I am currently helping someone who has a whole pipeline already made but want to adapt it using the LoadData module and have the images in OMERO.
The main issue is that the different pipelines had names for the different channels different to the one in OMERO eg ‘Nuclei’ instead of ‘DAPI’ etc… I was wondering if there was a way to change these names in CellProfiler or if I should then change the names in all the already established pipelines and modules ?
I thought about using the color2gray or gray2color but I’m not sure this would be the way to go since the LoadData module already separates the different channels.
I hope this is clear enough otherwise I’ll add screenshots…
Thanks for the help !