Problem opening older pipelines with new version of CellProfiler 3.1.9

hi everyone,

I want to use the following pipelines:
Pipeline_Main_Nieland_Sabatini.cp (75.5 KB) cp) (14.2 KB)
But when I try to import them it doesn’t work. Error message one is:

And the second error message after is:

How can this be fixed? Thank you in advance.


11675- that is a SUPER old pipeline! That’s a version of CellProfiler 2.0 from 2012, so I’m not surprised it doesn’t directly load.

In general, my strategy was going to be to open it in 2.2.0, then save it as a cppipe, and then open in 319, but since that pipeline apparently uses the RunImageJ module, the last CellProfiler version it will work in is 2.1.1, which I personally can’t run on my Mac (though downloads are still available on our website).

Note though we don’t support those older releases anymore, so if there are any bugs that are blocking, you may need to find a solution that doesn’t use RunImageJ so you can use more up-to-date versions of CellProfiler.

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Thanks a lot. That worked and in anyone else wants to use it you have to delete the RunImageJ module in CellProfiler 2.2.0. from the pipeline and then add the module tubeness back to pipeline in the 319 version. Because if you do not do that you will loose all the other modules after that one with the 319 version.

I anyway just want to use the pipeline to have something to start with and not entirely having to built one from scratch. So what I have now is a good start.

I am now facing another problem. I cannot open the following jar file and see what was done in that macro. Or let me know the modules to use in the new CellProfiler version?
tubeness2_0.jar (79.9 KB)

Thanks a lot in advance

I assume that’s the jar for the FIJI Plugins->Analyze->Tubeness filter, though maybe some ImageJ folks can confirm? In any case, it’s an ImageJ file.

If it behaves similarly to the current FIJI function I indicated above, the closest CellProfiler functions would be EnhanceOrSuppressFeatures in Neurite->Tube mode, or EnhanceEdges.

Totally forgot: Thanks a lot for your help. I had already used the right module. YAY :slight_smile:
Pipeline is already running quite smooth.

Stay safe!

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