Add Visium card to Examples in gallery#657
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The Visium mouse-brain notebook moved from tutorials/ to examples/ in
spatialdata-plot-notebooks (matching the convention: tutorials teach
the API on synthetic data, examples demonstrate it on real datasets).
Add the corresponding card + thumbnail to the gallery's Examples grid;
drop the "no examples yet" placeholder note that's now stale.
Tutorials section reframed to make the split explicit ("entry-point
material for learning the API on synthetic data" vs Examples'
"worked examples on real datasets you'd actually analyse").
Depends on scverse/spatialdata-plot-notebooks#2 for the file move; CI
will fail on this PR until that merges and the lib's submodule pull
catches up.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #657 +/- ##
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Coverage 77.07% 77.07%
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Files 11 11
Lines 3280 3280
Branches 774 774
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Hits 2528 2528
Misses 454 454
Partials 298 298 🚀 New features to boost your workflow:
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timtreis
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May 12, 2026
PR #657 added the card originally; the placeholder note slipped back in during a later rebase. Restores the card and ships the refreshed thumbnail from the updated notebook (publication-style figure colouring spots by Mbp expression on the H&E tissue).
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Summary
Adds the Visium mouse-brain notebook to the gallery's Examples section as a card with thumbnail. Reframes the Tutorials/Examples split to make it explicit:
Drops the now-stale "no examples yet" placeholder note from the Examples section.
Changes
No new dependencies. Local docs build verified clean under `-W`.
Dependency
Depends on scverse/spatialdata-plot-notebooks#2 which moves `visium_mouse_brain.ipynb` from `tutorials/` to `examples/`. The card on this PR links to `notebooks/examples/visium_mouse_brain`, which only resolves once #2 merges and the next docs build pulls fresh notebooks main (`post_checkout: git submodule update --init --remote --recursive`).