add import spatialdata_plot

Author: stephenwilliams22

notebooks/examples/visium_hd_mouse_brain.ipynb

@@ -15,7 +15,9 @@
       "/mnt/home/stephen.williams/micromamba/envs/spatialdata-io/lib/python3.12/site-packages/pyproj/network.py:59: UserWarning: pyproj unable to set PROJ database path.\n",
       "  _set_context_ca_bundle_path(ca_bundle_path)\n",
       "/mnt/home/stephen.williams/micromamba/envs/spatialdata-io/lib/python3.12/site-packages/xarray_schema/__init__.py:1: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
-      "  from pkg_resources import DistributionNotFound, get_distribution\n"
+      "  from pkg_resources import DistributionNotFound, get_distribution\n",
+      "/mnt/home/stephen.williams/micromamba/envs/spatialdata-io/lib/python3.12/site-packages/anndata/__init__.py:44: FutureWarning: Importing read_text from `anndata` is deprecated. Import anndata.io.read_text instead.\n",
+      "  return module_get_attr_redirect(attr_name, deprecated_mapping=_DEPRECATED)\n"
      ]
     },
     {
@@ -35,6 +37,7 @@
     "import tempfile\n",
     "import subprocess\n",
     "import scanpy as sc\n",
+    "import spatialdata_plot\n",
     "\n",
     "print(f\"spatialdata_io=={sdio.__version__}\")\n",
     "print(f\"spatialdata=={sdata.__version__}\")"
@@ -46,7 +49,8 @@
    "metadata": {},
    "source": [
     "# Download Visium HD example dataset from 10x public data repository\n",
-    "You'll need approximately 15 Gb of disk space"
+    "\n",
+    "You'll need approximately 15 Gb of disk space\n"
    ]
   },
   {
@@ -103,7 +107,7 @@
    "id": "d3179312",
    "metadata": {},
    "source": [
-    "# Read in Visium HD data"
+    "# Read in Visium HD data\n"
    ]
   },
   {
@@ -204,7 +208,7 @@
    "id": "cee7dab5",
    "metadata": {},
    "source": [
-    "# Visualize the images and segmentations"
+    "# Visualize the images and segmentations\n"
    ]
   },
   {
@@ -289,7 +293,7 @@
    "id": "a51d631b",
    "metadata": {},
    "source": [
-    "Now let's visualizes a relevant gene Hpca"
+    "Now let's visualizes a relevant gene Hpca\n"
    ]
   },
   {
@@ -352,7 +356,7 @@
    "id": "7a6e7f25",
    "metadata": {},
    "source": [
-    "# Quality control and filtering"
+    "# Quality control and filtering\n"
    ]
   },
   {
@@ -461,7 +465,7 @@
    "id": "dcf446f2",
    "metadata": {},
    "source": [
-    "# Normalization and Clustering"
+    "# Normalization and Clustering\n"
    ]
   },
   {
@@ -634,7 +638,8 @@
    "metadata": {},
    "source": [
     "# Calculate centroids\n",
-    "Use nucleus centroids for this calculation for use in analyses like cell cell communication "
+    "\n",
+    "Use nucleus centroids for this calculation for use in analyses like cell cell communication\n"
    ]
   },
   {