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rushin682 merged 2 commits into from
Aug 31, 2026
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Changelog and API reference follow-ups for the segmentation pipeline #11

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7fac19a
Add changelog entries for the segmentation pipeline
rushin682 Aug 31, 2026
d973fae
Drop default_zarr_path from the API reference
rushin682 Aug 31, 2026
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -20,3 +20,11 @@ and this project adheres to [Semantic Versioning][].
SpatialData zarr stores, optionally with aligned H&E images, tissue
segmentation, and Visium-like pseudo-spots; download a Xenium study's raw
assets from a `curl -O <url>` manifest.
- `spatialrefinery.segmentation`: nucleus segmentation on H&E whole-slide
images via InstanSeg (`instanseg`), and export of the resulting boundaries
as a SpatialData zarr store carrying the slide image, the nucleus polygons,
and a table over a template gene panel (`to_spatialdata`). Needs the
optional `segmentation` extra. The store is named for the slide's stem, so
`slide.ome.tif` yields `slide.zarr`.
- Tutorial notebook for the segmentation pipeline, taking an OME-TIFF through
segmentation to a written SpatialData zarr.
1 change: 0 additions & 1 deletion docs/api.md
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Expand Up @@ -61,7 +61,6 @@ extra -- see [Installation](installation.md).
:nosignatures:

geojson_to_spatialdata
default_zarr_path
```

:::{note}
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