Sopa

Added
- Support Xenium multimodal segmentation as a prior for Baysor (80)
- For snakemake, you can set a `BAYSOR_EXECUTABLE_PATH` environment variable to indicate the path of the Baysor executable
- Added [ComSeg](https://github.com/fish-quant/ComSeg) segmentation by tdefa (#76)

Fix
- Fix Xenium reader issue for recent machine versions (80)
- Fix type issue (`DataTree` and `DataArray`) related to `spatialdata>=0.2.0` (85)
- Fix `sjoin` issue related to `geopandas>=1.0.0`

Changed
- Fully depends on `spatialdata-io` for the MERSCOPE and the Xenium reader
- Use `DataArray` and `DataTree` typing instead of (Multiscale)SpatialImage (as in `spatialdata>=0.2.0`)

First post-publication release

Changed
- Using `rioxarray` as a default backend for MERSCOPE data if installed
- Lower RAM usage for channels aggregation
- Transcript-segmentation API more general (not Baysor-specific)

Fixed
- Encoding issue while writing the report (64)

Changed
- Renamed `embed_wsi_patches` to `infer_wsi_patches`
- `infer_wsi_patches` now accepts also callables
- Improves tile gathering speed and decreases overall computation of tile-wise inference

Changed
- Xenium reader now adds channel names, and support more recent versions (68)
- Renamed `sopa.embedding` into `sopa.patches`, and moved internal files
- Don't recompute `to_multiscale` if the right scales are already used for Xenium Explorer image writing

Added
- New tutorial on Xenium Explorer interoperability

Fix
- Fix polygon selection when no channel is provided
- Fix CosMX reader for proteins
- Fix FOV column issue for CosMX data (65)

Added
- Check the columns of CosMX data to see if the correct export module was used

Changed
- Ensure categorical variables are used for patches clustering

Added
- Can overlay a custom segmentation (merge boundaries)
- Xenium Explorer selection(s) can be added as shapes in a SpatialData object
- Optionnal OpenSlide backend for WSI data
- New `sopa.io.aicsimageio` reader for special formats (58)

Changed
- Rename `Aggregator.update_table` to `Aggregator.compute_table`