Supported by CCR Office of Science and Technology Resources (OSTR)

NanoString CosMx


The First Fully Integrated Single-Cell Spatial Solution

Key Applications

Cell Atlasing/Cell Typing

Discover and map cell types using expression profiles of known RNA and protein targets

Disease State

Visualize and quantify molecular (RNA / protein) and cellular organizational changes in a tissue

Ligand-Receptor Interaction

Analyze expression and interactions of up to 100 classic ligand-receptor pairs between interacting cells

Biomarker Discovery

Reveal differential gene expression and pathways in the same cell types depending on their spatial location

Tissue Microenvironment

Understand cellular neighborhoods by examining individual cells and their interacting neighboring cells

How It Works


Going from tissue sample to single-cell and subcellular insights has never been easier. With CosMx SMI, researchers can choose between preparing fresh frozen (FF) or even formalin-fixed paraffin embedded (FFPE) tissue samples with our 1000 plex RNA assay or 64-plex protein assay.

This streamlined workflow integrates with standard ISH protocols and eliminates the need for tissue expansion or clearing, cDNA synthesis, and amplification. Once tissue samples have been prepared, researchers can load their slides and associated CosMx reagents and allow the platform to perform the automated cyclic in situ hybridization chemistry.

While the tissues are being imaged on the CosMx SMI, a machine learning-driven algorithm performs cell segmentation on the images in parallel. Once a CosMx run has completed, these image files are ready to be analyzed and interpreted on AtoMx SIP with a few clicks.

Project Support

To get more information or to discuss a project, please contact Noemi Kedei, M.D., Facility Head

Contact CPTR