Table 1. overview of technical metrics of mentioned spatial transcriptomic technologies.
|
Method |
Resolution |
Multi- plexity |
Gene coverage |
Sample |
Strength |
Limitation |
|
smFISH |
Subcellular |
Low |
Low |
Fresh frozen/FFPE |
High detection sensitivity |
Low throughput |
|
RNAscope |
Subcellular |
Low |
Low |
Fresh frozen/FFPE |
High resolution and sensitivity |
Optical overlap |
|
seqFISH |
Subcellular |
Low |
~100 |
Fresh frozen |
Multiplexity |
Predefined probes; drop out error |
|
seqFISH+ |
Subcellular |
Low |
10,000 |
Fresh frozen |
Higher multiplexity |
Predefined probes; drop out error |
|
MERFISH |
Subcellular |
Low |
Hundreds to thousands |
Cultured cells/fresh frozen |
Super high resolution; error detection and correction |
Predefined probes; detect efficiency and accuracy |
|
osmFISH |
Subcellular |
Low |
Low |
Fresh frozen |
Low optical overlap |
Lower throughput and multiplexity |
|
ISS |
Subcellular |
Low |
Low |
Fresh frozen/FFPE |
Mutation and isoform detection; reduced background |
Optical overlap |
|
FISSEQ |
Subcellular |
Low |
Whole transcriptome |
Fresh frozen/FFPE |
Genome-wide detection |
Impaired sensitivity; time consuming; inefficient |
|
STARmap |
Subcellular |
Low |
Thousands |
Thick fresh frozen/FFPE |
No RT step; high specificity; error correction |
Complexity of image processing; small FOV |
|
LCM-seq/Geo-seq |
Single to a few cells |
Low |
Whole transcriptome |
Fresh frozen/FFPE |
High depth; tissue compatibility; full-length transcript |
Time-consuming; low throughput |
|
TIVA |
Single cell |
Low |
Whole transcriptome |
Live cells |
In vivo; natural state; isolate rare cell types |
Complexity of tag; efficiency of conjugation and hybridization |
|
Tomo-seq |
Tissue slice |
Medium |
Whole transcriptome |
Fresh frozen |
Not requiring specialized equipment |
Require similar samples; lack positional details; reconstruction artefact |
|
Niche-seq |
Single cell |
Low |
Whole transcriptome |
Live cells/in vitro tissue |
Isolation of rare immune cells; in vivo; natural state |
Need transgenic animal |
|
GeoM Dsp |
A few cells |
Low |
Hundreds |
Fresh frozen/FFPE |
Ability to analyze protein; compatible with fluorescent staining |
Throughput; costly |
|
ZipSeq |
Single cell |
Low |
Whole transcriptome |
Fresh frozen/FFPE |
Ability to analyze protein; combinatorial zipcode |
Complexity and hybridization efficiency of combinatorial zipcode; positional details lack |
|
ST/Visium |
50/100 μm spot |
High |
Whole transcriptome |
Fresh frozen |
High throughput |
Not single-cell resolution |
|
Slide-seq |
10 μm bead/subcellular |
High |
Whole transcriptome |
Fresh frozen |
Improved spatial resolution |
Low sensitivity; |
|
HDST |
2 μm bead/subcellular |
High |
Whole transcriptome |
Fresh frozen |
Subcellular resolution |
Low sensitivity |
|
DBiT-seq |
10/25/50 μm mosaic grid |
High |
Whole transcriptome |
Fresh frozen/FFPE |
Flexibility |
Risk of lateral expansion of barcode |
|
Seq-Scope |
0.5–0.8 μm distant cluster |
High |
Whole transcriptome |
Fresh frozen |
high resolution |
Require spatial barcode sequencing |
|
Stereo-seq |
220 nm |
High |
Whole transcriptome |
Fresh frozen |
Ability for larger tissue section; super high resolution |
Require spatial barcode sequencies; detection sensitivity |