CosMx™ SMI for Single-Cell Imaging

True Single-Cell In Situ Solution
CosMx™ SMI for Single-Cell Imaging instrument photo

Elevate your single-cell research with CosMx™ SMI

A Spatial Multiomics Single-Cell Imaging Platform

CosMx SMI is the first high-plex in situ analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. It is the flexible, spatial single-cell imaging platform that will drive deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery.

The CosMx™ SMI and decoder probes are not offered and/or delivered to the Federal Republic of Germany for use in the Federal Republic of Germany for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof in a method used in fluorescence in situ hybridization for detecting a plurality of analytes in a sample without the consent of the President and Fellows of Harvard College (Harvard Corporation) as owner of the German part of EP 2 794 928 B1. The use for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof is prohibited without the consent of the President and Fellows of Harvard College (Harvard Corporation).

Diagram showing how CosMx SMI for single-cell imaging delivers a comprehensive package from sample preparation to interactive data analysis.
CosMx SMI for single-cell imaging delivers a comprehensive package which includes validated reagents, instrument, and data analysis software for seamless sample-to-result.

Technical Overview

FFPE Compatibility
High Sensitivity
True Single-Cell Segmentation
FFPE Compatibility

Get single-cell gene expression in challenging FFPE tissues with spatial context.


Melanoma FFPE tissue probed with 1000-plex RNA panel to detect spatial localization of transcripts in intact tissue.

High Sensitivity

Detect low expressing genes with highly sensitive CosMx SMI


Genes Expression level Copies per cell (Max.)
MALAT1 High 256
FOS Medium 40
LY6D Low 24

Total number of cells analyzed = 800,327​
Total transcripts detected = 259,604,214​
Number of transcripts / cell (Max) = 2000​
Number of transcripts / cell (Mean) = 257

Shown here are the transcripts detected per cell in non-small cell lung cancer (NSCLC) FFPE tissue probed with a 1000-plex gene panel (left) and total transcript distribution in the NSCLC tissue (right). CosMx SMI offers high sensitivity and high dynamic range to capture low copy number gene transcripts at the single cell level.

True Single-Cell Segmentation

Multi-modal approach for true single-cell segmentation

Multi-modal cell segmentation process provides accurate cell boundaries detection. CosMx cell segmentation uses cell membrane and morphology marker protein images, machine-learning augmented cell segmentation algorithm and transcript-based segmentation refinement to achieve precise single-cell segmentation in morphologically intact tissue.

Redefining Spatial Biology with Single-Cell Imaging and Subcellular High-plex 3-Dimensional Resolution

How it works

CosMx SMI is an integrated system with mature cyclic fluorescent in situ hybridization (FISH) chemistry, high-resolution imaging readout, interactive data analysis and visualization software.

Easy Sample Preparation, Compatible with Any Sample Type

The molecular spatial imager for single-cell imaging streamlines and simplifies workflow
Streamlined and simple workflow that integrates with standard ISH protocol with no need for tissue expansion or clearing, cDNA synthesis or amplification. Go from sample to result faster.

Automated Cyclic in situ Hybridization Chemistry

Diagram illustrating single-cell imaging
Robust hybridization chemistry that provides higher sensitivity and supports high-plex assays in your tissue samples to uncover deeper biological insights.


CosMx Spatial Molecular Imager is the most flexible and robust spatial single-cell imaging platform for:

  • Cell Atlas and Characterization: Define cell types, cell states, tissue microenvironment phenotypes, and gene expression networks within spatial context.
  • Cell-cell Interaction: Understand biological process controlled by ligand-receptor interactions.
  • Spatial Biomarkers: Quantify change in gene expression based on treatment and identify single-cell subcellular biomarkers with spatial context.
Infectious Diseases
Developmental Biology

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Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue – AACR 2023

Single cell spatial molecular imaging of 76-plex proteins in clinical cancer samples in response to personalized treatment – AACR 2023

A complete pipeline for high-plex spatial proteomic profiling and analysis on the CosMx™ spatial molecular imager and AtoMx™ spatial informatics platform – AACR 2023

Spatial transcriptomic profiling of the human and mouse retina prepared with CryoJane Tape Transfer System using GeoMx and CosMx spatial analysis – AACR 2023

Spatial insights into tumor immune evasion illuminated with 1000-plex RNA profiling with CosMx Spatial Molecular Imager – AACR 2023

A spatially-resolved, single-cell analysis of human olfactory cleft mucosa highlights the transcriptional dysregulation in sustentacular cells with SARS-CoV-2 viral load

Single-Cell Imaging FAQs

Why is a single cell important?

Cells are a fundamental unit of life. A comprehensive understanding of how cells organize themselves in different layers of information to form tissues is not yet fully achieved.  Further, no matter how seemingly homogeneous a tissue might appear, it contains a diverse population of cells, all of which represent different manifestations of that tissue type. Learn more »

Why is single-cell analysis important?

Single-cell analysis encompasses the study of genomics, transcriptomics, proteomics, and metabolomics at single-cell resolution. As cells are the organism’s building blocks, they are organized in different layers of information to form tissues, and the position of each cell within a tissue has a physiological or morphological function. Learn more »

What is single-cell technique?

Single-cell techniques are advances in single-cell manipulation and amplification that have enabled the study of genomics, transcriptomics, and epigenomics at the level of a single cell. Learn more »

What is single-cell spatial transcriptomics?

Analysis of mRNA expression profile with spatial context at the level of a single cell is known as single-cell spatial transcriptomics. Each cell has a unique transcriptomic fingerprint as gene expression patterns can be heterogeneous even amongst similar cells in both standard and abnormal cell states. Learn more »

What is single-cell analysis used for?

Single-cell analysis can provide data on cellular phenotypes by studying the effects of genomic alterations, gene expression, and environmental influences at the level of a single cell. Learn more »

Related Resources

Brochure/eBook CosMx™ SMI – Brochure
Grant Support CosMx SMI Grant Package
Publication High-Plex Multiomic Analysis in FFPE Tissue at Single-Cellular and Subcellular Resolution by Spatial Molecular Imaging