imcyto pipeline won't return same output as CellProfiler

[SBata]

hi guys, I’m running into a problem with imcyto where if I run the segmentation.cppipe by itself in CellProfiler using tiffs from one of the ROIs, it works well ( = it finds various cells, markers etc…), however, when I run nf-core/imcyto with the exact same mcd file, I do not get any of the results I get running the tiffs separately. and those tiffs were taken from the work directory. for example, I get a nice mask for tumor cells if I run tiffs through CellProfiler, but if get no mask through nf-core/imcyto….any suggestions? and yes, I did use the same .cppipe file. tnx!