Update spatialdata notebooks

Author: keller-mark

docs/notebooks/spatial_data.ipynb

@@ -86,7 +86,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.16\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='Visium SpatialData Demo (visium_associated_xenium_io)',\n",
     ")\n",
     "# Add data to the configuration:\n",

docs/notebooks/spatial_data_blobs.ipynb

@@ -29,7 +29,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import spatialdata"
+    "import spatialdata\n",
+    "from os.path import join"
    ]
   },
   {
@@ -41,15 +42,6 @@
     "sdata = spatialdata.datasets.blobs()"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from os.path import join"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -65,16 +57,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sdata.write(spatialdata_filepath)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "sdata.table.uns"
+    "sdata.write(spatialdata_filepath, overwrite=True)"
    ]
   },
   {
@@ -109,15 +92,15 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='Visium SpatialData Demo (blobs)',\n",
     ")\n",
     "# Add data to the configuration:\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_store=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",
+    "    obs_segmentations_path=\"labels/blobs_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"blob\",\n",
@@ -185,6 +168,13 @@
     "vw = vc.widget()\n",
     "vw"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

docs/notebooks/spatial_data_kpmp_vis.ipynb

@@ -71,7 +71,7 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData\")\n",
     "\n",
     "t_obstype = \"Tubule\"\n",
     "a_obstype = \"Artery\"\n",
@@ -93,7 +93,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_tubules\",\n",
-    "        labels_path=\"labels/labels_tubules\",\n",
+    "        obs_segmentations_path=\"labels/labels_tubules\",\n",
     "        obs_feature_matrix_path=\"tables/table_tubules/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -106,7 +106,7 @@
     ").add_object(\n",
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
-    "        labels_path=\"labels/labels_arteries_arterioles\",\n",
+    "        obs_segmentations_path=\"labels/labels_arteries_arterioles\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
     "          \"fileUid\": \"labels_arteries_arterioles\",\n",
@@ -119,7 +119,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_cortical_interstitia\",\n",
-    "        labels_path=\"labels/labels_cortical_interstitia\",\n",
+    "        obs_segmentations_path=\"labels/labels_cortical_interstitia\",\n",
     "        obs_feature_matrix_path=\"tables/table_cortical_interstitia/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -133,7 +133,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_globally_sclerotic_glomeruli\",\n",
-    "        labels_path=\"labels/labels_globally_sclerotic_glomeruli\",\n",
+    "        obs_segmentations_path=\"labels/labels_globally_sclerotic_glomeruli\",\n",
     "        obs_feature_matrix_path=\"tables/table_globally_sclerotic_glomeruli/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -147,7 +147,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_non_globally_sclerotic_glomeruli\",\n",
-    "        labels_path=\"labels/labels_non_globally_sclerotic_glomeruli\",\n",
+    "        obs_segmentations_path=\"labels/labels_non_globally_sclerotic_glomeruli\",\n",
     "        obs_feature_matrix_path=\"tables/table_non_globally_sclerotic_glomeruli/X\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
@@ -161,7 +161,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_interstitialfibrosis_and_tubular_atrophy\",\n",
-    "        labels_path=\"labels/labels_interstitialfibrosis_and_tubular_atrophy\",\n",
+    "        obs_segmentations_path=\"labels/labels_interstitialfibrosis_and_tubular_atrophy\",\n",
     "        coordinate_system=\"global\",\n",
     "        coordination_values={\n",
     "          \"fileUid\": \"labels_interstitialfibrosis_and_tubular_atrophy\",\n",
@@ -174,7 +174,7 @@
     "    SpatialDataWrapper(\n",
     "        sdata_url=sdata_url,\n",
     "        table_path=\"tables/table_peritubular_capillaries\",\n",
-    "        labels_path=\"labels/labels_peritubular_capillaries\",\n",
+    "        obs_segmentations_path=\"labels/labels_peritubular_capillaries\",\n",
     "        obs_feature_matrix_path=\"tables/table_peritubular_capillaries/X\",\n",
     "        obs_set_paths=[\n",
     "            \"tables/table_peritubular_capillaries/obs/cortex_ifta_set\",\n",

docs/notebooks/spatial_data_merfish.ipynb

@@ -64,7 +64,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='SpatialData with MERFISH data',\n",
     ")\n",
     "# Add data to the configuration:\n",
@@ -80,7 +80,7 @@
     ")).add_object(SpatialDataWrapper(\n",
     "    sdata_url=sdata_url,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
-    "    labels_path=\"labels/dapi_labels\",\n",
+    "    obs_segmentations_path=\"labels/dapi_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"nucleus\",\n",
@@ -89,7 +89,7 @@
     ")).add_object(SpatialDataWrapper(\n",
     "    sdata_url=sdata_url,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
-    "    labels_path=\"labels/membrane_labels\",\n",
+    "    obs_segmentations_path=\"labels/membrane_labels\",\n",
     "    coordinate_system=\"global\",\n",
     "    coordination_values={\n",
     "        \"obsType\": \"cell\",\n",

docs/notebooks/spatial_data_merfish_2.ipynb

@@ -86,7 +86,7 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.17\",\n",
+    "    schema_version=\"1.0.18\",\n",
     "    name='MERFISH SpatialData Demo',\n",
     ")\n",
     "# Add data to the configuration:\n",

docs/notebooks/spatial_data_mouseliver.ipynb

@@ -248,15 +248,15 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData Demo\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData Demo\")\n",
     "\n",
     "# Instantiate the wrapper class, specifying data fields of interest.\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",
     "    table_path=\"tables/table\",\n",
     "    image_path=\"images/raw_image\",\n",
-    "    labels_path=\"labels/segmentation_mask\",\n",
+    "    obs_segmentations_path=\"labels/segmentation_mask\",\n",
     "    obs_feature_matrix_path=\"tables/table/X\",\n",
     "    obs_set_paths=[\"tables/table/obs/annotation\"],\n",
     "    obs_set_names=[\"Annotation\"],\n",
@@ -434,7 +434,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (zarr)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_path=adata_zarr_filepath,\n",
@@ -481,7 +481,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (h5ad)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (h5ad)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_path=adata_h5ad_filepath,\n",
@@ -613,7 +613,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image (ome-zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image (ome-zarr)\")\n",
     "\n",
     "# Add data.\n",
     "img_wrapper = ImageOmeZarrWrapper(\n",
@@ -696,7 +696,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image and segmentations (ome-tiff)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image and segmentations (ome-tiff)\")\n",
     "# Add data.\n",
     "wrapper = ImageOmeTiffWrapper(\n",
     "    img_path=ome_tiff_filepath,\n",

docs/notebooks/spatial_data_mouseliver_remote.ipynb

@@ -212,15 +212,15 @@
    "outputs": [],
    "source": [
     "# Create a VitessceConfig instance.\n",
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"SpatialData Demo\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"SpatialData Demo\")\n",
     "\n",
     "# Instantiate the wrapper class, specifying data fields of interest.\n",
     "wrapper = SpatialDataWrapper(\n",
     "    sdata_url=spatialdata_filepath,\n",
     "    # The following paths are relative to the root of the SpatialData Zarr store on-disk.\n",
     "    table_path=\"tables/table\",\n",
     "    image_path=\"images/raw_image\",\n",
-    "    labels_path=\"labels/segmentation_mask\",\n",
+    "    obs_segmentations_path=\"labels/segmentation_mask\",\n",
     "    obs_feature_matrix_path=\"tables/table/X\",\n",
     "    obs_set_paths=[\"tables/table/obs/annotation\"],\n",
     "    obs_set_names=[\"Annotation\"],\n",
@@ -349,7 +349,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (zarr)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_url=adata_zarr_filepath,\n",
@@ -396,7 +396,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"AnnData (h5ad)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"AnnData (h5ad)\")\n",
     "# Add data.\n",
     "wrapper = AnnDataWrapper(\n",
     "    adata_url=adata_h5ad_filepath,\n",
@@ -451,7 +451,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image (ome-zarr)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image (ome-zarr)\")\n",
     "\n",
     "# Add data.\n",
     "img_wrapper = ImageOmeZarrWrapper(\n",
@@ -534,7 +534,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vc = VitessceConfig(schema_version=\"1.0.17\", name=\"Image and segmentations (ome-tiff)\")\n",
+    "vc = VitessceConfig(schema_version=\"1.0.18\", name=\"Image and segmentations (ome-tiff)\")\n",
     "# Add data.\n",
     "wrapper = ImageOmeTiffWrapper(\n",
     "    img_url=ome_tiff_filepath,\n",