Add notebook (#369)

vitessce · Oct 2, 2024 · dc021eb · dc021eb
1 parent b02d767
commit dc021eb
Showing 1 changed file with 104 additions and 0 deletions.
diff --git a/docs/notebooks/widget_segmentations_beta.ipynb b/docs/notebooks/widget_segmentations_beta.ipynb
@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
+   "source": [
+    "# Vitessce Widget Tutorial"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from vitessce import (\n",
+    "    VitessceConfig,\n",
+    "    Component as cm,\n",
+    "    CoordinationType as ct,\n",
+    "    OmeTiffWrapper,\n",
+    "    MultiImageWrapper,\n",
+    "    CoordinationLevel as CL,\n",
+    "    ObsSegmentationsOmeTiffWrapper,\n",
+    "    ImageOmeTiffWrapper,\n",
+    "    get_initial_coordination_scope_prefix,\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vc = VitessceConfig(schema_version=\"1.0.16\")\n",
+    "dataset = vc.add_dataset(name='Spraggins').add_object(\n",
+    "    ImageOmeTiffWrapper(\n",
+    "        img_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2_bf.ome.tif\",\n",
+    "        offsets_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2_bf.offsets.json\"\n",
+    "    )\n",
+    ").add_object(\n",
+    "    ObsSegmentationsOmeTiffWrapper(\n",
+    "        img_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2.ome.tif\",\n",
+    "        offsets_url=\"https://storage.googleapis.com/vitessce-demo-data/kpmp-f2f-march-2023/S-1905-017737/S-1905-017737_PAS_2of2.offsets.json\",\n",
+    "        obs_types_from_channel_names=True\n",
+    "    )\n",
+    ")\n",
+    "\n",
+    "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
+    "lc = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
+    "\n",
+    "vc.link_views_by_dict([spatial, lc], {\n",
+    "    \"imageLayer\": CL([\n",
+    "        {\n",
+    "          \"photometricInterpretation\": \"RGB\"   \n",
+    "        }\n",
+    "    ]),\n",
+    "}, meta=True, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
+    "\n",
+    "vc.layout(spatial | lc);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw = vc.widget()\n",
+    "vw"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}