From bd92b48d3b6cfe67665ebbce278f69d2f4e8f5eb Mon Sep 17 00:00:00 2001 From: adamltyson Date: Tue, 5 Dec 2023 19:08:48 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20brainglo?= =?UTF-8?q?be/course-dec-2023@122bad5590828512ab25a3dca82e4d89e8c7b245=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- index.html | 169 +++++++++++++++++++++++++++++++---------------------- 1 file changed, 98 insertions(+), 71 deletions(-) diff --git a/index.html b/index.html index 15ef185..fe252ce 100644 --- a/index.html +++ b/index.html @@ -450,7 +450,7 @@

Command line installation

Create a new conda environment and install napari

conda create --name brainglobe python=3.10 -y
 conda activate brainglobe
-conda install napari -c conda-forge
+conda install -c conda-forge napari pyqt

Double-check that running

napari

opens a new napari window.

@@ -471,6 +471,33 @@

Command line installation

+
+

Command line installation (alternative)

+
+

Create a new conda environment and install napari with pip

+
conda create --name brainglobe python=3.10 -y
+conda activate brainglobe
+pip install "napari[pyqt5]"
+

Double-check that running

+
napari
+

opens a new napari window.

+
+
+
+
+
+
+ +
+

More details

+
+
+

More details about using conda are available at brainglobe.info

+
+
+
+
+

Install brainglobe napari plugins

@@ -483,12 +510,12 @@

Install brainglobe napari plugins

Run this first:

-
conda install hdf5
+
conda install hdf5

Install all brainglobe tools with

-
pip install brainglobe
+
pip install brainglobe

Initial checkup

@@ -559,29 +586,29 @@

BrainGlobe Atlas API

BrainGlobe Atlas API

-
from pprint import pprint
-from bg_atlasapi.bg_atlas import BrainGlobeAtlas
-atlas = BrainGlobeAtlas("allen_mouse_25um")
-
-# reference image
-reference_image = atlas.reference
-print(reference_image.shape)
-# (528, 320, 456)
-
-# hemispheres image (value 1 in left hemisphere, 2 in right)
-hemispheres_image = atlas.hemispheres
-print(hemispheres_image.shape)
-# (528, 320, 456)
-
-VISp = atlas.structures["VISp"]
-pprint(VISp)
-# {'acronym': 'VISp',
-#  'id': 385,
-#  'mesh': None,
-#  'mesh_filename': PosixPath('/home/user/.brainglobe/allen_mouse_25um_v0.3/meshes/385.obj')
-#  'name': 'Primary visual area',
-#  'rgb_triplet': [8, 133, 140],
-#  'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}
+
from pprint import pprint
+from bg_atlasapi.bg_atlas import BrainGlobeAtlas
+atlas = BrainGlobeAtlas("allen_mouse_25um")
+
+# reference image
+reference_image = atlas.reference
+print(reference_image.shape)
+# (528, 320, 456)
+
+# hemispheres image (value 1 in left hemisphere, 2 in right)
+hemispheres_image = atlas.hemispheres
+print(hemispheres_image.shape)
+# (528, 320, 456)
+
+VISp = atlas.structures["VISp"]
+pprint(VISp)
+# {'acronym': 'VISp',
+#  'id': 385,
+#  'mesh': None,
+#  'mesh_filename': PosixPath('/home/user/.brainglobe/allen_mouse_25um_v0.3/meshes/385.obj')
+#  'name': 'Primary visual area',
+#  'rgb_triplet': [8, 133, 140],
+#  'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}

Claudi, F., Petrucco, L., Tyson, A. L. et al (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” Journal of Open Source Software, v5(54), 2668

@@ -904,21 +931,21 @@

The IPython console

  • Navigate to Window > Console
  • In the console, run (each line separately)
    • -
    import napari
-from pathlib import Path
-from cellfinder_core.tools.IO import read_with_dask
-
-viewer = napari.viewer.current_viewer()
-
-# adapt "path/to/data" to your folder of tiffs
-path_to_data = Path("path/to/data") 
-viewer.open(path_to_data)
-
-print(viewer.layers)
-
-# which of these is quicker?
-%timeit -r 3 -n 1 viewer.open(path_to_data)
-%timeit -r 3 -n 1 viewer.add_image(read_with_dask(str(path_to_data)))
    +
    import napari
+from pathlib import Path
+from cellfinder_core.tools.IO import read_with_dask
+
+viewer = napari.viewer.current_viewer()
+
+# adapt "path/to/data" to your folder of tiffs
+path_to_data = Path("path/to/data") 
+viewer.open(path_to_data)
+
+print(viewer.layers)
+
+# which of these is quicker?
+%timeit -r 3 -n 1 viewer.open(path_to_data)
+%timeit -r 3 -n 1 viewer.add_image(read_with_dask(str(path_to_data)))

    Example script (demo)

    -
    import napari
-from bg_atlasapi import BrainGlobeAtlas
-from brainrender_napari.napari_atlas_representation import NapariAtlasRepresentation
-
-# setup a napari viewer and a brainglobe atlas
-viewer = napari.viewer.Viewer()
-viewer.dims.ndisplay = 3 # set to 3d mode
-atlas = BrainGlobeAtlas("allen_mouse_100um")
-
-# find all hippocampal regions
-hip_id = 1080 # the id of the hippocampus is 1080
-hip_regions = [
-    region["acronym"] 
-    for region in atlas.structures_list 
-    if hip_id in region["structure_id_path"]
-]
-
-# make a representation of the brainglobe atlas in napari
-napari_atlas = NapariAtlasRepresentation(atlas, viewer)
-
-# add all hippocampal regions to the napari viewer
-for hip_region in hip_regions:
-    napari_atlas.add_structure_to_viewer(hip_region)
-
-# add the whole brain mesh as a help for orientation
-napari_atlas.add_structure_to_viewer("root")
-
-# run this script
-if __name__ == "__main__":
-    napari.run()
    +
    import napari
+from bg_atlasapi import BrainGlobeAtlas
+from brainrender_napari.napari_atlas_representation import NapariAtlasRepresentation
+
+# setup a napari viewer and a brainglobe atlas
+viewer = napari.viewer.Viewer()
+viewer.dims.ndisplay = 3 # set to 3d mode
+atlas = BrainGlobeAtlas("allen_mouse_100um")
+
+# find all hippocampal regions
+hip_id = 1080 # the id of the hippocampus is 1080
+hip_regions = [
+    region["acronym"] 
+    for region in atlas.structures_list 
+    if hip_id in region["structure_id_path"]
+]
+
+# make a representation of the brainglobe atlas in napari
+napari_atlas = NapariAtlasRepresentation(atlas, viewer)
+
+# add all hippocampal regions to the napari viewer
+for hip_region in hip_regions:
+    napari_atlas.add_structure_to_viewer(hip_region)
+
+# add the whole brain mesh as a help for orientation
+napari_atlas.add_structure_to_viewer("root")
+
+# run this script
+if __name__ == "__main__":
+    napari.run()