v0.1.3

[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"

v0.1.2

[0.1.2] - 2024-03-30

Added

• (Visium HD) added reader, coauthored with @LLehner

Fixed

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

v0.1.1

[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

v0.1.0-rc0

[0.1.0] - 2024-03-24

Added

• (MCMICRO) support for TMAs (such as the data of exemplar-002)
• (Xenium) support for post-xenium aligned images (IF, HE)
• (Xenium) reader for the selection coordinates file from the Xenium Explorer
• (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

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

v0.0.9

Fixed

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

v0.0.8

Fixed

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

v0.0.7

Fixed bugs in Xenium and MERSCOPE.

v0.0.5

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

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

0.0.4

Add a Curio reader

v0.0.3

Merge pull request #40 from scverse/fix/categories

Fix/categories