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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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Cell segmentation in placental cells. #117

Closed svelagala007 closed 1 year ago

svelagala007 commented 1 year ago

Hello, I wanted to reach out and get some advice regarding cell segmentation for placental cells. This is very heterogeneous and it appears after segmentation, immune cells appear very large. They appear as large as the non-immune cells such as trophoblasts. I wanted to ask if there is a way to train for immune cells to increase accuracy of segmentation.

image image image image image image image image

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I would appreciate any recommendations.

Thanks

nilseling commented 1 year ago

Hi @svelagala007

that's a good point. Others performed multiple rounds of labelling and segmentation for each cell type. After all rounds you would need to combine the masks. Alternatively, you can only segment the nucleii and add one step to expand the nuclear segmentation masks. most of the time measuring the cytoplasmic signal close to the nucleus is still enough for phenotyping. Another alternative would be to use DeepCell implemented in steinbock - it performs quite well segmenting cells with different sizes and shapes in tissues.

nilseling commented 1 year ago

Closing now as I'm assuming this has been resolved.