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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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How to export cell mask from qupath? #48

Closed kaizen89 closed 3 years ago

kaizen89 commented 3 years ago

Hi, I have a naive question, I have an image overlay with 13 markers on which I performed cell segmentation on Qupath, I was wandering if you know hot to export the mask as a tif file to use with cytomapper. Thank you

nilseling commented 3 years ago

Hi @kaizen89

unfortunately I'm not so familiar with the scripting environment of qupath. But I googled around and found the post here: https://forum.image.sc/t/mask-script-doesnt-work-in-qupath-m4/33259 the corrected script works for me to export the segmentation masks. But these are exported as binary images (background: 0, cell: 1) and therefore not suitable for cytomapper. But the script could be a start for what you want to do. You could also ask the developers of qupath for help. At the end you will just need a segmentation mask where each cell is defined as a set of pixels with the same integer ID. Best,

Nils

kaizen89 commented 3 years ago

Thanks. While looking for a solution in qupath, what other tools would you recommend for multiplexed immunochemistry images?

nilseling commented 3 years ago

QuPath is probably the best option. There is also CytoMAP which offers more options for interactive multiplexed image analysis. Also check out steinbock and the ImcSegmentationPipeline for segmenting multiplexed images. As part of these pipelines, CellProfiler comes in quite handy. Nowadays, there are also some nice napari plugins available for this sort of analysis. This list is by far not complete, just tools that I had a look at in the past.

nilseling commented 3 years ago

I'll close this issue for now. Please reopen if I can support you with cytomapper related things :)

kaizen89 commented 3 years ago

Thanks, I finally found a script to export the cell mask with qupath here https://www.imagescientist.com/scripting-export-images#masks

nilseling commented 3 years ago

This is really useful, thanks!