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Changelog

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

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.

[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

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