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Anyone else using VisiumHD data to do ligand-receptor inference analysis?

Has anyone ever used any ligand-receptor inference method on VisiumHD data (particularly single cell segmented data)? I have been working with some data for several months and have tried a ton of method implementations in the LIANA+ ecosystem. I'm just curious which tools anyone else is using and how you are overcoming challenges when doing this sort of analysis. I'm using single cell segmented VisiumHD data and I've been conducting analysis to characterize cell-cell communication differences across different niches in tissue. The data is super sparse, so I've tried pseudo-bulking methods, and even those are still not enough to combat the sparsity. Every tool out there was made with Visium v1 (55 µm spots) and single cell in mind, so perhaps tools that were made with more higher res ST technology like GeoMx in mind may be worth looking into (idk)? I'm just super stuck with my analysis and not sure what else I should do...

ligand-receptor visiumhd spatial-transcriptomics cell-cell-communication
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updated by OmnibusX • OmnibusX • written by danielpintard • danielpintard

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I’ve tried CellPhoneDB on a 10x Visium HD demo dataset, and the results looked reasonably informative in my case.

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One thing that helped was using the 16 µm bin level, since it gives a spatial resolution that can still capture neighboring cells interacting with each other while being a bit more robust than working at the most extreme sparsity level.

I also wrote up the workflow and some interpretation of the results here, in case it’s useful for comparison with what you’re seeing: https://blog.omnibusx.com/dive-with-visium-hd-uncover-spatial-cell-communication-at-single-cell-clarity/

It may not solve all of the sparsity issues, but I hope it gives you another practical reference point.

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written by OmnibusX • OmnibusX

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