Preview for PR #2 7026ef4

Author: timtreis

pr-2/_sources/notebooks/tutorials/visium_breast_cancer.ipynb

@@ -9,9 +9,9 @@
     "\n",
     "This tutorial walks through visualising a real 10x Genomics Visium experiment with `spatialdata-plot`: H&E tissue image, spot polygons, gene expression overlays, and publication-style styling.\n",
     "\n",
-    "**Dataset**: [Human Breast Cancer (Block A Section 1)][10x] from 10x Genomics — fetched once via `scanpy.datasets.visium_sge` and cached by `pooch` for subsequent runs.\n",
+    "**Dataset**: [Human Breast Cancer (Block A Section 1)][10x] from 10x Genomics \u2014 fetched once via `scanpy.datasets.visium_sge` and cached by `pooch` for subsequent runs.\n",
     "\n",
-    "**Credit**: the example progression in this tutorial — H&E + spots, gene-expression overlays, outline styling — was originally curated by [@asarigun](https://github.com/asarigun) in [scverse/spatialdata-plot#590](https://github.com/scverse/spatialdata-plot/pull/590).\n",
+    "**Credit**: the example progression in this tutorial \u2014 H&E + spots, gene-expression overlays, outline styling \u2014 was originally curated by [@asarigun](https://github.com/asarigun) in [scverse/spatialdata-plot#590](https://github.com/scverse/spatialdata-plot/pull/590).\n",
     "\n",
     "[10x]: https://www.10xgenomics.com/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0"
    ]
@@ -43,14 +43,14 @@
      "data": {
       "text/plain": [
        "SpatialData object\n",
-       "├── Images\n",
-       "│     └── 'tissue': DataArray[cyx] (3, 2000, 2000)\n",
-       "├── Shapes\n",
-       "│     └── 'spots': GeoDataFrame shape: (3798, 2) (2D shapes)\n",
-       "└── Tables\n",
-       "      └── 'table': AnnData (3798, 36601)\n",
+       "\u251c\u2500\u2500 Images\n",
+       "\u2502     \u2514\u2500\u2500 'tissue': DataArray[cyx] (3, 2000, 2000)\n",
+       "\u251c\u2500\u2500 Shapes\n",
+       "\u2502     \u2514\u2500\u2500 'spots': GeoDataFrame shape: (3798, 2) (2D shapes)\n",
+       "\u2514\u2500\u2500 Tables\n",
+       "      \u2514\u2500\u2500 'table': AnnData (3798, 36601)\n",
        "with coordinate systems:\n",
-       "    ▸ 'global', with elements:\n",
+       "    \u25b8 'global', with elements:\n",
        "        tissue (Images), spots (Shapes)"
       ]
      },
@@ -283,7 +283,7 @@
    "source": [
     "## Coloring spots by a category\n",
     "\n",
-    "`color=` also accepts categorical columns — here, the `in_tissue` flag 10x sets to mark spots that fall on tissue."
+    "`color=` also accepts categorical columns \u2014 here, the `in_tissue` flag 10x sets to mark spots that fall on tissue."
    ]
   },
   {
@@ -375,9 +375,9 @@
    "source": [
     "## Where to next\n",
     "\n",
-    "- **API reference** — every parameter of `render_shapes`, `render_images`, and `show()` is documented in the [plotting API](https://spatialdata.scverse.org/projects/plot/en/latest/api.html).\n",
-    "- **Getting started tutorial** — if you skipped it, the [Getting started](./getting_started.ipynb) tutorial covers the same fluent API on the lightweight built-in `blobs` dataset.\n",
-    "- **Contributing** — found a missing example? Open a PR on [`spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks)."
+    "- **API reference** \u2014 every parameter of `render_shapes`, `render_images`, and `show()` is documented in the [plotting API](https://spatialdata.scverse.org/projects/plot/en/latest/api.html).\n",
+    "- **Getting started tutorial** \u2014 if you skipped it, the [Getting started](./getting_started.ipynb) tutorial covers the same fluent API on the lightweight built-in `blobs` dataset.\n",
+    "- **Contributing** \u2014 found a missing example? Open a PR on [`spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks)."
    ]
   }
  ],