Spatialdata-io

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

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

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

Fixed

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

Fixed

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