Spot Deconvolution with cell2location

Overview

Each Visium spot (55 um) holds several cells, so cell types are reported as an abundance per spot, not one label per spot. cell2location learns a signature per cell type from a scRNA-seq reference, then explains every spot's counts as a mixture of those signatures. Output: estimated cell counts and proportions per spot and type, maps on the tissue, and a marker check of each map.

When to Use

• Asked to "annotate cell types" or "find where cell types are" on Visium, Slide-seq or ST data
• Mapping a published scRNA-seq atlas onto a spot-based section
• Comparing cell type composition between tissue regions or sections
• Producing per-spot compositions for downstream niche or communication analysis
• Getting abundance estimates with posterior uncertainty (5% quantile)
• Use spatial-transcriptomics-cell-type-annotation instead when each observation is one cell (Xenium, MERFISH, CosMx)
• Use spatial-mapping-tangram (constrained deconvolution route) instead when you need single cells placed on segmented nuclei of the histology image