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CHANGELOG.md

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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.

[0.1.6] - xxxx-xx-xx

  • (MERSCOPE) added feature_key attribute for points (i.e., the 'gene' column) #210

[0.1.5] - 2024-09-25

Added

  • (Xenium) added dims parameter for more control in xenium_aligned_image()

Fixed

  • Passing rgb=None to image model parser for both visium and visiumhd, leading to 3-4 channel images being interpreted as RGB(A)
  • Fix header bug Visium data #200
  • (Visium HD) Fix path parsing when images are missing #204 #206

[0.1.4] - 2024-08-07

Changed

  • (Xenium) changed default target of table to labels; radii of circles computed from cells, not nuclei #179
  • (Visium HD) changed default geometry to squares from circles for the bins; added parameter to choose #183
  • (CosMx) dropping points element with zero-length from the cosmx reader #191

[0.1.3] - 2024-07-03

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