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Visium/Xenium spot interpolation and deconvolution
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Using the registration of Xenium to Visium, we binned cells (by centroid) and transcripts from Xenium into the Visium spots. This was done by proximity. The closest spot to a cell or transcript was identified as the spot a cell or transcript lies within. Robust Cell Type Decomposition (RCTD) with spacexr 2.0.142 in R was used to deconvolve Visium spots into cell types using the unsupervised scFFPE-seq reference. See the 10x Analysis Guide (https://www.10xgenomics.com/resources/analysis-guides/integrating-10x-visium-and-chromium-data-with-r).
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