CHANGELOG.md

Changelog

0.3.4

• StarDist moved to optional dependency group, global import removed
• b2c.stardist() accepts optional custom model/axes, and prints out parameter overrides

0.3.3

• b2c.view_cell_labels() to show cell-level metadata on the morphology segmentation

0.3.2

• b2c.view_labels() as a more lightweight, whole image level take on b2c.view_stardist_labels()
• b2c.actual_vs_inferred_image_shape() as an image dimension based assessment of source image validity
• custom image functions now can skip storing the image in the object, open up control over the image key, have the buffer included by default in both sets of generated keys, and print out any stored keys
• b2c.expand_labels() switches algorithm control to new algorithm argument
• b2c.salvage_secondary_labels() stores secondary label offset
• b2c.bin_to_cell() stores object ID as an integer in the cell object .obs

0.3.1

• add b2c.check_bin_image_overlap() for friendlier handling of users loading the incorrect image

0.3.0

• rework b2c.expand_labels() to be more robust:
  • evaluate a user-controlled k assigned bins for each unassigned bin
  • alternative expansion distance algorithm based on label area
  • max_call_distance is a new query by k array with maximum acceptable distance for each hit, making potential algorithmic expansion easier
  • simplify minima evaluation logic into two (queries with 1 and >1) rather than three steps

0.2.0

• add spaceranger_image_path to b2c.read_visium() in response to 10X creating a unified spaceranger spatial folder
• b2c.scaled_if_image() for processing IF images
• ignore out of bounds pixels in b2c.insert_labels()

0.1.1

• cap numpy at 1.x for the time being

0.1.0

• initial release