diff --git a/docs/_static/gallery/visium_mouse_brain.png b/docs/_static/gallery/visium_mouse_brain.png new file mode 100644 index 00000000..a1f80e5b Binary files /dev/null and b/docs/_static/gallery/visium_mouse_brain.png differ diff --git a/docs/gallery.md b/docs/gallery.md index e921d7d9..0a867667 100644 --- a/docs/gallery.md +++ b/docs/gallery.md @@ -1,7 +1,7 @@ # Gallery -Curated, runnable examples demonstrating `spatialdata-plot` on real -spatial-omics datasets and on the lightweight `blobs` dataset. +Runnable examples demonstrating `spatialdata-plot` on real spatial-omics +datasets and on the lightweight `blobs` dataset. Sources live in [`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks); @@ -10,7 +10,7 @@ against the latest `spatialdata-plot` release. ## Tutorials -End-to-end workflows on real datasets. +Entry-point material for learning the API on synthetic data. ::::{grid} 1 2 2 2 :gutter: 3 @@ -20,7 +20,7 @@ End-to-end workflows on real datasets. :link-type: doc :img-top: _static/gallery/getting_started.png -The fluent `.pl` API, layering, and styling — on the in-memory `blobs` +The fluent `.pl` API, layering, and styling on the in-memory `blobs` dataset. Ideal first read. ::: @@ -28,11 +28,21 @@ dataset. Ideal first read. ## Examples -```{note} -No focused examples yet — contributions welcome! See -[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md) -in the notebooks repo for how to add one. -``` +Worked examples on real datasets you'd actually analyse. + +::::{grid} 1 2 2 2 +:gutter: 3 + +:::{grid-item-card} Visium mouse brain +:link: notebooks/examples/visium_mouse_brain +:link-type: doc +:img-top: _static/gallery/visium_mouse_brain.png + +Render H&E tissue, overlay spots, color by gene expression and by cluster, +and finish with a publication-style figure. +::: + +:::: ```{toctree} :hidden: diff --git a/docs/notebooks b/docs/notebooks index e0ac82ac..3df9d61e 160000 --- a/docs/notebooks +++ b/docs/notebooks @@ -1 +1 @@ -Subproject commit e0ac82ace2e4a754a71682e6ee57ab24ec3ec353 +Subproject commit 3df9d61e454c96684b94452f767a4679bad54314