It depends a lot on whether one wants to measure platform- or tissue-specific differences, but also there’s a lot of readouts that can be confounded by section thickness.
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Back to the original point about clustering, some time ago there were preprints showing how to quantify and remove “diffuse” genes to improve clustering results.
I don’t share them bc I think the results were not super satisfactory. It is a completely open problem.
ResolVI seems to do a good job at reducing lateral diffusion artifacts in our hands… but still have not found a good metric to measure diffusion. I have seen it done by looking at RNA spillover at tissue borders, but borders are always tricky
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I don’t share them bc I think the results were not super satisfactory. It is a completely open problem.