Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

• spatialrefinery.core: a technology/converter registry (registry), shared spatial-omics helpers (utils), an image-to-pyramidal-OME-TIFF converter (converter, with an optional czi extra for Zeiss CZI via bioio), and a retrying, atomic-write asset downloader (downloader).

• spatialrefinery.io.xenium: convert 10x Genomics Xenium bundles to 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.