v1.0.7

[1.0.7] - 2024-03-29

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 (for instance, to use the GPU)

Fixed

• set_transformation issue for image alignment
• Import issue (#37, #39)

v1.0.6

[1.0.6] - 2024-03-13

Added

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

Changed

• Using MultiscaleSpatialImage by default for multiplex imaging technologies

Fixed

• Issue in report creation when channel names are integers

v1.0.5

[1.0.5] - 2024-03-01

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

v1.0.4

[1.0.4] - 2024-02-14

Fix

• Missing transcript count in cells due to concurrent writing processes (#20)

Changed

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

v1.0.3

[1.0.3] - 2024-02-12

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

v1.0.2

[1.0.2] - 2024-01-15

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

v1.0.1

[1.0.1] - 2024-01-10

Added

• Tutorial on CLI usage
• Tutorial on image alignment with the Xenium Explorer
• Multi-step segmentation (#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

v1.0.0

First post-preprint release

Our preprint can be found here: https://www.biorxiv.org/content/10.1101/2023.12.22.571863v1

Stable version

Sopa v1.0.0 should now be stable. Don't hesitate to open new issues to continue improving the repository.

v0.2.1

First public version

Preprint coming soon