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broadinstitute / Tangram

Spatial alignment of single cell transcriptomic data.
BSD 3-Clause "New" or "Revised" License
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Tangram Deconvolution #115

Open abhishekmaj08 opened 6 months ago

abhishekmaj08 commented 6 months ago

Hello, I have a question about the deconvolution process. As I understand it, there are 2 steps: (1) segmentation by watershed algorithms that gives the cell_count and (2) deconvolution by alignment. I was wondering how well does Tangram perform when in step (1) the provided image is not DAPI? If the segmentation process does not perform properly, then that should affect the cell_count and in turn the deconvolution by alignment step right? So what should I use in the segmentation step in case of a non-DAPI image.

Thanks

gaddamshreya1 commented 5 months ago

Hi @abhishekmaj08 ,

Thank you for your interest in Tangram! Here are some other tutorials by Squidpy for segmentation that maybe useful for you:

I would recommend trying these segmentation methods whichever fits your use case. However, you can also use any other segmentation methods, get cell count per spot and continue with deconvolution.