Cell segmentation and gene imputation for imaging-based spatial transcriptomics

Imaging-based spatial transcriptomics technologies are revolutionary tools for biomedical investigation, but the power is currently limited by small number of measured genes and tricky cell segmentation. Here we introduce RedeFISH to simultaneously conduct cell segmentation and gene imputation for imaging-based spatial transcriptomics with the aid of single-cell RNA sequencing data. Extensive benchmarking across various spatial platforms and tissue types shows the validity and power of the cell-segmented, whole-transcriptome spatial data generated by RedeFISH.