docs/notebooks/widget_imaging_beta.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {
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   },
   "source": [
    "# Vitessce Widget Tutorial"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Visualization of Multi-Modal Imaging Data\n",
    "We visualize IMS, PAS, and AF imaging data overlaid from the Spraggins Lab of the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University, uploaded to the HuBMAP data portal."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "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",
    ")\n",
    "from os.path import join"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Configure Vitessce\n",
    "Set up the images from the three different assays, with the `use_physical_size_scaling` set to `True` so that the IMS image scales to the other images based on their physical sizes."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "vc = VitessceConfig(schema_version=\"1.0.16\", name='Spraggins Multi-Modal', description='PAS + IMS + AF From https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca')\n",
    "dataset = vc.add_dataset(name='Spraggins').add_file(\n",
    "    url='https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif?token=',\n",
    "    file_type=\"image.ome-tiff\",\n",
    "    coordination_values={\n",
    "        \"fileUid\": \"PAS\",\n",
    "    },\n",
    ")\n",
    "\n",
    "imageScopes = vc.add_coordination_by_dict({\n",
    "    \"imageLayer\": CL([\n",
    "      {\n",
    "        \"fileUid\": 'PAS',\n",
    "        \"spatialLayerOpacity\": 1,\n",
    "        \"spatialLayerVisible\": True,\n",
    "        \"photometricInterpretation\": 'RGB',\n",
    "        \"imageChannel\": CL([\n",
    "          {\n",
    "            \"spatialTargetC\": 0,\n",
    "            \"spatialChannelColor\": [255, 0, 0],\n",
    "            \"spatialChannelVisible\": True,\n",
    "            \"spatialChannelOpacity\": 1.0,\n",
    "            \"spatialChannelWindow\": [0, 255],\n",
    "          },\n",
    "          {\n",
    "            \"spatialTargetC\": 1,\n",
    "            \"spatialChannelColor\": [0, 255, 0],\n",
    "            \"spatialChannelVisible\": True,\n",
    "            \"spatialChannelOpacity\": 1.0,\n",
    "            \"spatialChannelWindow\": [0, 255],\n",
    "          },\n",
    "          {\n",
    "            \"spatialTargetC\": 2,\n",
    "            \"spatialChannelColor\": [0, 0, 255],\n",
    "            \"spatialChannelVisible\": True,\n",
    "            \"spatialChannelOpacity\": 1.0,\n",
    "            \"spatialChannelWindow\": [0, 255],\n",
    "          },\n",
    "        ]),\n",
    "      }\n",
    "    ])\n",
    "})\n",
    "\n",
    "metaCoordinationScope = vc.add_meta_coordination()\n",
    "metaCoordinationScope.use_coordination_by_dict(imageScopes)\n",
    "\n",
    "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
    "lc = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
    "\n",
    "spatial.use_meta_coordination(metaCoordinationScope)\n",
    "lc.use_meta_coordination(metaCoordinationScope)\n",
    "\n",
    "vc.layout(spatial | lc);"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2. Create the Vitessce widget"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a5efa92286df4ad58cf94cfb3d12b703",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VitessceWidget(config={'version': '1.0.16', 'name': 'Spraggins Multi-Modal', 'description': 'PAS + IMS + AF Fr…"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vw = vc.widget(custom_js_url='http://localhost:8000/packages/main/prod/dist/index.min.js')\n",
    "vw"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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