v2.1.1

[2.1.1] - 2025-07-16

Added

• Log a warning in sopa.io.visium_hd if the fullres image is too small (potentially a user error)
• Added a allow_holes argument to sopa.segmentation.tissue to decide whether to keep holes or not
• correction argument in sopa.spatial.mean_distance to account for the bias related to group proportions (experimental)
• The Docker CI now also pushes the images with the latest tag

Changed

• CosMx reader: use flip_image=False by default (#231)

Fixed

• _smoothen_cell returns an empty polygon if the cell can't be smoothened (#279)
• Remove NaN genes before transcript-based segmentation (#283)
• Broken link in the docs @ChristopherBottomsOMRF (#284)
• Added again the command ps to all Docker images for Nextflow