Sopa

Fix
- Missing transcript count in cells due to concurrent writing processes (20)

Changed
- Explorer images should have a higher contrast (not clipping values anymore)

Breaking changes
- `pixelsize` argument has been renamed to `pixel_size` (the snakemake pipeline is only deprecating it for now)

Added
- The `phenocycler` reader can now also read `.tif` files (not just `.qptiff`)
- Added missing legend in the HTML report under the "Channels" section (15)
- The cell area is also stored in the table (in `.obs["area"]`)

Changed
- The `uniform` toy dataset now has two coordinate systems (better test case)
- Faster table conversion to the Xenium Explorer

Fixed
- Tight patching more stable with epsilon constant

Fix
- When geometries are `GeometryCollection`, convert them back to Polygons (11)
- Give `min_area` parameter to the right Baysor function in snakemake

Added
- API tutorial
- `sopa.spatial` tutorial
- Docstrings for the snakemake pipeline utils
- Show right micron scale in the Xenium Explorer

Changed
- `sopa.stats` is now called `sopa.spatial`

Added

- Tutorial on CLI usage
- Tutorial on image alignment with the Xenium Explorer
- Multi-step segmentation ([8](https://github.com/gustaveroussy/sopa/issues/8))
- Tutorial for multi-step segmentation and custom segmentation
- Improved installation guide

Fix
- CLI issue (missing file) when used without Snakemake

Change

- Use `.parquet` instead of `.zarr.zip` format to store intermediate boundary polygons

Added

- First official release
- Preprint at https://www.biorxiv.org/content/10.1101/2023.12.22.571863v1