radiantkit version 0.1.0

Radial Image Analysis Toolkit (RadIAnTkit or simply radiantkit) is a Python3.12+ package containing tools for full-stack image analysis for YFISH images, such as used in the GPSeq pipeline. This is a detached fork of the original, now archived, repository at github.com/ggirelli/radiantkit.

Pipeline summary

• Convert proprietary microscope formats CZI (Zeiss) and ND2 (Nikon) to the TIFF format.

• Segment nuclei in 2D or 3D.

• Select nuclei in G1-phase of the cell cycle, based on DNA staining and nuclear volume.

• Extract segmented objects and measure their features (e.g., volume, integral of intensity, shape descriptors).

• Measure radial patterns as radial profiles (with different center definitions), and characterize them (e.g., peaks, inflection points, contrast).

• And finally, generate interactive reports.

Contents:

• Example usage
  • Extract images as tiff files from nd2
  • Segment nuclei
  • Extract radial profiles
  • Select nuclei
  • Generate a report
  • Example script
• Details
  • nd2_to_tiff
  • tiff_findoof
  • tiff_segment
  • radial_population
  • report
• Installation
  • Requirements
  • Install
  • Check your installation
  • When Python < 3.12
  • Docker
• Changelog
  • 0.1.0
• Codebase
  • Class inheritance
• Future / to do
  • Refactoring