NanoString Releases Single Cell Spatial Transcriptomics Dataset Highlighting Data Quality of CosMx Spatial Molecular Imager

New liver tissue dataset highlights high sensitivity and specificity of CosMx system, and the biological power of spatially analyzing 1000 RNA targets

NanoString Technologies, Inc. (NASDAQ: NSTG), a leading provider of life science tools for discovery and translational research, today announced a public release of new data generated by the CosMx™ Spatial Molecular Imager (SMI). This data was generated from formalin-fixed paraffin-embedded (FFPE) human liver samples and showcases the best-in-class data quality of the CosMx SMI. The dataset highlights CosMx SMI’s high sensitivity, with the capability to detect and quantify an average of 1,150 transcripts per cell and to maximize biological insights by detecting 676 unique genes. The dataset also represents CosMx SMI’s high specificity, with more than 99% of identified counts on targeted genes.

CosMx SMI enables high-resolution imaging of more than 1,000 RNA and over 64 protein analytes within morphologically intact whole tissue sections. The CosMx instrument allows researchers to visualize and quantify gene and protein expression at single cell and subcellular resolutions within both fresh frozen and FFPE tissue samples. Using a multi-modality approach, including protein imaging, CosMx SMI delivers best-in-class cell segmentation. This high-plex in situ analysis also enables researchers to perform cell typing, cell state, functional, and cell-cell interaction analyses in a single experiment generating high-resolution cell atlases.

NanoString used the CosMx SMI to characterize liver FFPE tissue from normal and hepatocellular carcinoma patients. The CosMx human liver data provides subcellular expression map of 1,000 genes and a single cell tissue atlas that categorizes each cell in the tissue as one of 18 unique cell types. The complete dataset consists of over 800,000 single cells and ~700 million transcripts, and a single-cell tissue atlas across a ~180 mm2 area of liver tissue. The high-plex analysis provided deep insight into the cell and tissue changes that occur in cancer, including infiltration of diverse immune cells.

“The CosMx SMI provides researchers with the ability to profile more genes than any other single cell in situ imager. As this dataset demonstrates, the market-leading plex of CosMx yields high sensitivity and specificity. The AtoMx™ Spatial Informatics Platform (SIP) enables powerful insights into the rich datasets generated by the CosMx,” said Joe Beechem, chief scientific officer, NanoString Technologies.

This spatial in situ imaging and molecular data is released in an open-source AtoMx SIP export format, which can be accessed through NanoString’s website ( This will allow analyses by the research community and facilitate open-source informatics tools development for the class-leading AtoMx SIP. The AtoMx SIP is a flexible cloud-based informatics platform that provides the secure, scalable storage and analysis that spatial biology researchers need to drive their workflow from study design to peer-reviewed publication. AtoMx SIP is compatible with both the CosMx SMI platform and the GeoMx® Digital Spatial Profiler (DSP). A cloud-based platform obviates the need for laboratories to invest in their own costly informatics infrastructure and reduces spatial biology analysis compute times from days to hours. Users have the flexibility to apply a pre-defined data analysis pipeline, to customize these pipelines using their own code, and to access open-source tools developed by the bio-informatics community.

The CosMx SMI and AtoMx SIP are the newest products in the company's industry-leading spatial analysis portfolio, joining the GeoMx DSP. The GeoMx DSP is a fully-automated spatial profiler allowing multi-cellular analysis of whole transcriptome for both human and mouse applications, and customizable for other species.

To learn more about NanoString's CosMx Spatial Molecular Imager, visit

About NanoString Technologies, Inc.

NanoString Technologies, a leader in spatial biology, offers an ecosystem of innovative discovery and translational research solutions, empowering our customers to map the universe of biology. The GeoMx® Digital Spatial Profiler, cited in more than 190 peer-reviewed publications, is a flexible and consistent solution combining the power of whole tissue imaging with gene expression and protein data for spatial whole transcriptomics and proteomics from one FFPE slide. The CosMx™ Spatial Molecular Imager is an FFPE-compatible, single-cell imaging platform powered by spatial multiomics enabling researchers to map single cells in their native environments to extract deep biological insights and novel discoveries from one experiment. The AtoMx Spatial Informatics Platform is a cloud-based informatics solution with advanced analytics and global collaboration capabilities, enabling powerful spatial biology insights anytime, anywhere. At the foundation of our research tools is our nCounter® Analysis System, cited in more than 6,500 peer-reviewed publications, which offers a secure way to easily profile the expression of hundreds of genes, proteins, miRNAs, or copy number variations, simultaneously with high sensitivity and precision.

For more information, visit

NanoString, NanoString Technologies, the NanoString logo, CosMx, GeoMx, AtoMx and nCounter are trademarks or registered trademarks of NanoString Technologies, Inc. in various jurisdictions.


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