CellProfiler Pipeline compatibility issues


My lab uses CellProfiler 2.1.1 version for doing segmentation. However, I have a new Mac computer (with Mac OS Big Sur) and it only lets me use CellProfiler 4.07 version. Due to compatibility issues I can’t use the pipeline we established in that version for generating Fishquant (FQ) outlines.

I tried to create a new pipeline with this version. However, I noticed that there are changes in the modules from the old version not available in this new version (I attach a link with a powerpoint highlighting these differences). As I am new, I can’t find the right modules to use in order to incorporate these missing features in my new Pipeline. I tried following this blog that is a guide discussing converting pipelines from CellProfiler 2.0 to 3.0 but they don’t discuss all the features that are found in our 2.1.1 pipeline in order to convert them to my 4.07 version.

In the end when I generated FQ Outlines (from the modifications I did) I got the message: MORE THAN ONE POLYGON FOUND. Will choose largest. This leads to the creation of an FQ outline for a single cell instead of the individual cells from the segmentation files (Please see file in URL for how this looks).

Could someone help me figure out what modules in the 4.07 version I should be adding in order to incorporate all the features of my 2.1.1 pipeline?

Thank you!

URL: Cellprofiler.pptx - Google Drive

Hi @Jacob_S ,

Inspite of more variation between CP2.1.1 to CP4.0.7, one could reproduce the pipeline with the same modules but with more options. Between these two versions there is difference in the process of segmentation itself, so there would be slight with the measurements. But you have all the measurements available still like your previous version. When I checked you ppt, you new pipeline, you were almost right. In few places I have mentioned if there is change, rest looks ok. PFA.
Still I am not able to understand you error that you are getting. It would be great if you share the pipeline with some same image to check if we could reproduce the error & check the issue.
Cellprofiler.pdf (4.4 MB)