High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

CytoSPACE maps individual cells from a reference single-cell RNA sequencing atlas to spatial transcriptomics data. Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE, an optimization method for mapping individual cells from a single-cell RNA sequencing atlas to spatial expression profiles. Across diverse platforms and tissue types, we show that CytoSPACE outperforms previous methods with respect to noise tolerance and accuracy, enabling tissue cartography at single-cell resolution.