Fig. 1

Imaging-based ST strategies. a seqFISH decodes transcripts in space by sequential staining/imaging cycles. b Compared to seqFISH, smHCR can achieve ~ 20 fold signal amplification to detect single mRNA in situ. c MERFISH implements thousands of RNA imaging using a combinatorial FISH labeling with encoding schemes that correct errors. d seqFISH+ performs in situ RNA imaging using 20 probes in four-wheel coding. e ISS-methods by sequencing by ligation (ISS, IISS). f Electro-seq combines bioelectronics with ISS enabling electrophysiological and gene expression profiling. g Non-targeted sequencing, such as FISSEQ and ExSeq, enables unbiased covering sequencing of the whole transcriptome. ST spatial transcriptomic, FISH fluorescence in situ hybridization, seqFISH+ sequential FISH+, smHCR single-molecule hybridization chain reaction, MERFISH multiplexed error-robust FISH, ISH in situ hybridization, ISS in situ sequencing, IISS improved in situ sequencing, FISSEQ fluorescent in situ sequencing, Electro-seq in situ electro-sequencing