Spatialdata

Changed

- Using `DataArray` directly instead of the subclass `SpatialImage` (removed install constraint for the `spatial_image` package) 587
- Using `DataTree` directly instead of the subclass `MultiscaleSpatialImage` (removed install constraint for the `multiscale_spatial_image` package) 587
- Changed `element`parameter (deprecation in v0.3.0) of `transform_element_to_coordinate_system` to a string `element_name` 611

Major

- Added operation: `to_polygons()` quentinblampey 560
- Extended `rasterize()` to support all the data types quentinblampey 566
- Added operation: `rasterize_bins()` quentinblampey 578
- Added operation: `map_raster()` to apply functions block-wise to raster data ArneDefauw 588

Minor

- Removed `pygeos` dependency omsai 545
- Channel coordinate annotations on images now persist through `rasterize()` clwgg 544
- Added `datasets` module
- Extended `get_values()` to `AnnData` tables 579
- Added `get_element_instances()` (replaces `_get_unique_label_values_as_index()`) 582
- Added `get_element_annotators()`, retrieving the tables that annotate a particular SpatialElement 595

Fixed

- Preserve channel names of multi-scale images in `transform` (379)
- Fix `filter_by_coordinate_system` with SpatialData object having a table not annotating an element (619)

- (MERSCOPE) added `feature_key` attribute for points (i.e., the `'gene'` column) 210
- (Visium HD) get transformation matrices even when only images are parsed 215

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