CellProfiler with StarDist

StarDist may give a nicer nucleus segmentation with less tweaking of parameters than the built-in IdentifyPrimaryObjects module. There is a plugin for running StarDist in CellProfiler: https://github.com/CellProfiler/CellProfiler-plugins/blob/master/runstardist.py.

Installing the plugin may be difficult, however. In this case you can use labels created by an automated StarDist run. The drawback is that this is done with default parameters, it may or may not be optimal for your images.

Fiji macro and example CellProfiler pipeline: https://github.com/UH-LMU/FijiStarDistCellProfiler.