dcollins15
commented
4 months ago Thanks for using Seurat!
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Hi,
As you may know, some spatial transcriptomics technologies such as Visium contains more than 1 cell per spot. I have been wondering as you have developed a method to perform deconvolution based on an annotated single cell RNA sequencing reference, what is your opinion about integrated an unsupervised deconvolution such as fuzzy c-mean clustering ?
I have been trying some packages but none have worked on Visium data. So I tried to use your "integration with single data for spatial" method based on a first clustering (SCTransform, Umap, Findcluster...) from the spatial data as a reference to predict potential mixture in the same spatial data. It works to some extent but I was wondering if it was a correct way to use it as a fuzzy clustering ?
Best,