docs: update tutorials

navis-org · Jan 11, 2024 · 064c89a · 064c89a
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diff --git a/docs/source/tutorials/flywire_annotations.ipynb b/docs/source/tutorials/flywire_annotations.ipynb
diff --git a/docs/source/tutorials/flywire_connectivity.ipynb b/docs/source/tutorials/flywire_connectivity.ipynb
diff --git a/docs/source/tutorials/flywire_mirror.ipynb b/docs/source/tutorials/flywire_mirror.ipynb
@@ -13,7 +13,7 @@
     "accidentally flipped along the left-right (i.e. \"x\") axis. A detailed explanation\n",
     "of this observation can be found in `Schlegel et al <https://www.biorxiv.org/content/10.1101/2023.06.27.546055v2.full>`_.\n",
     "\n",
-    "Importantly, the official `side` labels we provide for FlyWire are biologically\n",
+    "Importantly, the official ``side`` labels we provide for FlyWire are biologically\n",
     "correct. Let's illustrate this:\n",
     "\n",
     ".. note:\n",
@@ -34,19 +34,27 @@
     "import navis.interfaces.neuprint as neu\n",
     "\n",
     "from fafbseg import flywire\n",
+    "import fafbseg.flywire.NeuronCriteria as NC\n",
     "\n",
     "client = neu.Client(\"https://neuprint.janelia.org\", dataset=\"hemibrain:v1.2.1\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Found 8 neurons matching the given criteria.\n"
+     ]
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "59c4160c24894003964a44dfe6b2510a",
+       "model_id": "68d1dbd1ef77446e90012b86c57c66ad",
        "version_major": 2,
        "version_minor": 0
       },
@@ -60,7 +68,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "0b0570118962469d957fb87a44f08a33",
+       "model_id": "4d4d98bf2d394bf485d3888e971d2244",
        "version_major": 2,
        "version_minor": 0
       },
@@ -73,12 +81,14 @@
     }
    ],
    "source": [
-    "# Fetch a neuron on the left side of the brain\n",
+    "# Fetch a couple neurons on the left side of the brain\n",
     "# (note that \"side\" always refers to where the soma is)\n",
-    "da1 = flywire.search_annotations(\"hemibrain_type:DA1_lPN\", materialization=630)\n",
-    "da1_left = da1[da1.side == \"left\"]\n",
-    "meshes = flywire.get_mesh_neuron(da1_left.root_id.values, dataset=\"flat_630\", lod=3)\n",
-    "meshes = navis.downsample_neuron(meshes, 5)  # slightly downsample neurons"
+    "meshes = flywire.get_mesh_neuron(\n",
+    "    NC(type=\"DA1_lPN\", side=\"left\"), dataset=\"flat_630\", lod=3\n",
+    ")\n",
+    "\n",
+    "# Slightly downsample neurons for visualization\n",
+    "meshes = navis.downsample_neuron(meshes, 5)"
    ]
   },
   {