Schematic overview of methods based on imaging profiling of the entire specimen. a In situ hybridisation/fluorescence staining where bound oligonucleotide probes reveal spatial expression via fluorescent dyes. b Digital Spatial Profiling where digital barcodes tag bound oligonucleotides and allow multiplexed spatial profiling. c DNA microscopy where chemical DNA reactions permit spatial imaging. d seqFISH+ where accurate fluorescent barcoding is performed sequentially to improve throughput and generate spatial atlases in situ. e DistMap where Drop-seq technology integrates scRNA-seq data and ISH imaging to reveal spatial gene expression. f STARmap where genes are sequenced in situ using padlock amplification. g Tomo-seq where cryogenic tissue sections are individually analysed by bulk RNA-seq and spatial data triangulated in three axes. h Geo-seq where cryogenic tissue samples are obtained through laser capture microdissection and analysed through bulk RNA-seq with results spatially mapped. i High-definition spatial transcriptomics where cDNA synthesis is performed in situ and spatially barcoded prior to RNA-seq. j Slide-seq where mRNA is barcoded in situ and spatially indexed by SOLiD. k novoSpaRc where scRNA-seq is digitally profiled to virtually reconstruct the tissue. l NASC-seq where 4sU labelling identifies temporal and spatial features of single-cell data. Single-cell RNA-seq (scRNA-seq), in situ hybridisation (ISH), sequencing by oligonucleotide ligation and detection (SOLiD).