The First Fully Integrated Single-Cell Spatial Solution

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Glowing orb of tissue

CosMx™ SMI and AtoMx™ SIP combine cutting-edge instrumentation with AI-powered analysis

Meet CosMx™ Spatial Molecular Imager, the first fully-integrated single-cell spatial biology solution powered by AtoMx™ Spatial Informatics Platform.

An Unmatched Single-Cell Spatial Solution

CosMx™ Spatial Molecular Imager (SMI) allows researchers to comprehensively map single cells in their native environment and extract deeper biological insights from a single experiment.​

To help accelerate discoveries with CosMx SMI, we’ve built a new cloud-based analysis solution: AtoMx™ Spatial Informatics Platform (SIP). On CosMx SMI, secondary analysis occurs so further analysis can be performed with ease on AtoMx SIP. You can then analyze and visualize CosMx SMI single-cell spatial data with ease. 

Understanding cell types, cell to cell interactions, and cell states enhances our ability to interpret biology and disease. 

Overlay cell segmentation and normalized gene expression directly on your tissue and visualize CosMx SMI single-cell data real time with AtoMx SIP.

CosMx SMI’s ultra-high plex technology can quantify and image 1000 RNA and 64 Protein targets at single-cell and subcellular resolution. This technology enables cell typing and pathway analysis to resolve cell state, cell function, cell-cell interactions, and cell signaling. ​

AtoMx SIP’s powerful data analysis and visualization software for CosMx SMI enables researchers to obtain novel insights from millions of single cells with a click of a button, and no coding experience is required to analyze single-cell data. We developed this best-in-class suite of analysis modules to help accelerate data to discovery. Let AtoMx SIP simplify data analysis so that you can focus on scientific discoveries and publish research faster.

Analyze CosMx SMI Data

Complimentary AtoMx SIP for 1 Year

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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.

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Want to learn how you can harness the power of spatial biology with CosMx and AtoMx? Fill out the form below.

Related Resources

Brochure CosMx™ SMI – Brochure
Product Bulletin AtoMx™ SIP – Product Bulletin
Grant Support CosMx SMI Grant Package
Webinar Introduction to the CosMx Webinar series and “The single-cell spatial revolution: CosMx SMI”