Table 1.

Technical highlights of four technical routes in spatial transcriptomics.

In situ hybridization (ISH)-based technologies
Method	Application	Detection efficiency	Features	Refs
seqFISH	Fresh-frozen	84 %	Targeted, expensive experiments	[9], [42]
MERFISH	Fresh-frozen	80 %	Targeted, high robustness of probe design method, expensive experiments	[9], [17]
seqFISH+	Fresh-frozen	49 %	Targeted, expensive experiments	[9], [18]
DSP	Fresh-frozen or FFPE	NA	Targeted, commercially available	[19]
Split-FISH	Fresh-frozen	NA	Targeted, no tissue clearance required，expensive experiments	[9], [20]
EEL FISH	Fresh-frozen	13.2 %	Targeted, transferring RNA using electrophoresis, low-cost experiments	[21]
SMI	Fresh-frozen or FFPE	One or two copies per cell	Targeted, high signal to noise ratio detection, commercially available	[22]
In situ sequencing (ISS)-based technologies
Method	Application	Detection efficiency	Features	Refs
ISS	Fresh-frozen or FFPE	< 1 %	Targeted, low throughput, commercially available	[42], [103]
FISSEQ	Fresh-frozen or FFPE	< 0.005 %	Unbiased, whole transcriptome, low capture efficiency，commercially available	[42], [103], [187]
STARmap	Fresh-frozen	higher than single-cell RNA sequencing	Targeted, reverse transcription-free	[25]
HybISS	Fresh-frozen or FFPE	higher than ISS	Targeted, higher throughput than ISS	[26]
BOLORAMIS	Cell lines	10–30 %	Targeted, reverse transcription-free	[29]
Next generation sequencing (NGS)-based technologies
Method	Application	Resolution	Features	Refs
ST/Visium	Fresh-frozen/Fresh-frozen or FFPE	100/55 µm	Unbiased, whole transcriptome, low capture efficiency, commercially available	[31], [188], [189]
slide-seq	Fresh-frozen	10 µm	Unbiased, whole transcriptome, low capture efficiency	[33]
HDST	Fresh-frozen	2 µm	Unbiased, whole transcriptome, low capture efficiency	[34]
DBiT-seq	Fresh-frozen or FFPE	10 µm	Unbiased, whole transcriptome, low capture efficiency	[35]
slide-seqV2	Fresh-frozen	10 µm	Unbiased, whole transcriptome, higher capture efficiency than slide-seq	[36]
Seq-Scope	Fresh-frozen	0.5–0.8 µm	Unbiased, whole transcriptome, low capture efficiency	[37]
stereo-seq	Fresh-frozen	500/715 nm	Unbiased, whole transcriptome, low capture efficiency, largest detection area	[38]
Spatial information reconstruction technologies
Method	Application	Algorithm	Features	Refs
tomo-seq	Fresh-frozen	Iterative Proportional Fitting (IPF)	Unbiased, imaging-free, whole transcriptome, low capture efficiency	[40]
STRP-seq	Fresh-frozen	Tomographer	Unbiased, imaging-free, whole transcriptome, low capture efficiency	[41]