Table 1 Imaging-Based ST Technologies
From: Advances in spatial transcriptomics and its application in the musculoskeletal system
Method | Inventor | Year established | Sample type | Advantages | Limitations | Gene detection efficiency | Targeted/ transcriptome-wide | Spatial resolution | Commercial platform (vendor) | References |
|---|---|---|---|---|---|---|---|---|---|---|
ISH-based | ||||||||||
smFISH | Femino et al. | 1998 | FF/FFPE | High sensitivity | Low throughput | Nearly 100% | Targeted | Subcellular | RNAscope (Bio-Techne) | |
seqFISH | Lubeck et al. | 2014 | FF/FFPE | Multiplexing | High cost, high error, optical crowding, limited view | 84% | Targeted | Subcellular | Molecular Cartography (Resolve Biosciences) | |
MERFISH | Chen et al. | 2015 | FF/FFPE | Multiplexing, improved detection robustness | High cost, limited view | 80%–95% | Targeted | Subcellular | MERSCOPE (Vizgen) | |
seqFISH+ | Eng et al. | 2019 | FF | Higher level of multiplexing, each image displays part of the transcripts, reducing optical crowding | High cost, time-consuming, limited view: analysis of small tissue profiles, only 1 mm2 | 49% | Targeted | Subcellular | NA | |
EEL FISH | Borm et al. | 2022 | FF | Multiplexing, high throughput, low cost, gapless RNA capture, eliminates tissue background impact | Low detection sensitivity | 2.6%–13.2% | Targeted | Subcellular | Rebus Esper (Rebus Biosystems) | |
CosMx SMI | Nanostring | 2022 | FF/FFPE | Automated equipment, targeted detection of RNA and proteins at the spatial level, high signal-to-noise ratio | Low throughput | One or two copies per cell | Targeted | Subcellular | CosMx SMI (Nanostring) | |
ISS-based | ||||||||||
FISSEQ | Lee et al. | 2014 | FF/FFPE | Whole transcriptome analysis | Limited read length, extremely low detection efficiency, high proportion of rRNA reads, low throughput, expensive, optical crowding | < 0.005% | Transcriptome-wide | Subcellular | RC2 (ReadCoor) | |
STARmap | Wang et al. | 2018 | FF | High signal-to-noise ratio, high sensitivity, high precision, capable of resolving thick tissue sections | Low throughput, limited view | Slightly better than scRNA-seq | Targeted | Subcellular | Plexa In Situ Analyzer (Stellaromics) | |
Exseq | Alon et al. | 2021 | FF/FFPE | Optional targeted and non-targeted, nanoscale subcellular spatial resolution | Long imaging time | ~43.4% (Targeted) | Targeted or transcriptome-wide | Subcellular | NA | |
Xenium | 10x Genomics | 2023 | FF/FFPE | High detection sensitivity for low-level expressed genes, high specificity, fast data output capability | Platform capable of combined proteomic analysis pending release | 1.4 times higher than scFFPE-seq | Targeted | Subcellular | Xenium (10x Genomics) | |
Electro-seq | Li et al. | 2023 | Live cells | Paired detection of 3D transcriptional states and electrophysiological states | The causal relationship between gene expression and electrophysiology still needs further exploration | NA | Targeted | Cellular | NA | |
