Changelog

0.1.0

This marks the first release in the new repository. The archived parent can be found at github.com/ggirelli/radiantkit

Added the option –gaussian sigma to tiff_segment. That will low pass filter images with a Gaussian kernel as a first step in the segmentation pipeline. Solves issues with noisy image.
Added the option –slice2d to radial_population which will tell radiantkit to only extract intensities at the plane with the largest cross sectional area for each nuclei. Expected to be useful for nuclei grown and attached to coverslips.

Runs with Python 3.12 and probably also 3.13 but probably not with older versions.
Updated dependency list in pyproject.toml.
The documentation has been updated, although it is far from complete.
Changes reflection API changes in pandas and scikit-image.
Don’t care what the axes are called in the tif files, the first axis will be considered as the axial direction “Z”.
Fixed: Correct titles in the settings screens (several had the same title, “Object extraction”).
In radial_population: Files containing the word mask are not allowed to be used as regular images and will be silently ignored. This solves the issues that masks could be confused with normal images when the inreg was not properly configured.
It is considered an error (previously a warning) if there is more than one image per channel for any FOV when loading images from a folder.

Progressbars that were in the way for debugging (a few rich.track), can be enabled again in util.py