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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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Imaging mass cytometry #13

Closed mkeays closed 4 years ago

mkeays commented 4 years ago

Hello,

I am looking for open source, automation-friendly software to do end-to-end processing for imaging mass cytometry data, and I was wondering if Cytokit would fit the bill? I have data similar to the example dataset here.

Thanks, Maria

eric-czech commented 4 years ago

Hi Maria,

I don't believe any IMC images were used to train the CellProfiler nuclei detection U-Net that Cytokit uses so it's probably not a great idea, or at least it would be hard to justify applying it without validating the model for that imaging modality first.

Out of curiosity though I ran it on one of your H3 images and the results are better than I thought, but still not as good as fluorescent images (w.r.t. nuclei detection):

Screen Shot 2019-11-06 at 5 12 25 PM

I think you'll probably get more mileage out of some package or plugin specifically for IMC. Sorry!

mkeays commented 4 years ago

Hi Eric,

Thanks for your quick reply and for explaining -- I will look at some other packages.

Thanks! Maria