Sopa

Added
- CosMX reader with image stitching (experimental)

Changed
- Default `min_transcripts` set in snakemake configs
- Minimum number of transcripts per patch set to 4000 (41)
- Config files refactoring (configs added or renamed)
- Readers refactoring
- Section with error during report are not displayed (instead of throwing an error)

Added:
- Support multiple tables

Fixed
- Spatial elements not saved when data is not backed

Hotfix: resolve issues related to `spatialdata>=1.0.0`

Changed
- Improvements in the CLI and API tutorials
- Sequential segmentation now requires `patchify` to be run independently
- Dependency `spatialdata>=0.1.1`

Added
- Kwargs can be provided to Cellpose model init

Fixed
- `set_transformation` issue for image alignment
- Import issue 37 39

Added
- Spatial join between shapes (`from sdata.spatial import sjoin`)
- H&E tutorial (basic usage)
- New backend for the MERSCOPE reader (requires `rioxarray`, currently experimental, should use less RAM)

Changed
- Using `MultiscaleSpatialImage` by default for multiplex imaging technologies

Fixed
- Issue in report creation when channel names are integers

Changed
- Faster image writing for the Xenium Explorer (about x5 speedup)
- Cellpose default model set to `"cyto3"` (new cellpose version)
- Cell GeoDataFrame index consistent with `obs_names`

Added
- Support for python 3.9 to 3.11 (we still recommend `python==3.10`)
- Support WSI analysis: reader, tissue segmentation, patch embedding (tutorials coming soon)
- Supporting multiple region-of-interest queries
- Can load a custom cellpose model using the `pretrained_model`/`model_type` argument