Import label mask images to CellProfiler

[Christian_Tischer]

Hi All,

I am 100% sure I asked this already but I could not find the post.

Let’s say we use StarDist for nucleus segmentation and get a label mask image as an output. Is there a way to load this into Cellprofiler and convert it into objects? I think this would require a “Label mask to Objects” module in CellProfiler, but I don’t think that exists, does it?

cc @aklemm @VolkerH

[aklemm (Anna Klemm)]

@Christian_Tischer

for nucleus segmentation and get a label mask image as an output. Is there a way to load this into Cellprofiler and convert it int

Hi @Christian_Tischer

there is the ConvertImageToObjects module that does that. I am using the latest version, ver 4.0.7.

Cheers
Anna

[bcimini (Beth Cimini)]

You can also load it in the NamesAndTypes module as image type “Objects”; I haven’t tried it specifically with StarDist output but anything that’s a label matrix should in theory work.

[Christian_Tischer]

Thanks @bcimini and @aklemm
This is super helpful to know!