Cell membrane presence or absence

Hi all,

I am trying to set up an Ilastik classifyer with three labels in order to identidy cells with a full circle cellular membrane, cells without a full membrane and negative areas (outside the section, blood vessels, folds, etc). My strategy so far has been the following:

Label one: negative areas
Label two: cell membrane
Label three: cytoplasms (no nucleus in the inside)

Any ideas on how to compile that or is there is an existing pipeline for that? Also, is there any step to set up automatically flourescence intensity and background reducing?

Thank you!

Hi Anna,

Are you trying to bring the classes/labels that you built in Ilastik to CellProfiler?
If that’s the case, you can mask your image with each of the labels using “MaskImage” module, and then use “IdentifyPrimaryObject” to detect your desired areas/cells.

Depend on your image, you might be able to detect all of your cells/desired areas in just CellProfiler as well.
You can find some general examples here: https://cellprofiler.org/examples/


Hi @sealnit,

welcome to the image.sc forum!

I am not a biologist so I don’t have a no visuals in my head when reading your question. Would it be possible for you to post an example image with maybe some annotations/drawings inside to explain that problem a bit more visually? :slight_smile:


Hi Sealnit

I have bit of experience merging Ilastik probability maps will cellprofiler to identify the objects you are interested in. Its actually quite an easy a reliable pipeline once you create it. Im more than happy to help if you want to send me a direct email to chat more.


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