. Author manuscript; available in PMC: 2023 Jan 31.

Published in final edited form as: Nat Rev Genet. 2021 Jun 18;22(10):627–644. doi: 10.1038/s41576-021-00370-8

Table 1 |.

Widely used spatial transcriptomics techniques and instruments

Type	Technique	Characteristics	Mechanism notes	Refs
Hiqh-plex RNA imaging	In situ sequencing for RNA analysis in preserved tissue and cells	25–90 reads per cell¹⁰, 69-gene panel³¹	Genes of interest must be selected to design gene target-specific ‘padlock probes’	¹⁰
	STARmap	160-gene panel, ~250 reads per cell	Uses ‘padlock probe’ mechanism and integrates hydrogel-tissue chemistry for 3D spatial resolution	¹⁴³
	Multiplexed error-robust FISH (MERFISH)	135-gene panel, ~100 reads per cell²⁹	Each gene has an associated binary code (wherein 1 means fluorescence for a certain part of the sequence, and 0 means no fluorescence)	^11,152
	Sequential FISH (seqFISH, seqFISH+)	249-gene panel, ~30 reads per cell¹³	Each gene has an associated colour sequence code (24 colour probes per gene) with 60 different pseudo-colour options	^12–14
Spatial barcoding	Spatial transcriptomics	100 μm diameter capture spot resolution	100 μm from original spatial transcriptomics publication¹⁵	¹⁵
	Visium spatial gene expression	55 μm diameter	55 μm resolution translates to 3–30 cells per capture spot¹⁶ (original technique¹⁵is widely accessible through this 10× Genomics Visium Platform: spatialtran-scriptomics.com)	¹⁶
	High-definition spatial transcriptomics (HDST)	2 μm diameter	Direct improvement in resolution on spatial transcriptomics¹⁵, but not as accessible	¹⁶¹
	Slide-seq, Slide-seq v2	10 μm diameter	Uses beads instead of capture spots, with the poly-T oligomers projecting radially around the bead; employs slides	^17,18

This table lists a widely used subset of the technologies; for more comprehensive reviews of spatial transcriptomics technologies, we refer readers to REFS^162–164. Characteristics of high-plex RNA imaging (HPRI) methods are from exemplary studies that performed the method on intact tissue (rather than tissue culture). For reference, single-cell RNA sequencing (scRNA-seq) methods typically measure 10⁴–10⁶ reads per cell. FISH, fluorescence in situ hybridization.