Hello, Just when I start to analyze the pictures, it shows the error like this.
Can anybody help me with it?
I crop the picture by Image J first, so I do not know if I should not crop it ?
Cropping images beforehand should be just fine.
Do you mind uploading your .cpproj file so we can take a look at your settings? It seems the pipeline is having trouble somewhere!
Yes, of course. And also it is strange that I repeat it one more time, I could get the file. But sometimes I could not.
Final pipeline Hoechst and PCNA cellprofiler.cppipe (20.7 KB)
Hmm…I think the next step is for you find a situation where it is consistently producing the problem - my best guess is that it fails for some image sets/filenames and not others and that is why it’s not consistent. If you can figure out which images it fails on it might provide a clue to the problem.
I don’t know that the expected results are. I don’t know what you are asking.
As per your pipeline, it seems fine. As @AnneCarpenter mentioned you might have check with the particular image which shows error or not give the desired output.
As per above screenshot your number of nuclei image doesn’t match with cell images, but according to your pipeline your it should be equal.
In your saveImages module you might want to enable “No” for overwrite existing files because this could be dangerous!!
Another suggestion could be, in your Testmode please check if you are segmenting nuclei & its corresponding cells.
You had given the same name in two modules for example in Primary object “nuclei” & also in convert objectto image also same name. Not sure if this could be problem in save images (of course it would save the latest module output)
Sharing some sample images, also might help us to help you better!!
Hope this helps!!
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