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. 2022 Dec 13;23:256. doi: 10.1186/s13059-022-02824-6

Table 1.

Summary of single cell or subcellular spatial omics technologies. The table only includes single cell or subcellular resolution spatial omics technology, excluding spatial barcoding methods as it loses the organization context (e.g., CITE-seq, ZipSeq, ExSeq, XYZeq, and sci-space). MERSCOPE employs MERFISH as a platform solution. Slide-SeqV2 and DBiT-seq could be near single-cell. The plex numbers are based on the maximum validated or claimed in publications, as of March 2022. Ab-based Antibody-based methods (multiplexed spectrometry), mFISH Multiplexed FISH (probe-based methods), NGS Next-generation sequencing, SR Not specified and stated as subcellular resolution; falls within the capacity of resolution microscopy, WT Whole transcriptome

Technology Type Target Resolution (nm) Year Company Plex
FISSEQ NGS RNA 600 2014 FISSEQ 8742
MIBI Ab-based RNA, protein 350 2014 IonPath 40
IMC Ab-based RNA, protein 1000 2014 Fluidigm 37
ChipCytometry Ab-based Protein 500 2019 Canopy 120
MERFISH mFISH RNA 100 2015 Vizgen 10,000
CyCIF Ab-based Protein 110 2015 Rarecyte 261
seqFISH+a mFISH RNA 100 2016 Spatial Genomics 10,000
STARmap NGS RNA SR 2018 N/A 1020
Phenocycler (CODEX) Ab-based RNA, protein 260 2018 Akoya 100
osmFISH mFISH RNA SR 2018 N/A 48
Slide-seqV2b NGS RNA 10,000 2020 N/A WT
HDST NGS RNA 2000 2019 N/A WT
Split-FISH mFISH RNA SR 2020 N/A 317
HybISS mFISH RNA SR 2020 N/A 124
DBiT-seq NGS RNA, Protein 10,000 2020 AtlasXomics WT
Stereo-Seq NGS RNA 500 2021 BGI STOmics WT
ExSeq NGS RNA 1000 2021 N/A WT
Molecular Cartography mFISH RNA 200 2021 Resolve Biosciences 100
Cell DIVE Ab-based Protein SR 2021 Cytiva 60
CosMxc mFISH RNA, protein 50 2022 NanoString Technologies 960
Xeniumc mFISH RNA, protein 50 2022 10X Genomics 1000
Visium HD NGS RNA 5000 2021 10X Genomics WT
Esper mFISH RNA 260 2021 Rebus Biosystems 30
Seq-scope NGS RNA 600 2021 N/A WT
PIXEL-seqc NGS RNA 1000 2021 N/A WT
MOSAICA mFISH RNA 100 2022 N/A 60
MICS Ab-based Protein 100 2022 Miltenyi Biotec 100
EEL FISHc mFISH RNA 200 2022 Rebus Biosystems 440
coppaFISHc mFISH RNA SR 2022 N/A 72

aupdated version of seqFISH; bupdated version of Slide-seq

cIn preprint or not publicly available yet