CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments (opens in new tab)

Author summary Spatial transcriptomics reveals how cells are organized within tissues by mapping where genes are expressed. To achieve both scale and resolution, many approaches now combine spatial imaging with single-cell RNA-seq references to reconstruct complete transcriptomes in situ. New methods such as CISI, FISHnCHIPs, and ATLAS accelerate this process by measuring combinations of co-expressed genes rather than each gene individually. These aggregate measurements simplify experiments b...