As I find more great things to do better with CellProfiler, I’ve been on a posting spree. Thanks in advance for your patience and help.
I have built a pipeline for analysing timelapse experiments looking at fluorescent reporters in worm embryos. The segmentation of the embryos is from brightfield images (so that reporter expression does not affect the size of the identified embryo). I then use Track Objects to follow the embryos through the frames. I am happy with the performance of this part of the pipeline.
My main problem is that I would like to save the ‘TrackObjects’ colour-coded image so I can manually check no funny business went on. The help for the module says that the image produced can be saved by a SaveImages module downstream. However when I try this I simply get a blank image. I have tried different formats and colourmaps but to no avail.
I have attached a shortened pipeline to illustrate the problem along with a short sequence of images that can be processed with it.