From 7fac19a98dbe22411ae1f9b1fc5a4ca1295c7d70 Mon Sep 17 00:00:00 2001 From: Rushin Gindra Date: Mon, 31 Aug 2026 20:55:57 +0200 Subject: [PATCH 1/2] Add changelog entries for the segmentation pipeline Covers the segmentation module, the optional extra, the zarr store naming, and the tutorial notebook. --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c217be..af6febf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 ` 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. From d973fae617c5f2119e45b0392799ec09ed3a1e33 Mon Sep 17 00:00:00 2001 From: Rushin Gindra Date: Mon, 31 Aug 2026 20:59:10 +0200 Subject: [PATCH 2/2] Drop default_zarr_path from the API reference It is a naming helper, not an entry point; the two functions above it are the documented surface. --- docs/api.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/api.md b/docs/api.md index ccf7a50..d9eb9d9 100644 --- a/docs/api.md +++ b/docs/api.md @@ -61,7 +61,6 @@ extra -- see [Installation](installation.md). :nosignatures: geojson_to_spatialdata - default_zarr_path ``` :::{note}