ngff/issues).
 
 ### Array data
 
-This library only models the *structure* of a Zarr hierarchy, i.e. the layout of Zarr groups and arrays, and their metadata; it provides no functionality for efficiently reading or writing large Zarr arrays. Consider [`tensorstore`](https://google.github.io/tensorstore/) or [`dask`](https://www.dask.org/) for this purpose.
-
+This library only models the *structure* of a Zarr hierarchy, i.e. the layout of Zarr groups and arrays, and their metadata; it provides no functionality for efficiently reading or writing data from Zarr arrays. Use [`zarr-python`](https://github.com/zarr-developers/zarr-python) or [`tensorstore`](https://google.github.io/tensorstore/) for getting data in and out of Zarr arrays.
 
 # Examples
 
 ## Reading a Multiscale group
 
-This example demonstrates how to use the `Group` class defined in `pydantic_ome_ngff.v04.multiscale` to model an existing multiscale group.
+This example demonstrates how to use the [`Group`](./api/v04/multiscale.md#Group) class defined in [`pydantic_ome_ngff.v04.multiscale`](./api/v04/multiscale.md) to model a multiscale group from cloud storage.
 
 ```python
 from pydantic_ome_ngff.v04.multiscale import Group
@@ -120,7 +119,7 @@ print(arrays)
 
 ## Creating a multiscale group
 
-`pydantic-ome-ngff` provides simple way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. 
+`pydantic-ome-ngff` provides a direct way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. Note that the data in these arrays will not be accessed -- the arrays are used to create models of Zarr arrays, and so their `shape` and `dtype` attributes are necessary.
 
 The basic workflow is as follows:
 
@@ -251,7 +250,6 @@ print(group_model.model_dump())
 # we make an in-memory zarr store for demo purposes
 # with real data, you would use `zarr.storage.DirectoryStore` or `zarr.storage.FSStore`
 store = zarr.MemoryStore()
-path = 'foo'
 stored_group = group_model.to_zarr(store, path='foo')
 
 # check that the expected arrays are present

From a3e4b4fe48d2ace6831f17f0c2ba00c3f908cb29 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:29:16 +0100
Subject: [PATCH 53/69] bump deps, using latest version of pydantic-zarr

---
 poetry.lock    | 269 ++++++++++++++++++++++++++-----------------------
 pyproject.toml |   2 +-
 2 files changed, 143 insertions(+), 128 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index dfb1fab..c7f35c2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "aiohttp"
@@ -177,33 +177,33 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "black"
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 [package.dependencies]
@@ -445,6 +445,20 @@ files = [
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 ]
 
+[[package]]
+name = "eval-type-backport"
+version = "0.1.3"
+description = "Like `typing._eval_type`, but lets older Python versions use newer typing features."
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.extras]
+tests = ["pytest"]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.0"
@@ -574,13 +588,13 @@ files = [
 
 [[package]]
 name = "fsspec"
-version = "2024.2.0"
+version = "2024.3.1"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -629,13 +643,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "0.41.3"
+version = "0.42.1"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -764,13 +778,13 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "markdown"
-version = "3.5.2"
+version = "3.6"
 description = "Python implementation of John Gruber's Markdown."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -944,13 +958,13 @@ mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.13"
+version = "9.5.14"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1364,13 +1378,13 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "pydantic"
-version = "2.6.3"
+version = "2.6.4"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1474,16 +1488,17 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pydantic-zarr"
-version = "0.6.1"
+version = "0.7.0"
 description = "pydantic models for zarr"
 optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = "<4.0,>=3.9"
 files = [
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 ]
 
 [package.dependencies]
+eval-type-backport = ">=0.1.3,<0.2.0"
 pydantic = ">=2.0.0,<3.0.0"
 typing-extensions = {version = ">=4.7.1,<5.0.0", markers = "python_version < \"3.12\""}
 zarr = ">=2.14.2,<3.0.0"
@@ -1666,13 +1681,13 @@ pyyaml = "*"
 
 [[package]]
 name = "referencing"
-version = "0.33.0"
+version = "0.34.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1930,44 +1945,44 @@ files = [
 
 [[package]]
 name = "ruff"
-version = "0.3.2"
+version = "0.3.3"
 description = "An extremely fast Python linter and code formatter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ruff-0.3.2-py3-none-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = "sha256:77f2612752e25f730da7421ca5e3147b213dca4f9a0f7e0b534e9562c5441f01"},
-    {file = "ruff-0.3.2-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:9966b964b2dd1107797be9ca7195002b874424d1d5472097701ae8f43eadef5d"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:b83d17ff166aa0659d1e1deaf9f2f14cbe387293a906de09bc4860717eb2e2da"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:bb875c6cc87b3703aeda85f01c9aebdce3d217aeaca3c2e52e38077383f7268a"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:be75e468a6a86426430373d81c041b7605137a28f7014a72d2fc749e47f572aa"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:967978ac2d4506255e2f52afe70dda023fc602b283e97685c8447d036863a302"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1231eacd4510f73222940727ac927bc5d07667a86b0cbe822024dd00343e77e9"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2c6d613b19e9a8021be2ee1d0e27710208d1603b56f47203d0abbde906929a9b"},
-    {file = "ruff-0.3.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c8439338a6303585d27b66b4626cbde89bb3e50fa3cae86ce52c1db7449330a7"},
-    {file = "ruff-0.3.2-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:de8b480d8379620cbb5ea466a9e53bb467d2fb07c7eca54a4aa8576483c35d36"},
-    {file = "ruff-0.3.2-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:b74c3de9103bd35df2bb05d8b2899bf2dbe4efda6474ea9681280648ec4d237d"},
-    {file = "ruff-0.3.2-py3-none-musllinux_1_2_i686.whl", hash = "sha256:f380be9fc15a99765c9cf316b40b9da1f6ad2ab9639e551703e581a5e6da6745"},
-    {file = "ruff-0.3.2-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:0ac06a3759c3ab9ef86bbeca665d31ad3aa9a4b1c17684aadb7e61c10baa0df4"},
-    {file = "ruff-0.3.2-py3-none-win32.whl", hash = "sha256:9bd640a8f7dd07a0b6901fcebccedadeb1a705a50350fb86b4003b805c81385a"},
-    {file = "ruff-0.3.2-py3-none-win_amd64.whl", hash = "sha256:0c1bdd9920cab5707c26c8b3bf33a064a4ca7842d91a99ec0634fec68f9f4037"},
-    {file = "ruff-0.3.2-py3-none-win_arm64.whl", hash = "sha256:5f65103b1d76e0d600cabd577b04179ff592064eaa451a70a81085930e907d0b"},
-    {file = "ruff-0.3.2.tar.gz", hash = "sha256:fa78ec9418eb1ca3db392811df3376b46471ae93792a81af2d1cbb0e5dcb5142"},
+    {file = "ruff-0.3.3-py3-none-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = "sha256:973a0e388b7bc2e9148c7f9be8b8c6ae7471b9be37e1cc732f8f44a6f6d7720d"},
+    {file = "ruff-0.3.3-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:cfa60d23269d6e2031129b053fdb4e5a7b0637fc6c9c0586737b962b2f834493"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1eca7ff7a47043cf6ce5c7f45f603b09121a7cc047447744b029d1b719278eb5"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:e7d3f6762217c1da954de24b4a1a70515630d29f71e268ec5000afe81377642d"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:b24c19e8598916d9c6f5a5437671f55ee93c212a2c4c569605dc3842b6820386"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:5a6cbf216b69c7090f0fe4669501a27326c34e119068c1494f35aaf4cc683778"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:352e95ead6964974b234e16ba8a66dad102ec7bf8ac064a23f95371d8b198aab"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:8d6ab88c81c4040a817aa432484e838aaddf8bfd7ca70e4e615482757acb64f8"},
+    {file = "ruff-0.3.3-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:79bca3a03a759cc773fca69e0bdeac8abd1c13c31b798d5bb3c9da4a03144a9f"},
+    {file = "ruff-0.3.3-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:2700a804d5336bcffe063fd789ca2c7b02b552d2e323a336700abb8ae9e6a3f8"},
+    {file = "ruff-0.3.3-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:fd66469f1a18fdb9d32e22b79f486223052ddf057dc56dea0caaf1a47bdfaf4e"},
+    {file = "ruff-0.3.3-py3-none-musllinux_1_2_i686.whl", hash = "sha256:45817af234605525cdf6317005923bf532514e1ea3d9270acf61ca2440691376"},
+    {file = "ruff-0.3.3-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:0da458989ce0159555ef224d5b7c24d3d2e4bf4c300b85467b08c3261c6bc6a8"},
+    {file = "ruff-0.3.3-py3-none-win32.whl", hash = "sha256:f2831ec6a580a97f1ea82ea1eda0401c3cdf512cf2045fa3c85e8ef109e87de0"},
+    {file = "ruff-0.3.3-py3-none-win_amd64.whl", hash = "sha256:be90bcae57c24d9f9d023b12d627e958eb55f595428bafcb7fec0791ad25ddfc"},
+    {file = "ruff-0.3.3-py3-none-win_arm64.whl", hash = "sha256:0171aab5fecdc54383993389710a3d1227f2da124d76a2784a7098e818f92d61"},
+    {file = "ruff-0.3.3.tar.gz", hash = "sha256:38671be06f57a2f8aba957d9f701ea889aa5736be806f18c0cd03d6ff0cbca8d"},
 ]
 
 [[package]]
 name = "setuptools"
-version = "69.1.1"
+version = "69.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-69.1.1-py3-none-any.whl", hash = "sha256:02fa291a0471b3a18b2b2481ed902af520c69e8ae0919c13da936542754b4c56"},
-    {file = "setuptools-69.1.1.tar.gz", hash = "sha256:5c0806c7d9af348e6dd3777b4f4dbb42c7ad85b190104837488eab9a7c945cf8"},
+    {file = "setuptools-69.2.0-py3-none-any.whl", hash = "sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c"},
+    {file = "setuptools-69.2.0.tar.gz", hash = "sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
@@ -2207,20 +2222,20 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "8339793aab56453a96e746e6928015ed41de0f0e73e6c2ef7061f8db12a7a33d"
+content-hash = "dc936c7cf7eeb3a697c4638769c15a46060153aa495c72138291531330ee3566"
diff --git a/pyproject.toml b/pyproject.toml
index 8b3d0ad..b241c32 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ packages = [{include = "pydantic_ome_ngff", from="src"}]
 
 [tool.poetry.dependencies]
 python = "^3.9"
-pydantic-zarr = "0.6.1"
+pydantic-zarr = "0.7.0"
 rich = "^13.6.0"
 
 [tool.poetry.group.dev.dependencies]

From 2923fdd3fe0b04316147450b998c3a223a5cac37 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:35:28 +0100
Subject: [PATCH 54/69] add chunks keyword argument to from_arrays, and
 corresponding normalization function

---
 src/pydantic_ome_ngff/v04/multiscale.py | 55 ++++++++++++++++++++++---
 1 file changed, 49 insertions(+), 6 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index fc6fbad..c4211d0 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -1,6 +1,8 @@
 from __future__ import annotations
 from typing import TYPE_CHECKING
 from collections import Counter
+from typing_extensions import Literal
+import numpy as np
 
 if TYPE_CHECKING:
     from typing_extensions import Self
@@ -19,6 +21,7 @@
 import pydantic_ome_ngff.v04.transform as tx
 import zarr
 from zarr.errors import ArrayNotFoundError, ContainsGroupError
+from zarr.util import guess_chunks
 
 VALID_NDIM = (2, 3, 4, 5)
 NUM_TX_MAX = 2
@@ -229,7 +232,7 @@ class GroupAttrs(BaseModel):
     multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
 
 
-class Group(GroupSpec[GroupAttrs, ArraySpec | GroupSpec]):
+class Group(GroupSpec[GroupAttrs, Union[ArraySpec, GroupSpec]]):
     """
     A model of a Zarr group that implements OME-NGFF Multiscales metadata.
 
@@ -314,6 +317,7 @@ def from_arrays(
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
+        chunks: tuple[int, ...] | tuple[tuple[int, ...]] | Literal["auto"] = "auto",
         **kwargs: Any,
     ) -> Self:
         """
@@ -341,10 +345,22 @@ def from_arrays(
             A description of the type of multiscale image represented by this group. Optional.
         metadata: Dict[str, Any] | None, default = None
             Arbitrary metadata associated with this multiscale collection. Optional.
+        chunks: tuple[int] | tuple[tuple[int, ...]] | Literal["auto"], default = "auto"
+            The chunks for the arrays in this multiscale group.
+            If the string "auto" is provided, each array will have chunks set to the zarr-python default value, which depends on the shape and dtype of the array.
+            If a single sequence of ints is provided, then this defines the chunks for all arrays.
+            If a sequence of sequences of ints is provided, then this defines the chunks for each array.
         """
+
+        chunks_normalized = normalize_chunks(
+            chunks,
+            shapes=[s.shape for s in arrays],
+            typesizes=[s.dtype.itemsize for s in arrays],
+        )
+
         members_flat = {
-            "/" + key.lstrip("/"): ArraySpec.from_array(arr, **kwargs)
-            for key, arr in zip(paths, arrays, strict=True)
+            "/" + key.lstrip("/"): ArraySpec.from_array(arr, cnks, **kwargs)
+            for key, arr, cnks in zip(paths, arrays, chunks_normalized)
         }
 
         multimeta = MultiscaleMetadata(
@@ -354,9 +370,7 @@ def from_arrays(
             axes=axes,
             datasets=[
                 create_dataset(path=path, scale=scale, translation=translation)
-                for path, scale, translation in zip(
-                    paths, scales, translations, strict=True
-                )
+                for path, scale, translation in zip(paths, scales, translations)
             ],
             coordinateTransformations=None,
         )
@@ -429,3 +443,32 @@ def check_array_ndim(self) -> "Group":
                             raise ValueError(msg)
 
         return self
+
+
+def normalize_chunks(
+    chunks: Any, shapes: tuple[tuple[int, ...]], typesizes: tuple[tuple[int]]
+) -> tuple[tuple[int, ...]]:
+    """
+    If chunks is "auto", then use zarr default chunking based on the largest array for all the arrays.
+    If chunks is a sequence of ints, then use those chunks for all arrays.
+    If chunks is a sequence of sequences of ints, then use those chunks for each array.
+    """
+    if chunks == "auto":
+        # sort shapes by descending size
+        params_sorted_descending = sorted(
+            zip(shapes, typesizes), key=lambda v: np.prod(v[0]), reverse=True
+        )
+        return (guess_chunks(*params_sorted_descending[0]),) * len(shapes)
+    if isinstance(chunks, Sequence):
+        if all(isinstance(element, int) for element in chunks):
+            return (chunks,) * len(shapes)
+        if all(isinstance(element, Sequence) for element in chunks):
+            if all(map(lambda v: all(isinstance(k, int) for k in v), chunks)):
+                return tuple(map(tuple, chunks))
+            else:
+                raise ValueError(
+                    f"Expected a sequence of sequences of ints. Got {chunks} instead."
+                )
+    raise TypeError(
+        f'Input must be a sequence or the string "auto". Got {type(chunks)}'
+    )

From f5156b862a89c5aa5bc81b3790145fc19df25316 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:37:19 +0100
Subject: [PATCH 55/69] add from __future__ imports, and use Union instead of |

---
 src/pydantic_ome_ngff/v04/transform.py | 8 ++++----
 tests/v04/test_label.py                | 1 +
 tests/v04/test_transform.py            | 1 +
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/transform.py b/src/pydantic_ome_ngff/v04/transform.py
index f07d807..8e34a04 100644
--- a/src/pydantic_ome_ngff/v04/transform.py
+++ b/src/pydantic_ome_ngff/v04/transform.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Annotated, Literal, Sequence
+from typing import Annotated, Literal, Sequence, Union
 
 from pydantic import BeforeValidator
 
@@ -145,9 +145,9 @@ def scale_translation(
     return (vec_scale, vec_trans)
 
 
-Scale = VectorScale | PathScale
-Translation = VectorTranslation | PathTranslation
-Transform = Scale | Translation
+Scale = Union[VectorScale, PathScale]
+Translation = Union[VectorTranslation, PathTranslation]
+Transform = Union[Scale, Translation]
 
 
 def ensure_dimensionality(
diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index f94365d..02bbd82 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from typing import List, Literal
 import pytest
 from pydantic import ValidationError
diff --git a/tests/v04/test_transform.py b/tests/v04/test_transform.py
index 95619ab..3dfe537 100644
--- a/tests/v04/test_transform.py
+++ b/tests/v04/test_transform.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from typing import Sequence, Tuple
 import pytest
 from pydantic_ome_ngff.v04.transform import (

From b8e55abf8ce5b1fc82eded433ccedce03a55951e Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:37:52 +0100
Subject: [PATCH 56/69] add chunks to from_array tests

---
 tests/v04/test_multiscales.py | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index d7239b4..46acbd0 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -1,8 +1,9 @@
 from __future__ import annotations
-from typing import Dict, Tuple
+from typing import Dict, Literal, Tuple
 from pydantic import ValidationError
 import pytest
 import jsonschema as jsc
+from zarr.util import guess_chunks
 from pydantic_zarr.v2 import ArraySpec
 from pydantic_ome_ngff.v04.multiscale import (
     MultiscaleMetadata,
@@ -383,12 +384,14 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
 @pytest.mark.parametrize("path_pattern", ["{0}", "s{0}", "foo/{0}"])
 @pytest.mark.parametrize("metadata", [None, {"foo": 10}])
 @pytest.mark.parametrize("ndim", [2, 3, 4, 5])
+@pytest.mark.parametrize("chunks", ["auto", "tuple", "tuple-of-tuple"])
 def test_from_arrays(
     name: str | None,
     type: str | None,
     path_pattern: str,
     metadata: Dict[str, int] | None,
     ndim: int,
+    chunks: Literal["auto", "tuple", "tuple-of-tuple"],
 ) -> None:
     arrays = [np.arange(x**ndim).reshape((x,) * ndim) for x in [3, 2, 1]]
     paths = [path_pattern.format(idx) for idx in range(len(arrays))]
@@ -416,6 +419,18 @@ def test_from_arrays(
     else:
         axes = [*all_axes[4:], *all_axes[:3]]
 
+    if chunks == "auto":
+        chunks_arg = chunks
+        chunks_expected = (
+            guess_chunks(arrays[0].shape, arrays[0].dtype.itemsize),
+        ) * len(arrays)
+    elif chunks == "tuple":
+        chunks_arg = (2,) * ndim
+        chunks_expected = (chunks_arg,) * len(arrays)
+    elif chunks == "tuple-of-tuple":
+        chunks_arg = tuple((idx,) * ndim for idx in range(1, len(arrays) + 1))
+        chunks_expected = chunks_arg
+
     group = Group.from_arrays(
         paths=paths,
         axes=axes,
@@ -425,6 +440,7 @@ def test_from_arrays(
         name=name,
         type=type,
         metadata=metadata,
+        chunks=chunks_arg,
     )
 
     group_flat = group.to_flat()
@@ -435,8 +451,10 @@ def test_from_arrays(
     assert group.attributes.multiscales[0].coordinateTransformations is None
     assert group.attributes.multiscales[0].axes == axes
     for idx, array in enumerate(arrays):
-        assert array.shape == group_flat["/" + paths[idx]].shape
-        assert array.dtype == group_flat["/" + paths[idx]].dtype
+        array_model: ArraySpec = group_flat["/" + paths[idx]]
+        assert array.shape == array_model.shape
+        assert array.dtype == array_model.dtype
+        assert chunks_expected[idx] == array_model.chunks
         assert group.attributes.multiscales[0].datasets[
             idx
         ].coordinateTransformations == (

From e6407f7394923494fc00d98ec5386c21a8d31ebb Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 13:39:52 +0100
Subject: [PATCH 57/69] chore: update lockfile

---
 poetry.lock | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/poetry.lock b/poetry.lock
index c7f35c2..29226c8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2238,4 +2238,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "dc936c7cf7eeb3a697c4638769c15a46060153aa495c72138291531330ee3566"
+content-hash = "2675a477b55c6cd7ada8aeae2a51d11d86d2758644d83321fa248d3f3a2f163c"

From d80a120181b9df8fd25b9fb71353da9fb1ea9cc4 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 14:49:32 +0100
Subject: [PATCH 58/69] chore: add python 3.9 to ci

---
 .github/workflows/ci.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 01a3c42..067f317 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -20,6 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
+          - "3.9"
           - "3.10"
           - "3.10"
           - "3.12"

From 26f1fe853eef969eea1c065e7255d40d1b63c48b Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 14:55:22 +0100
Subject: [PATCH 59/69] docs: fix example

---
 docs/index.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/index.md b/docs/index.md
index 82a1229..1cb7671 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -172,7 +172,8 @@ group_model = Group.from_arrays(
     arrays=arrays,
     scales=scales,
     translations=translations,
-    chunks=store_chunks)
+    chunks=store_chunks,
+    compressor=None)
 
 print(group_model.model_dump())
 """

From d1808e22a87eefa9e247f6d76fa711227ff1901d Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 14:56:38 +0100
Subject: [PATCH 60/69] feat: expand function signature of from_arrays to
 include compressor, order, fill value

---
 src/pydantic_ome_ngff/v04/multiscale.py | 26 +++++++++++++++++++++----
 tests/v04/test_multiscales.py           |  9 +++++++++
 2 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index c4211d0..b6e77b6 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -6,6 +6,7 @@
 
 if TYPE_CHECKING:
     from typing_extensions import Self
+    from numcodecs.abc import Codec
 
 from typing import Annotated, Any, Dict, List, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
@@ -19,6 +20,7 @@
 from pydantic_ome_ngff.v04.base import version
 from pydantic_ome_ngff.v04.axis import Axis, AxisType
 import pydantic_ome_ngff.v04.transform as tx
+from numcodecs import Zstd
 import zarr
 from zarr.errors import ArrayNotFoundError, ContainsGroupError
 from zarr.util import guess_chunks
@@ -311,14 +313,16 @@ def from_arrays(
         paths: Sequence[str],
         axes: Sequence[Axis],
         arrays: Sequence[ArrayLike | ChunkedArrayLike],
-        scales: Sequence[Sequence[int | float]],
-        translations: Sequence[Sequence[int | float]],
+        scales: Sequence[tuple[int | float]],
+        translations: Sequence[tuple[int | float]],
         *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
         chunks: tuple[int, ...] | tuple[tuple[int, ...]] | Literal["auto"] = "auto",
-        **kwargs: Any,
+        compressor: Codec = Zstd(3),
+        fill_value: Any = 0,
+        order: Literal["C", "F", "auto"] = "auto",
     ) -> Self:
         """
         Create a `Group` from a sequence of multiscale arrays and spatial metadata.
@@ -350,6 +354,12 @@ def from_arrays(
             If the string "auto" is provided, each array will have chunks set to the zarr-python default value, which depends on the shape and dtype of the array.
             If a single sequence of ints is provided, then this defines the chunks for all arrays.
             If a sequence of sequences of ints is provided, then this defines the chunks for each array.
+        fill_value: Any, default = 0
+            The fill value for the Zarr arrays.
+        compressor: `Codec`
+            The compressor to use for the arrays. Default is `numcodecs.ZStd`.
+        order: "auto" | "C" | "F"
+            The memory layout used for chunks of Zarr arrays. The default is "auto", which will infer the order from the input arrays, and fall back to "C" if that inference fails.
         """
 
         chunks_normalized = normalize_chunks(
@@ -359,7 +369,15 @@ def from_arrays(
         )
 
         members_flat = {
-            "/" + key.lstrip("/"): ArraySpec.from_array(arr, cnks, **kwargs)
+            "/" + key.lstrip("/"): ArraySpec.from_array(
+                arr,
+                cnks,
+                attributes={},
+                compressor=compressor,
+                filters=None,
+                fill_value=fill_value,
+                order=order,
+            )
             for key, arr, cnks in zip(paths, arrays, chunks_normalized)
         }
 
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 46acbd0..80a849c 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -385,6 +385,7 @@ def test_multiscale_group_datasets_rank(default_multiscale: MultiscaleMetadata)
 @pytest.mark.parametrize("metadata", [None, {"foo": 10}])
 @pytest.mark.parametrize("ndim", [2, 3, 4, 5])
 @pytest.mark.parametrize("chunks", ["auto", "tuple", "tuple-of-tuple"])
+@pytest.mark.parametrize("order", ["auto", "C", "F"])
 def test_from_arrays(
     name: str | None,
     type: str | None,
@@ -392,6 +393,7 @@ def test_from_arrays(
     metadata: Dict[str, int] | None,
     ndim: int,
     chunks: Literal["auto", "tuple", "tuple-of-tuple"],
+    order: Literal["auto", "C", "F"],
 ) -> None:
     arrays = [np.arange(x**ndim).reshape((x,) * ndim) for x in [3, 2, 1]]
     paths = [path_pattern.format(idx) for idx in range(len(arrays))]
@@ -431,6 +433,11 @@ def test_from_arrays(
         chunks_arg = tuple((idx,) * ndim for idx in range(1, len(arrays) + 1))
         chunks_expected = chunks_arg
 
+    if order == "auto":
+        order_expected = "C"
+    else:
+        order_expected = order
+
     group = Group.from_arrays(
         paths=paths,
         axes=axes,
@@ -441,6 +448,7 @@ def test_from_arrays(
         type=type,
         metadata=metadata,
         chunks=chunks_arg,
+        order=order,
     )
 
     group_flat = group.to_flat()
@@ -452,6 +460,7 @@ def test_from_arrays(
     assert group.attributes.multiscales[0].axes == axes
     for idx, array in enumerate(arrays):
         array_model: ArraySpec = group_flat["/" + paths[idx]]
+        assert array_model.order == order_expected
         assert array.shape == array_model.shape
         assert array.dtype == array_model.dtype
         assert chunks_expected[idx] == array_model.chunks

From fd0c19a0b7396d1e6120d382c32b2602468a5d98 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 21:28:48 +0100
Subject: [PATCH 61/69] feat: use tuples instead of lists

---
 src/pydantic_ome_ngff/v04/label.py      | 11 +++++++----
 src/pydantic_ome_ngff/v04/multiscale.py | 20 ++++++++++----------
 src/pydantic_ome_ngff/v04/plate.py      |  9 ++++-----
 src/pydantic_ome_ngff/v04/transform.py  |  8 ++++----
 src/pydantic_ome_ngff/v04/well.py       |  4 ++--
 5 files changed, 27 insertions(+), 25 deletions(-)

diff --git a/src/pydantic_ome_ngff/v04/label.py b/src/pydantic_ome_ngff/v04/label.py
index 59295de..94913a6 100644
--- a/src/pydantic_ome_ngff/v04/label.py
+++ b/src/pydantic_ome_ngff/v04/label.py
@@ -1,6 +1,9 @@
 from __future__ import annotations
 import warnings
-from typing import List, Literal, Optional, Tuple, Annotated
+from typing import Literal, Optional, Tuple, Annotated, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import List
 
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_ome_ngff.base import VersionedBase
@@ -92,8 +95,8 @@ class ImageLabel(VersionedBase):
     version: Annotated[
         Literal["0.4"] | None, AfterValidator(parse_version)
     ] = NGFF_VERSION
-    colors: Annotated[Optional[List[Color]], AfterValidator(parse_colors)] = None
-    properties: Optional[List[Property]] = None
+    colors: Annotated[Optional[tuple[Color, ...]], AfterValidator(parse_colors)] = None
+    properties: Optional[tuple[Property, ...]] = None
     source: Optional[Source] = None
 
     @model_validator(mode="after")
@@ -112,7 +115,7 @@ class GroupAttrs(multiscale.GroupAttrs):
     ----------
     image_label: `ImageLabel`
         Image label metadata.
-    multiscales: List[v04.multiscales.Multiscales]
+    multiscales: tuple[v04.multiscales.Multiscales]
         Multiscale image metadata.
     """
 
diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index b6e77b6..9b4b3ad 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -8,7 +8,7 @@
     from typing_extensions import Self
     from numcodecs.abc import Codec
 
-from typing import Annotated, Any, Dict, List, Sequence, Union, cast
+from typing import Annotated, Any, Dict, Sequence, Union, cast
 from pydantic import AfterValidator, BaseModel, Field, model_validator
 from pydantic_zarr.v2 import GroupSpec, ArraySpec
 from pydantic_ome_ngff.utils import (
@@ -193,11 +193,11 @@ class MultiscaleMetadata(StrictVersionedBase):
         The type of the multiscale image. Optional. Defaults to `None`.
     metadata: Dict[str, Any] | None
         Metadata for this multiscale image. Optional. Defaults to `None`.
-    datasets: List[Dataset]
+    datasets: tuple[Dataset]
         A collection of descriptions of arrays that collectively comprise this multiscale image.
-    axes: List[Axis]
+    axes: tuple[Axis]
         A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
-    coordinateTransformations: List[tx.Scale, tx.Translation]
+    coordinateTransformations: tuple[tx.Scale] | tuple[tx.Scale, tx.Translation] | None
         Coordinate transformations that express a scaling and translation shared by all elements of
         `datasets`.
     """
@@ -207,9 +207,9 @@ class MultiscaleMetadata(StrictVersionedBase):
     name: Any = None
     type: Any = None
     metadata: Dict[str, Any] | None = None
-    datasets: Annotated[List[Dataset], Field(..., min_length=1)]
+    datasets: Annotated[tuple[Dataset, ...], Field(..., min_length=1)]
     axes: Annotated[
-        list[Axis],
+        tuple[Axis, ...],
         AfterValidator(ensure_axis_length),
         AfterValidator(ensure_axis_names),
         AfterValidator(ensure_axis_types),
@@ -227,11 +227,11 @@ class GroupAttrs(BaseModel):
 
     Attributes
     ----------
-    multiscales: List[MultiscaleMetadata]
+    multiscales: tuple[MultiscaleMetadata]
         A list of `MultiscaleMetadata`. Each element of `multiscales` specifies a multiscale image.
     """
 
-    multiscales: Annotated[List[MultiscaleMetadata], Field(..., min_length=1)]
+    multiscales: Annotated[tuple[MultiscaleMetadata, ...], Field(..., min_length=1)]
 
 
 class Group(GroupSpec[GroupAttrs, Union[ArraySpec, GroupSpec]]):
@@ -310,12 +310,12 @@ def from_zarr(cls, node: zarr.Group) -> Group:
     @classmethod
     def from_arrays(
         cls,
+        arrays: Sequence[ArrayLike | ChunkedArrayLike],
+        *,
         paths: Sequence[str],
         axes: Sequence[Axis],
-        arrays: Sequence[ArrayLike | ChunkedArrayLike],
         scales: Sequence[tuple[int | float]],
         translations: Sequence[tuple[int | float]],
-        *,
         name: str | None = None,
         type: str | None = None,
         metadata: Dict[str, Any] | None = None,
diff --git a/src/pydantic_ome_ngff/v04/plate.py b/src/pydantic_ome_ngff/v04/plate.py
index e5d7e0f..01aaee6 100644
--- a/src/pydantic_ome_ngff/v04/plate.py
+++ b/src/pydantic_ome_ngff/v04/plate.py
@@ -1,5 +1,4 @@
 from __future__ import annotations
-from typing import List
 
 from pydantic import (
     BaseModel,
@@ -44,11 +43,11 @@ class PlateMetadata(VersionedBase):
     _version = version
     version: str | None = version
     name: str | None = None
-    acquisitions: List[Acquisition]
-    columns: List[Entry]
-    rows: List[Entry]
+    acquisitions: tuple[Acquisition, ...]
+    columns: tuple[Entry, ...]
+    rows: tuple[Entry, ...]
     field_count: PositiveInt
-    wells: List[WellMetadata]
+    wells: tuple[WellMetadata, ...]
 
 
 class GroupAttrs(BaseModel):
diff --git a/src/pydantic_ome_ngff/v04/transform.py b/src/pydantic_ome_ngff/v04/transform.py
index 8e34a04..3217d64 100644
--- a/src/pydantic_ome_ngff/v04/transform.py
+++ b/src/pydantic_ome_ngff/v04/transform.py
@@ -73,12 +73,12 @@ class VectorTranslation(StrictBase):
     ----------
     type: Literal["translation"]
         The string "translation".
-    translation: Sequence[float | int]
+    translation: tuple[float | int]
         A sequence of numbers that define an N-dimensional translation transformation.
     """
 
     type: Literal["translation"] = "translation"
-    translation: Annotated[Sequence[float | int], BeforeValidator(listify_numpy)]
+    translation: Annotated[tuple[float | int, ...], BeforeValidator(listify_numpy)]
 
 
 class VectorScale(StrictBase):
@@ -91,12 +91,12 @@ class VectorScale(StrictBase):
     ----------
     type: Literal["scale"]
         The string "scale".
-    scale: Sequence[float | int]
+    scale: tuple[float | int]
         A sequence of numbers that define an  N-dimensional scaling transformation.
     """
 
     type: Literal["scale"] = "scale"
-    scale: Annotated[Sequence[float | int], BeforeValidator(listify_numpy)]
+    scale: Annotated[tuple[float | int, ...], BeforeValidator(listify_numpy)]
 
 
 def ndim(
diff --git a/src/pydantic_ome_ngff/v04/well.py b/src/pydantic_ome_ngff/v04/well.py
index 7605ddf..26bfd89 100644
--- a/src/pydantic_ome_ngff/v04/well.py
+++ b/src/pydantic_ome_ngff/v04/well.py
@@ -1,5 +1,5 @@
 from __future__ import annotations
-from typing import List, Union
+from typing import Union
 
 from pydantic import BaseModel, ValidationError, field_validator
 from pydantic_zarr.v2 import ArraySpec, GroupSpec
@@ -22,7 +22,7 @@ class WellMetadata(VersionedBase):
 
     _version = version
     version: str | None = version
-    images: List[Image]
+    images: tuple[Image, ...]
 
 
 class GroupAttrs(BaseModel):

From b5e6ba98246182e8849268ec60740785e5a06846 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 21:29:20 +0100
Subject: [PATCH 62/69] update tests for tuples

---
 tests/v04/test_label.py       | 2 +-
 tests/v04/test_multiscales.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/v04/test_label.py b/tests/v04/test_label.py
index 02bbd82..66c4434 100644
--- a/tests/v04/test_label.py
+++ b/tests/v04/test_label.py
@@ -13,7 +13,7 @@ def test_imagelabel(version: Literal["0.4"] | None):
     model = ImageLabel(colors=[color], version=version)
     dumped = model.model_dump()
 
-    assert dumped["colors"] == [color.model_dump()]
+    assert dumped["colors"] == (color.model_dump(),)
     # check that if the version is None, then we didn't write it out
     if version == "0.4":
         assert dumped["version"] == NGFF_VERSION
diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 80a849c..5413591 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -457,7 +457,7 @@ def test_from_arrays(
     assert group.attributes.multiscales[0].type == type
     assert group.attributes.multiscales[0].metadata == metadata
     assert group.attributes.multiscales[0].coordinateTransformations is None
-    assert group.attributes.multiscales[0].axes == axes
+    assert group.attributes.multiscales[0].axes == tuple(axes)
     for idx, array in enumerate(arrays):
         array_model: ArraySpec = group_flat["/" + paths[idx]]
         assert array_model.order == order_expected

From 88290a495ad16fc6c28ee84f92535fdd1cef9238 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 21:29:30 +0100
Subject: [PATCH 63/69] add validation example

---
 docs/index.md | 126 ++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 91 insertions(+), 35 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index 1cb7671..d3b6e72 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -48,24 +48,24 @@ group_model = Group.from_zarr(zgroup)
 multi_meta = group_model.attributes.multiscales
 print(multi_meta)
 """
-[
+(
     MultiscaleMetadata(
         version='0.4',
         name=None,
         type=None,
         metadata=None,
-        datasets=[
+        datasets=(
             Dataset(
                 path='0',
                 coordinateTransformations=(
                     VectorScale(
                         type='scale',
-                        scale=[
+                        scale=(
                             1.0,
                             0.5002025531914894,
                             0.3603981534640209,
                             0.3603981534640209,
-                        ],
+                        ),
                     ),
                 ),
             ),
@@ -74,12 +74,12 @@ print(multi_meta)
                 coordinateTransformations=(
                     VectorScale(
                         type='scale',
-                        scale=[
+                        scale=(
                             1.0,
                             0.5002025531914894,
                             0.7207963069280418,
                             0.7207963069280418,
-                        ],
+                        ),
                     ),
                 ),
             ),
@@ -88,25 +88,25 @@ print(multi_meta)
                 coordinateTransformations=(
                     VectorScale(
                         type='scale',
-                        scale=[
+                        scale=(
                             1.0,
                             0.5002025531914894,
                             1.4415926138560835,
                             1.4415926138560835,
-                        ],
+                        ),
                     ),
                 ),
             ),
-        ],
-        axes=[
+        ),
+        axes=(
             Axis(name='c', type='channel', unit=None),
             Axis(name='z', type='space', unit='micrometer'),
             Axis(name='y', type='space', unit='micrometer'),
             Axis(name='x', type='space', unit='micrometer'),
-        ],
+        ),
         coordinateTransformations=None,
-    )
-]
+    ),
+)
 """
 
 # to get the Zarr arrays referenced by the multiscale metadata, we access them by name from the Zarr group.
@@ -180,43 +180,43 @@ print(group_model.model_dump())
 {
     'zarr_version': 2,
     'attributes': {
-        'multiscales': [
+        'multiscales': (
             {
                 'version': '0.4',
                 'name': None,
                 'type': None,
                 'metadata': None,
-                'datasets': [
+                'datasets': (
                     {
                         'path': 's0',
                         'coordinateTransformations': (
-                            {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
+                            {'type': 'scale', 'scale': (1.0, 2.0, 2.0, 2.0)},
                             {
                                 'type': 'translation',
-                                'translation': [0.0, 0.0, 0.0, 0.0],
+                                'translation': (0.0, 0.0, 0.0, 0.0),
                             },
                         ),
                     },
                     {
                         'path': 's1',
                         'coordinateTransformations': (
-                            {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
+                            {'type': 'scale', 'scale': (2.0, 4.0, 4.0, 4.0)},
                             {
                                 'type': 'translation',
-                                'translation': [0.5, 1.0, 1.0, 1.0],
+                                'translation': (0.5, 1.0, 1.0, 1.0),
                             },
                         ),
                     },
-                ],
-                'axes': [
+                ),
+                'axes': (
                     {'name': 't', 'type': 'time', 'unit': 'second'},
                     {'name': 'z', 'type': 'space', 'unit': 'nanometer'},
                     {'name': 'y', 'type': 'space', 'unit': 'nanometer'},
                     {'name': 'x', 'type': 'space', 'unit': 'nanometer'},
-                ],
+                ),
                 'coordinateTransformations': None,
-            }
-        ]
+            },
+        )
     },
     'members': {
         's0': {
@@ -269,37 +269,93 @@ foo
 print(stored_group.attrs.asdict())
 """
 {
-    'multiscales': [
+    'multiscales': (
         {
             'version': '0.4',
             'name': None,
             'type': None,
             'metadata': None,
-            'datasets': [
+            'datasets': (
                 {
                     'path': 's0',
                     'coordinateTransformations': (
-                        {'type': 'scale', 'scale': [1.0, 2.0, 2.0, 2.0]},
-                        {'type': 'translation', 'translation': [0.0, 0.0, 0.0, 0.0]},
+                        {'type': 'scale', 'scale': (1.0, 2.0, 2.0, 2.0)},
+                        {'type': 'translation', 'translation': (0.0, 0.0, 0.0, 0.0)},
                     ),
                 },
                 {
                     'path': 's1',
                     'coordinateTransformations': (
-                        {'type': 'scale', 'scale': [2.0, 4.0, 4.0, 4.0]},
-                        {'type': 'translation', 'translation': [0.5, 1.0, 1.0, 1.0]},
+                        {'type': 'scale', 'scale': (2.0, 4.0, 4.0, 4.0)},
+                        {'type': 'translation', 'translation': (0.5, 1.0, 1.0, 1.0)},
                     ),
                 },
-            ],
-            'axes': [
+            ),
+            'axes': (
                 {'name': 't', 'type': 'time', 'unit': 'second'},
                 {'name': 'z', 'type': 'space', 'unit': 'nanometer'},
                 {'name': 'y', 'type': 'space', 'unit': 'nanometer'},
                 {'name': 'x', 'type': 'space', 'unit': 'nanometer'},
-            ],
+            ),
             'coordinateTransformations': None,
-        }
-    ]
+        },
+    )
 }
 """
+```
+
+
+## Data validation
+
+This library attempts to detect invalid OME-NGFF containers and provide useful error messages when something is broken. The following examples illustrate a few ways in which OME-NGFF metadata can be broken, and what the error messages look like.
+
+```python
+from pydantic import ValidationError
+from pydantic_zarr.v2 import ArraySpec
+from pydantic_ome_ngff.v04.multiscale import Group
+from pydantic_ome_ngff.v04.axis import Axis
+import numpy as np
+
+arrays = np.zeros((10,10)), np.zeros((5,5))
+scales = ((1,1), (2,2))
+translations = ((0,0), (0.5, 0.5))
+paths = ('s0','s1')
+axes = (
+    Axis(name='y', unit='nanometer', type='space'),
+    Axis(name='x', unit='nanometer', type='space')
+)
+
+# create a valid multiscale group
+group_model = Group.from_arrays(arrays, paths=paths, axes=axes, scales=scales, translations=translations)
+
+# convert that group to a dictionary, so we can break it
+group_model_missing_array = group_model.model_dump()
+
+# remove one of the arrays. this invalidates the multiscale metadata
+group_model_missing_array['members'].pop('s0')
+
+try:
+    Group(**group_model_missing_array)
+except ValidationError as e:
+    print(e)
+    """
+    1 validation error for Group
+      Value error, Dataset s0 was specified in multiscale metadata, but no array with that name was found in the hierarchy. All arrays referenced in multiscale metadata must be contained in the group. [type=value_error, input_value={'zarr_version': 2, 'attr...: 'zstd', 'level': 3}}}}, input_type=dict]
+        For further information visit https://errors.pydantic.dev/2.6/v/value_error
+    """
+
+group_model_wrong_array = group_model.model_dump()
+
+# insert an array with incorrect dimensionality
+group_model_wrong_array['members']['s0'] = ArraySpec.from_array(np.arange(10)).model_dump()
+
+try:
+    Group(**group_model_wrong_array)
+except ValidationError as e:
+    print(e)
+    """
+    1 validation error for Group
+      Value error, Transform type='scale' scale=(1, 1) has dimensionality 2, which does not match the dimensionality of the array found in this group at s0 (1). Transform dimensionality must match array dimensionality. [type=value_error, input_value={'zarr_version': 2, 'attr...: 'zstd', 'level': 3}}}}, input_type=dict]
+        For further information visit https://errors.pydantic.dev/2.6/v/value_error
+    """
 ```
\ No newline at end of file

From 472d75e5b5810a317ce13f370f6fccf53fbfae0f Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 23:18:50 +0100
Subject: [PATCH 64/69] docs

---
 docs/index.md                           | 128 +++++++++++++++++++++++-
 src/pydantic_ome_ngff/v04/multiscale.py |   8 +-
 2 files changed, 131 insertions(+), 5 deletions(-)

diff --git a/docs/index.md b/docs/index.md
index d3b6e72..bfef04b 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -117,7 +117,7 @@ print(arrays)
 """
 ```
 
-## Creating a multiscale group
+## Creating a multiscale group from arrays
 
 `pydantic-ome-ngff` provides a direct way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. Note that the data in these arrays will not be accessed -- the arrays are used to create models of Zarr arrays, and so their `shape` and `dtype` attributes are necessary.
 
@@ -304,6 +304,132 @@ print(stored_group.attrs.asdict())
 """
 ```
 
+## Creating a multiscale group directly
+
+It's also possible to create a multiscale group without using the `from_arrays` method demonstrated in the previous example, but it's a bit more involved.
+
+```python
+from pydantic_zarr.v2 import ArraySpec
+from pydantic_ome_ngff.v04.multiscale import Group, MultiscaleMetadata, create_dataset, GroupAttrs
+from pydantic_ome_ngff.v04.axis import Axis
+import numpy as np
+import zarr
+
+# define the axes
+axes = [
+    Axis(name='t', unit='second', type='time'),
+    Axis(name='z', unit='nanometer', type='space'),
+    Axis(name='y', unit='nanometer', type='space'),
+    Axis(name='x', unit='nanometer', type='space')
+]
+
+ndim = len(axes)
+
+# the chunk size we want to use for our Zarr arrays
+store_chunks = (1, 2, 2, 2)
+
+# simulate a multiscale pyramid
+shapes = (10,) * ndim, (5,) * ndim
+dtypes = ('uint8', 'uint8')
+
+# arrays will be named s0, s1, etc
+paths = [f's{idx}' for idx in range(len(shapes))]
+
+# downsampling by 2 in each axis
+scales = [
+    [1.0, 2.0, 2.0, 2.0],
+    [2.0, 4.0, 4.0, 4.0],
+]
+
+# s0 is at the origin; s1 is at the offset induced by downsampling
+translations = [
+    [0.0, 0.0, 0.0, 0.0],
+    [0.5, 1.0, 1.0, 1.0]
+]
+
+datasets = tuple(create_dataset(p, s, t) for p, s, t in zip(paths, scales, translations))
+
+multiscales = MultiscaleMetadata(
+    datasets=datasets,
+    axes=axes)
+
+attributes = GroupAttrs(multiscales=(multiscales,))
+members = {p: ArraySpec(shape=s, dtype=d, chunks=store_chunks) for p,s,d in zip(paths, shapes, dtypes)}
+
+group = Group(attributes=attributes, members = members)
+
+print(group.model_dump())
+"""
+{
+    'zarr_version': 2,
+    'attributes': {
+        'multiscales': (
+            {
+                'version': '0.4',
+                'name': None,
+                'type': None,
+                'metadata': None,
+                'datasets': (
+                    {
+                        'path': 's0',
+                        'coordinateTransformations': (
+                            {'type': 'scale', 'scale': (1.0, 2.0, 2.0, 2.0)},
+                            {
+                                'type': 'translation',
+                                'translation': (0.0, 0.0, 0.0, 0.0),
+                            },
+                        ),
+                    },
+                    {
+                        'path': 's1',
+                        'coordinateTransformations': (
+                            {'type': 'scale', 'scale': (2.0, 4.0, 4.0, 4.0)},
+                            {
+                                'type': 'translation',
+                                'translation': (0.5, 1.0, 1.0, 1.0),
+                            },
+                        ),
+                    },
+                ),
+                'axes': (
+                    {'name': 't', 'type': 'time', 'unit': 'second'},
+                    {'name': 'z', 'type': 'space', 'unit': 'nanometer'},
+                    {'name': 'y', 'type': 'space', 'unit': 'nanometer'},
+                    {'name': 'x', 'type': 'space', 'unit': 'nanometer'},
+                ),
+                'coordinateTransformations': None,
+            },
+        )
+    },
+    'members': {
+        's0': {
+            'zarr_version': 2,
+            'attributes': {},
+            'shape': (10, 10, 10, 10),
+            'chunks': (1, 2, 2, 2),
+            'dtype': '|u1',
+            'fill_value': 0,
+            'order': 'C',
+            'filters': None,
+            'dimension_separator': '/',
+            'compressor': None,
+        },
+        's1': {
+            'zarr_version': 2,
+            'attributes': {},
+            'shape': (5, 5, 5, 5),
+            'chunks': (1, 2, 2, 2),
+            'dtype': '|u1',
+            'fill_value': 0,
+            'order': 'C',
+            'filters': None,
+            'dimension_separator': '/',
+            'compressor': None,
+        },
+    },
+}
+"""
+```
 
 ## Data validation
 
diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index 9b4b3ad..1ca012a 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -193,11 +193,11 @@ class MultiscaleMetadata(StrictVersionedBase):
         The type of the multiscale image. Optional. Defaults to `None`.
     metadata: Dict[str, Any] | None
         Metadata for this multiscale image. Optional. Defaults to `None`.
-    datasets: tuple[Dataset]
+    datasets: tuple[Dataset, ...]
         A collection of descriptions of arrays that collectively comprise this multiscale image.
-    axes: tuple[Axis]
-        A list of `Axis` objects that define the semantics for the different axes of the multiscale image.
-    coordinateTransformations: tuple[tx.Scale] | tuple[tx.Scale, tx.Translation] | None
+    axes: tuple[Axis, ...]
+        A tuple of `Axis` objects that define the semantics for the different axes of the multiscale image.
+    coordinateTransformations: tuple[tx.Scale] | tuple[tx.Scale, tx.Translation] | None. Defaults to `None`.
         Coordinate transformations that express a scaling and translation shared by all elements of
         `datasets`.
     """

From 297338ddfc3574b0da6f128d2f9636967452d741 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 20 Mar 2024 23:20:53 +0100
Subject: [PATCH 65/69] docstring

---
 src/pydantic_ome_ngff/v04/multiscale.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pydantic_ome_ngff/v04/multiscale.py b/src/pydantic_ome_ngff/v04/multiscale.py
index 1ca012a..642a2e9 100644
--- a/src/pydantic_ome_ngff/v04/multiscale.py
+++ b/src/pydantic_ome_ngff/v04/multiscale.py
@@ -245,7 +245,7 @@ class Group(GroupSpec[GroupAttrs, Union[ArraySpec, GroupSpec]]):
 
     attributes: GroupAttrs
         The attributes of this Zarr group, which should contain valid `GroupAttrs`.
-    members Dict[Str, ArraySpec | GroupSpec]:
+    members: Dict[Str, ArraySpec | GroupSpec]:
         The members of this Zarr group. Should be instances of `pydantic_zarr.GroupSpec` or `pydantic_zarr.ArraySpec`.
 
     """

From e7228f75d5d12d7b47d609cef25ab7a293c8f150 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Thu, 21 Mar 2024 11:36:04 +0100
Subject: [PATCH 66/69] more text about

---
 docs/index.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/index.md b/docs/index.md
index bfef04b..80dbce8 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -119,7 +119,7 @@ print(arrays)
 
 ## Creating a multiscale group from arrays
 
-`pydantic-ome-ngff` provides a direct way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. Note that the data in these arrays will not be accessed -- the arrays are used to create models of Zarr arrays, and so their `shape` and `dtype` attributes are necessary.
+`pydantic-ome-ngff` provides a direct way to create multiscale metadata from a collection of arrays accompanied by spatial metadata. Note that the data in these arrays will not be accessed -- the arrays are used to create models of Zarr arrays, and so their `shape` and `dtype` attributes are necessary, and other attributes (like `chunks`, if present), can be used to template the resulting Zarr arrays.
 
 The basic workflow is as follows:
 

From 53fcc82a4c305ffa8cf15fea628611f3b8a154b9 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 27 Mar 2024 15:40:59 +0100
Subject: [PATCH 67/69] chore: bump deps

---
 poetry.lock | 66 ++++++++++++++++++++++++++---------------------------
 1 file changed, 33 insertions(+), 33 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 29226c8..bba67bb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -486,18 +486,18 @@ files = [
 
 [[package]]
 name = "filelock"
-version = "3.13.1"
+version = "3.13.3"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.13.1-py3-none-any.whl", hash = "sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c"},
-    {file = "filelock-3.13.1.tar.gz", hash = "sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e"},
+    {file = "filelock-3.13.3-py3-none-any.whl", hash = "sha256:5ffa845303983e7a0b7ae17636509bc97997d58afeafa72fb141a17b152284cb"},
+    {file = "filelock-3.13.3.tar.gz", hash = "sha256:a79895a25bbefdf55d1a2a0a80968f7dbb28edcd6d4234a0afb3f37ecde4b546"},
 ]
 
 [package.extras]
-docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.24)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
 typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
@@ -682,13 +682,13 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "7.0.2"
+version = "7.1.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_metadata-7.0.2-py3-none-any.whl", hash = "sha256:f4bc4c0c070c490abf4ce96d715f68e95923320370efb66143df00199bb6c100"},
-    {file = "importlib_metadata-7.0.2.tar.gz", hash = "sha256:198f568f3230878cb1b44fbd7975f87906c22336dba2e4a7f05278c281fbd792"},
+    {file = "importlib_metadata-7.1.0-py3-none-any.whl", hash = "sha256:30962b96c0c223483ed6cc7280e7f0199feb01a0e40cfae4d4450fc6fab1f570"},
+    {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
 ]
 
 [package.dependencies]
@@ -697,7 +697,7 @@ zipp = ">=0.5"
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -958,13 +958,13 @@ mkdocs = ">=1.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.14"
+version = "9.5.15"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material-9.5.14-py3-none-any.whl", hash = "sha256:a45244ac221fda46ecf8337f00ec0e5cb5348ab9ffb203ca2a0c313b0d4dbc27"},
-    {file = "mkdocs_material-9.5.14.tar.gz", hash = "sha256:2a1f8e67cda2587ab93ecea9ba42d0ca61d1d7b5fad8cf690eeaeb39dcd4b9af"},
+    {file = "mkdocs_material-9.5.15-py3-none-any.whl", hash = "sha256:e5c96dec3d19491de49ca643fc1dbb92b278e43cdb816c775bc47db77d9b62fb"},
+    {file = "mkdocs_material-9.5.15.tar.gz", hash = "sha256:39f03cca45e82bf54eb7456b5a18bd252eabfdd67f237a229471484a0a4d4635"},
 ]
 
 [package.dependencies]
@@ -1360,13 +1360,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.6.2"
+version = "3.7.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "pre_commit-3.6.2-py2.py3-none-any.whl", hash = "sha256:ba637c2d7a670c10daedc059f5c49b5bd0aadbccfcd7ec15592cf9665117532c"},
-    {file = "pre_commit-3.6.2.tar.gz", hash = "sha256:c3ef34f463045c88658c5b99f38c1e297abdcc0ff13f98d3370055fbbfabc67e"},
+    {file = "pre_commit-3.7.0-py2.py3-none-any.whl", hash = "sha256:5eae9e10c2b5ac51577c3452ec0a490455c45a0533f7960f993a0d01e59decab"},
+    {file = "pre_commit-3.7.0.tar.gz", hash = "sha256:e209d61b8acdcf742404408531f0c37d49d2c734fd7cff2d6076083d191cb060"},
 ]
 
 [package.dependencies]
@@ -1945,28 +1945,28 @@ files = [
 
 [[package]]
 name = "ruff"
-version = "0.3.3"
+version = "0.3.4"
 description = "An extremely fast Python linter and code formatter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ruff-0.3.3-py3-none-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl", hash = "sha256:973a0e388b7bc2e9148c7f9be8b8c6ae7471b9be37e1cc732f8f44a6f6d7720d"},
-    {file = "ruff-0.3.3-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:cfa60d23269d6e2031129b053fdb4e5a7b0637fc6c9c0586737b962b2f834493"},
-    {file = "ruff-0.3.3-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1eca7ff7a47043cf6ce5c7f45f603b09121a7cc047447744b029d1b719278eb5"},
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+    {file = "ruff-0.3.4.tar.gz", hash = "sha256:f0f4484c6541a99862b693e13a151435a279b271cff20e37101116a21e2a1ad1"},
 ]
 
 [[package]]

From fa3f922d889da4af8c059166b4d559d39edf121e Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 27 Mar 2024 15:41:56 +0100
Subject: [PATCH 68/69] test: parametrize
 test_coordinate_transforms_invalid_ndims

---
 tests/v04/test_multiscales.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 5413591..73c9753 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -112,8 +112,8 @@ def test_multiscale_unique_axis_names() -> None:
         Dataset(
             path="path",
             coordinateTransformations=(
-                VectorScale(scale=[1, 1, 1]),
-                VectorTranslation(translation=[0, 0, 0]),
+                VectorScale(scale=[1, 1]),
+                VectorTranslation(translation=[0, 0]),
             ),
         )
     ]
@@ -123,7 +123,7 @@ def test_multiscale_unique_axis_names() -> None:
             name="foo",
             axes=axes,
             datasets=datasets,
-            coordinateTransformations=(VectorScale(scale=[1, 1, 1]),),
+            coordinateTransformations=(VectorScale(scale=[1, 1]),),
         )
 
 
@@ -216,10 +216,15 @@ def test_multiscale_axis_length(num_axes: int) -> None:
         )
 
 
-def test_coordinate_transforms_invalid_ndims() -> None:
+@pytest.mark.parametrize(
+    "scale, translation", [((1, 1), (1, 1, 1)), ((1, 1, 1), (1, 1))]
+)
+def test_coordinate_transforms_invalid_ndims(
+    scale: tuple[int, ...], translation: tuple[int, ...]
+) -> None:
     tforms = [
-        VectorScale(scale=(1, 1)),
-        VectorTranslation(translation=(1, 1, 1)),
+        VectorScale(scale=scale),
+        VectorTranslation(translation=translation),
     ]
     with pytest.raises(
         ValidationError,

From 9e915f7b9a1097e7effb77b6f47fb0c629a73a56 Mon Sep 17 00:00:00 2001
From: Davis Bennett <davis.v.bennett@gmail.com>
Date: Wed, 27 Mar 2024 15:44:51 +0100
Subject: [PATCH 69/69] test: shorten the names of some test functions

---
 tests/v04/test_multiscales.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/v04/test_multiscales.py b/tests/v04/test_multiscales.py
index 73c9753..cec131a 100644
--- a/tests/v04/test_multiscales.py
+++ b/tests/v04/test_multiscales.py
@@ -219,7 +219,7 @@ def test_multiscale_axis_length(num_axes: int) -> None:
 @pytest.mark.parametrize(
     "scale, translation", [((1, 1), (1, 1, 1)), ((1, 1, 1), (1, 1))]
 )
-def test_coordinate_transforms_invalid_ndims(
+def test_transform_invalid_ndims(
     scale: tuple[int, ...], translation: tuple[int, ...]
 ) -> None:
     tforms = [
@@ -247,7 +247,7 @@ def test_coordinate_transforms_invalid_ndims(
         * 5,
     ],
 )
-def test_coordinate_transforms_invalid_length(
+def test_transform_invalid_length(
     transforms: list[Transform],
 ) -> None:
     with pytest.raises(
@@ -269,7 +269,7 @@ def test_coordinate_transforms_invalid_length(
         ],
     ],
 )
-def test_coordinate_transforms_invalid_first_element(
+def test_transform_invalid_first_element(
     transforms: Tuple[Transform, Transform],
 ) -> None:
     with pytest.raises(
@@ -288,7 +288,7 @@ def test_coordinate_transforms_invalid_first_element(
         ],
     ),
 )
-def test_coordinate_transforms_invalid_second_element(
+def test_transform_invalid_second_element(
     transforms: Tuple[VectorScale, VectorScale],
 ) -> None:
     with pytest.raises(