Quantification of Spots

In spot-based spatial transcriptomics platforms such as Visium and Xenium, individual RNA molecules are detected as diffraction-limited spots in imaging data. Each spot must be assigned to a specific gene based on its barcode sequence and optical coordinates, and then aggregated into a count matrix of genes by spatial positions. This notebook demonstrates the quantification of spot-based spatial data using the exprmat package. When a high-resolution segmentation mask is available, spot-level signals can be further aggregated to the cell level, producing a cell-by-gene count matrix that bridges spatial and single-cell resolution. The notebook covers spot decoding, signal extraction, and count matrix assembly for downstream spatial analysis.