CellProfiler Pixel classification

@bcimini @VolkerH
I would need a simple (random forest) based pixel classification in CellProfiler.
Is there something useable for CP3.*.*?

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I am aware of this plugin which calls ilastik:


I haven’t tried it myself. Maybe the Cellprofiler team can give you additional information.

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Thanks!

@agoodman @ilastik_team

  1. Has the predict plugin been recently tested?
  2. How do you add a plugin to CellProfiler?

Hi @Christian_Tischer,

I have never tried to use it with cp3, but would be very interested in how this turns out. So in case you give it a go, please give me a call so I can sit in :wink:

@k-dominik and I gave it a try and we got it to work. Attached are an example image, CellProfiler pipeline and ilastik project.
Archive.zip (46.9 KB)

There are however few things that could be improved and @k-dominik nicely agreed to have a look.

cc @edward.law

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