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.

[0.1.3] - xxxx-xx-xx

Added

(Xenium) support reading multi-polygon selection files from the Xenium Explorer
(ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
(Stereo-seq) Added reader @LLehner @timtreis @florianingelfinger #70
(MERSCOPE) Optional rioxarray backend for MERSCOPE data (reads chunks)
(MERSCOPE) Can choose which elements should be loaded

Fixed

(Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique. obs_names_make_unique is now called internally to enforce unique index values allowing for join operations.

Changed

(MERSCOPE) "global" coordinate system is used as a default instead of "microns"

[0.1.2] - 2024-03-30

Added

(Visium HD) added reader, coauthored by @LLehner

Fixed

(Xenium) reader for 1.0.1 (paper data) and unknown versions
(Xenium) fix in reading "minimalistic" Xenium datasets #132

[0.1.1] - 2024-03-24

Added

(Xenium) support for post-xenium aligned images (IF, HE)
(Xenium) reader for the selection coordinates file from the Xenium Explorer
(Xenium) support for the new Xenium 2.0.0 (multimodal segmentation)
(Xenium) reading multiscale labels from cells.zarr.zip
(MCMICRO) support for TMAs (such as the data of exemplar-002)
(DBiT-seq) reader
converter functions experimental.to_legacy_anndata() and experimental.from_legacy_anndata()
(Visium) support for raw reads (capture locations not under tissue)

Fixed

(Xenium) fixed index (fail on write)
(Xenium) renamed cells_as_shapes to cells_as_circles; set default to True
(MERSCOPE) don't try to load unexisting elements #87
(Visium) fixed axes ordering

[0.0.9] - 2023-11-06

Fixed

(Xenium) bug when converting feature_name #81, from @fbnrst
(Visium) visium() supports file counts without dataset_id #91

[0.0.8] - 2023-10-02

Fixed

(Xenium) coerce cell id to str #64
(MERSCOPE) fix coordinate transformation #68
(MERSCOPE) Improvements/fixes: merscope reader #73

[0.0.7] - 2023-07-23

Fixed

Bugs in Xenium and MERSCOPE

[0.0.5] - 2023-06-21

Added

MERFISH reader (from @quentinblampey)
CODEX reader (from @LLehner)

Fixed

Issues on Visium reader (thanks @ilia-kats) and Xenium reader

[0.0.4] - 2023-05-23

Added

Curio reader

[0.0.3] - 2023-05-22

Merged

Merge pull request #40 from scverse/fix/categories

[0.0.2] - 2023-05-04

Changed

Revert version regex (#37)

[0.0.1] - 2023-05-04

Tested

Test installation from pypi