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Notebook for MERFISH example stored via SpatialData (#455)
* WIP: nb for example from tmt * Use remote data
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‎docs/notebooks/spatial_data_merfish.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"nbsphinx": "hidden"
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},
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"source": [
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"# Vitessce Widget Tutorial"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Visualization of a SpatialData object, blobs example"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Import dependencies\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"sdata_url = \"https://data-2.vitessce.io/data/moffitt/merfish_mouse_ileum.sdata.zarr\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from vitessce import (\n",
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" VitessceConfig,\n",
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" ViewType as vt,\n",
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" CoordinationType as ct,\n",
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" CoordinationLevel as CL,\n",
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" SpatialDataWrapper,\n",
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" get_initial_coordination_scope_prefix\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Configure Vitessce\n",
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"\n",
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"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."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"vc = VitessceConfig(\n",
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" schema_version=\"1.0.17\",\n",
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" name='SpatialData with MERFISH data',\n",
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")\n",
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"# Add data to the configuration:\n",
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"\n",
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"dataset = vc.add_dataset(name='MERFISH').add_object(SpatialDataWrapper(\n",
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" sdata_url=sdata_url,\n",
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" # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
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" image_path=\"images/stains\",\n",
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" coordinate_system=\"global\",\n",
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" coordination_values={\n",
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" \"fileUid\": \"stains\"\n",
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" }\n",
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")).add_object(SpatialDataWrapper(\n",
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" sdata_url=sdata_url,\n",
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" # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
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" labels_path=\"labels/dapi_labels\",\n",
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" coordinate_system=\"global\",\n",
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" coordination_values={\n",
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" \"obsType\": \"nucleus\",\n",
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" \"fileUid\": \"dapi\"\n",
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" }\n",
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")).add_object(SpatialDataWrapper(\n",
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" sdata_url=sdata_url,\n",
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" # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
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" labels_path=\"labels/membrane_labels\",\n",
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" coordinate_system=\"global\",\n",
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" coordination_values={\n",
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" \"obsType\": \"cell\",\n",
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" \"fileUid\": \"membrane\"\n",
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" }\n",
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"))\n",
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"\n",
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"# Add views (visualizations) to the configuration:\n",
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"spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
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"layer_controller = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
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"\n",
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"vc.link_views_by_dict([spatial, layer_controller], {\n",
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" 'imageLayer': CL([{\n",
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" \"fileUid\": \"stains\",\n",
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" 'photometricInterpretation': 'BlackIsZero',\n",
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" 'spatialLayerOpacity': 1.0,\n",
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" 'spatialLayerVisible': True,\n",
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" 'imageChannel': CL([\n",
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" {\n",
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" 'spatialChannelVisible': True,\n",
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" \"spatialTargetC\": 0, # DAPI, Nucleus\n",
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" \"spatialChannelColor\": [0, 0, 255],\n",
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" \"spatialChannelOpacity\": 1.0\n",
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" },\n",
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" {\n",
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" 'spatialChannelVisible': True,\n",
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" \"spatialTargetC\": 1, # Membrane, Cell\n",
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" \"spatialChannelColor\": [255, 255, 255],\n",
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" \"spatialChannelOpacity\": 1.0\n",
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" }\n",
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" ])\n",
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" }]),\n",
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"}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
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"\n",
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"vc.link_views_by_dict([spatial, layer_controller], {\n",
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" 'segmentationLayer': CL([{\n",
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" \"fileUid\": \"membrane\",\n",
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" 'spatialLayerOpacity': 1.0,\n",
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" 'spatialLayerVisible': True,\n",
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" 'segmentationChannel': CL([{\n",
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" 'spatialChannelVisible': True,\n",
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" 'obsType': 'cell',\n",
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" \"spatialChannelColor\": [200, 200, 200],\n",
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" \"obsColorEncoding\": \"spatialChannelColor\",\n",
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" }]),\n",
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" }, {\n",
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" \"fileUid\": \"dapi\",\n",
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" 'spatialLayerOpacity': 1.0,\n",
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" 'spatialLayerVisible': True,\n",
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" 'segmentationChannel': CL([{\n",
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" 'spatialChannelVisible': True,\n",
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" 'obsType': 'nucleus',\n",
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" \"spatialChannelColor\": [255, 255, 255],\n",
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" \"obsColorEncoding\": \"spatialChannelColor\",\n",
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" }]),\n",
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" }]),\n",
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"}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
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"\n",
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"# Layout the views\n",
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"vc.layout(spatial | layer_controller);"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Render the widget"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"vw = vc.widget()\n",
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"vw"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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