Program to analyse Omero high-throughput microscopy images

This is a beta version of the program; additional bug fixes and testing necessary Requires a connection to an active Omero server

Contributors

Robert Zach, Haoran Yue, Alex Herbert and Helfrid Hochegger

Purpose of the program

Analysing hightroughput imaging data using Omero Screen data base.

Images are first pre-processed using flatfield correction, then segmenthed using optimised cellpose models. Single cell features (default,: area, min max intensities) for each channel are extracted and stored in a final data frame.

The input metadata are provided via an Excel file (see data/sample_metadata.xlsx)

TODO Generate module to make Figures for cell cycle data

TODO Add omero screen metadata storage functionality

TODO use classifier for mitotic interphase separation and free up H3 channel