This repository is an exploratory resource to accelerate opensource analysis of CosMx™ Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
Great question.
Short answer, perhaps to become a short article later:
We don't background-subtract the count matrix, for two reasons:
There just aren't enough negprobes to get an accurate estimate of each cell's background level. If there are 20 negprobes, then a cell's total negprobe counts are binomial distributed with n = 20, p = the background rate, usually ~0.05. This is just too noisy.
Subtracting would turn our sparse counts matrix into a dense matrix, which uses too much memory.
Is it needed? If so, how to perform such operation on the count matrix, either based on expression of negative probes or something else?