From fcc6ab1d5455aa814d15bc9d56814c5e04d767bb Mon Sep 17 00:00:00 2001
From: Mark Keller <7525285+keller-mark@users.noreply.github.com>
Date: Wed, 27 Nov 2024 16:45:10 -0500
Subject: [PATCH] Add blobs notebook for image rendering (#387)

---
 docs/notebooks/spatial_data_blobs.ipynb | 214 ++++++++++++++++++++++++
 1 file changed, 214 insertions(+)
 create mode 100644 docs/notebooks/spatial_data_blobs.ipynb

diff --git a/docs/notebooks/spatial_data_blobs.ipynb b/docs/notebooks/spatial_data_blobs.ipynb
new file mode 100644
index 0000000..47f49a5
--- /dev/null
+++ b/docs/notebooks/spatial_data_blobs.ipynb
@@ -0,0 +1,214 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
+   "source": [
+    "# Vitessce Widget Tutorial"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Visualization of a SpatialData object"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Import dependencies\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import spatialdata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata = spatialdata.datasets.blobs()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from os.path import join"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "spatialdata_filepath = join(\"data\", \"blobs.spatialdata.zarr\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata.write(spatialdata_filepath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sdata.table.uns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from vitessce import (\n",
+    "    VitessceConfig,\n",
+    "    ViewType as vt,\n",
+    "    CoordinationType as ct,\n",
+    "    CoordinationLevel as CL,\n",
+    "    SpatialDataWrapper,\n",
+    "    get_initial_coordination_scope_prefix\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Configure Vitessce\n",
+    "\n",
+    "Vitessce needs to know which pieces of data we are interested in visualizing, the visualization types we would like to use, and how we want to coordinate (or link) the views."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vc = VitessceConfig(\n",
+    "    schema_version=\"1.0.16\",\n",
+    "    name='Visium SpatialData Demo (blobs)',\n",
+    ")\n",
+    "# Add data to the configuration:\n",
+    "wrapper = SpatialDataWrapper(\n",
+    "    sdata_path=spatialdata_filepath,\n",
+    "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
+    "    image_path=\"images/blobs_image\",\n",
+    "    labels_path=\"labels/blobs_labels\",\n",
+    "    coordinate_system=\"global\",\n",
+    "    coordination_values={\n",
+    "        \"obsType\": \"blob\",\n",
+    "        \"fileUid\": \"my_unique_id\"\n",
+    "    }\n",
+    ")\n",
+    "dataset = vc.add_dataset(name='Blobs').add_object(wrapper)\n",
+    "\n",
+    "# Add views (visualizations) to the configuration:\n",
+    "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
+    "layer_controller = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
+    "\n",
+    "vc.link_views_by_dict([spatial, layer_controller], {\n",
+    "    'imageLayer': CL([{\n",
+    "        \"fileUid\": \"my_unique_id\",\n",
+    "        'photometricInterpretation': 'BlackIsZero',\n",
+    "        'spatialLayerOpacity': 0.9,\n",
+    "        'imageChannel': CL([\n",
+    "            {\n",
+    "                \"spatialTargetC\": 0,\n",
+    "                \"spatialChannelColor\": [255, 0, 0],\n",
+    "                \"spatialChannelOpacity\": 1.0\n",
+    "            }\n",
+    "        ])\n",
+    "    }]),\n",
+    "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
+    "\n",
+    "vc.link_views_by_dict([spatial, layer_controller], {\n",
+    "    'segmentationLayer': CL([{\n",
+    "        'segmentationChannel': CL([{\n",
+    "            'spatialChannelVisible': False,\n",
+    "            'obsType': 'blob',\n",
+    "        }]),\n",
+    "    }]),\n",
+    "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
+    "\n",
+    "# Layout the views\n",
+    "vc.layout(spatial | layer_controller);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Render the widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vw = vc.widget()\n",
+    "vw"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "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": "3.9.20"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}