Spatialdata-io

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

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

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"

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

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

Fixed

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