v2.1.5

[2.1.5] - 2025-10-11

Added

• Use the default proseg presets if infer_presets = True (default) and if not yet provided in the command_line_suffix
• Exclude the CosMX control genes from the transcript patches and the aggregation
• Added optional only_excluded argument in count_transcripts to count the genes that are normally excluded from the counts (#329)

Fixed

• Ensure that cell expansion with no overlap preserves a polygon output (#318)
• Fixed proseg usage on CosMx data (#323)
• Don't perform segmentation on extremely small patches @Marius1311 (#282)
• Fixed incorrect prior cell ID assignment to float dtype instead of int in the CosMx reader when fov is not None (#335)
• Do not save the cache column in the transcript patches to allow moving the .zarr directory before segmentation

Broken changes

• The CosMX reader now stores the transcript coordinates in microns instead of pixels, so Baysor/Comseg config needs to be adjusted (#323)