Spatial Barcode Deconvolution for Single-Cell Position Mapping

The patent introduces spatial barcodes as intermediary elements that are incorporated into nucleic acid capture probes. These barcodes act as mediators that link the captured analytes (nucleic acids) with their specific spatial locations in the tissue sample. The spatial barcode sequence encodes position information, allowing computational correlation between analyte capture and spatial coordinates without requiring direct physical linkage.

The patent creates a spatial copy or map of the tissue architecture by assigning unique barcode sequences to specific locations in the tissue section. This barcode map serves as a digital replica of the spatial organization, which can then be computationally correlated with the captured analyte data to reconstruct spatial relationships without physically maintaining the original tissue structure.

The patent segments the tissue sample into discrete spatial units (such as individual cells or subcellular regions) and assigns unique spatial barcodes to each segment. This segmentation allows comprehensive tracking of position information for multiple cells simultaneously, with each cell's captured analytes tagged with its specific location barcode, enabling reconstruction of spatial heterogeneity at single-cell resolution.

The spatial barcode system serves multiple functions simultaneously: it identifies spatial location, tracks individual cells, and enables correlation of diverse analyte types with their positions. The universal barcode approach can be applied to various analyte classes (mRNA, proteins, metabolites) and multiple cells in parallel, providing comprehensive spatial heterogeneity data without requiring separate methods for each analyte type.