Category | Name | Level | Sample preparation | Labels | Visualization | Comments | Refs. |
---|---|---|---|---|---|---|---|
Non-specific technique | H&E staining | Nonspecific structure | FFPE | Hematoxylin and eosin | Visible light | Low-cost; high flux helped by deep learning: poordiscrimination of cell subtypes | |
Probe-based in situ imaging | IHC | Peptide and protein | FFPE | Antibody-reporter (usually florescent protein) | Fluorescence, insoluble pigment, etc. | Limited detectable targets simultaneously | [26] |
FISH | DNA | FFPE | Oligonucleotides-florescent reporter | Fluorescence | Limited detectable targets simultaneously | [27] | |
CODEX | Peptide and protein | Fresh-frozen | Antibody-oligonucleotides | Fluorescence | Extended detectible targets simultaneously | [28] | |
CODEX-FFPE | Peptide and protein | FFPE | Antibody-oligonucleotides | Fluorescence | Extended detectible targets simultaneously | [10] | |
seqFISH, seqFISH + , corFISH | mRNA (sub-transcriptome) | Live section | Oligonucleotides-florescent reporter | Fluorescence | > 10,000 detectible genes simultaneously; subcellular resolution ratio | ||
MIBI, MIBI-TOF | Peptide and protein | FFPE, immobilized cell suspension | Antibodies-isotypes | Secondary ion beam | Extended detectible targets simultaneously | ||
IMC | Protein, etc. | FFPE | Antibodies-high mass tag | Ion beam | Subcellular resolution ratio; probes are not necessarily needed | ||
Spatial transcriptome | Microarray-based spatial transcriptomics | Transcriptome | Live section, FFPE | Spatial transcriptome | Pathology + Computational analysis | Restricted cellular resolution | [36] |
Microarray-based spatial transcriptomics + sc-RNAseq | Transcriptome | Live section + single-cell suspension | Spatial transcriptome | Computational matching | Mapping is based on region-cluster matching by multimodal intersection analysis | [37] | |
ZipSeq | Transcriptome | Live section | Antibody/lignoceric-oligonucleotides-zipcode | Computational matching | Exquisite design in advance is required for accuracy | [38] | |
Spatial proteome | MALDI MSI | Proteome | Fresh frozen, FFPE | – | Ion imaging | Label-free; de novo investigation |