Strange pattern in pct_counts_mt from bin2cell deconvolved VisiumHD data
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10 hours ago

Hey everyone! I have been working with some VisiumHD data and ran Bin2Cell on it to group the 2 µm bins into larger bins that reflect single cells. After I ran the B2C pipeline, I took my new, deconvolved spatial data object and ran a standard scRNA-seq analysis workflow. When I calculated QC metrics, I noticed this strange, sort of banding pattern that occurs in the plot (seen below). I assume this may be an artefact of the B2C pipeline, but I am pretty lost as to what could cause this. I just have never seen a pct_count_mt plot like this before! Would love to hear others ideas and hypotheses!

plot of cells and how much of their transcriptome is of mitochondrial origin

spatial-transcriptomics bin2cell VisiumHD • 599 views
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Update: take a look at the plot below

enter image description here

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