Add interactive region annotation tutorial#5
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Adds examples/interactive_annotate.ipynb covering the new `sdata.pl.annotate()` API from scverse/spatialdata-plot#684. Uses the same `squidpy.datasets.visium_hne_sdata()` dataset as visium_mouse_brain.ipynb so the download cache is shared. Structure follows the existing examples/ pattern: - Intro + dataset citation + install hint for the [interactive] extra - Load → render the image so the reader sees what to annotate - Widget invocation shown in a markdown fenced block (the static docs build can't execute the anywidget JS runtime; live-kernel users copy the snippet) - GIF placeholder cell — replace interactive_annotate.gif with a real recording before merging - "What the widget produces": a code cell that builds the equivalent ShapesModel directly via shapely + ShapesModel.parse, so downstream cells reproduce in the docs build without the widget - Overlay with render_shapes; polygon-crop via sd.polygon_query - Watermark block matching the other tutorials Wires the new entry into examples/index.md alongside the Visium card. Outstanding before merge: - Replace the hippocampus polygon coordinates with values from an actual annotation pass against visium_hne_sdata - Record interactive_annotate.gif (~3-5 s of drawing/saving) - Add interactive_annotate.png thumbnail for the gallery grid card Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pixi 0.54.2 refuses to load `[tool.pixi]` with dotted-key children (`workspace.channels = [...]`, `dependencies.python = ">=3.11"`, …) and requires one of `[tool.pixi.workspace]` / `.project` / `.package` as a real TOML table header. Rewrite the inline-dotted block into explicit `[tool.pixi.workspace]`, `[tool.pixi.dependencies]`, `[tool.pixi.pypi-dependencies]`, and `[tool.pixi.tasks]` sections so `pixi install` and `pixi run kernel-install` actually work. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Move existing thumbnails from beside their notebooks to a shared `_static/img/` directory (Sphinx convention) so all gallery media lives in one place: examples/visium_mouse_brain.png -> _static/img/visium_mouse_brain.png tutorials/getting_started.png -> _static/img/getting_started.png tutorials/color_and_palette.png -> _static/img/color_and_palette.png Update the `:img-top:` references in `examples/index.md` and `tutorials/index.md` to point at `../_static/img/<slug>.png`. Add step 6 to `CONTRIBUTING.md` documenting the convention: gallery thumbnails and notebook-embedded GIFs / screenshots go under `_static/img/`, never next to the notebook itself. Renumber the following CI step accordingly. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
The widget pivoted from the custom anywidget+JS canvas to the external `anybioimage` library's `BioImageViewer` (see scverse/spatialdata-plot#684). Update the tutorial to match: - Intro: replace the anywidget/SVG architecture blurb with a description of the `BioImageViewer` backend. - Launch section: rewrite the API signature from the old positional `annotate(coordinate_system, element, persist=True)` to the new keyword-only chain-step form `.pl.render_images(...).pl.annotate( coordinate_systems=...)`. Drop the lasso tool (no longer present) and the JS-canvas-specific shortcut list. Replace the "Write to disk" button with a `sdata.write_element(<name>)` follow-up note. - Polygon query cell: pass the actual shapely geometry rather than the whole `GeoDataFrame`. spatialdata's `polygon_query` overload for `DataArray`/`DataTree` calls `GeoDataFrame(geometry=[polygon])` internally, which fails with `GeometryTypeError: Unknown geometry type: 'featurecollection'` if passed a nested gdf. - Watermark: drop `anywidget` (transitive dep that isn't imported by any executable cell) to keep the watermark report honest. - Add a `warnings.filterwarnings("ignore")` housekeeping cell ahead of the squidpy dataset load so the notebook's recorded outputs don't leak Zarr v3 deprecation chatter into the docs build. - Add the recorded GIF (`_static/img/interactive_annotate.gif`) and a placeholder PNG thumbnail (regenerate before merging). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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📖 Docs preview: https://scverse.org/spatialdata-plot-notebooks/pr-5/gallery.html Built from ef91a72; redeployed on every push. |
timtreis
changed the title
0.4.0 ships `sdata.pl.annotate()` (scverse/spatialdata-plot#684), so the tutorial can require the published wheel instead of an editable path. Re-executed the notebook to refresh the watermark output to 0.4.0. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Adds
examples/interactive_annotate.ipynbforsdata.pl.annotate(), backed byanybioimage'sBioImageViewer.squidpy.datasets.visium_hne_sdata()and renders the H&E.interactive_annotate.gifshows the live UX in the rendered docs.ShapesModel.parse(...)cell stands in for a real draw + Save so downstream cells (overlay,polygon_query) execute reproducibly in CI.examples/index.md: gallery card + toctree entry.