CosMx Spatial Molecular Imager
What is the CosMx SMI?
CosMx® Spatial Molecular Imager (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.
Single-Cell Imaging at Subcellular Resolution
The CosMx SMI delivers high-plex in situ imaging at subcellular resolution with the highest plex, more than 21,000 RNA targets and unbiased sensitivity, including multiomic same cell workflow and an integrated spatial informatics solution, the AtoMx® Spatial Informatics Platform.
Single Cell Spatial Transcriptomics 101: Intro to CosMx SMI
Join us for an introduction to the CosMx SMI and see how high-plex single-cell spatial biology can unlock deeper biological insights. From understanding why spatial biology matters to evaluating 1K, 6K, and whole transcriptome capabilities, this session provides the knowledge researchers need to maximize scientific discovery.
Explore a Human Whole Transcriptome Breast Cancer Atlas
See how CosMx SMI enables human whole transcriptome spatial biology discovery in breast cancer tissue with single-cell and subcellular resolution. This interactive Minerva story highlights tumor architecture, cellular interactions, and pathway-level spatial insights generated from FFPE breast cancer samples.
Why CosMx SMI?
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High Sensitivity
Unmatched detection efficiency to deliver the highest number of transcripts and unique genes per cell
Subcellular Whole Transcriptome Imaging
First spatial platform to image the entire protein-encoding transcriptome inside every single cell
Same-Cell Multiomics
Add another dimension to your data with comprehensive, same-cell RNA and Protein insights
Accurate 3D Cell Segmentation
Best in class AI algorithms for the most accurate definition of cell boundaries and assignment of transcripts to individual cells
Section 3 – Social Proof/Testimonials
“We are impressed with ease of use with which the CosMx SMI enabled single cell spatial transcriptomics across various tissue types, even in archival FFPE tissue. The high-plex protein assay makes the CosMx SMI a true multiomic solution. The CosMx SMI’s large capture area allows analysis from valuable clinical trial samples using tissue microarrays, enabling characterization of 100s of samples weekly.”
Dr. Nigel B Jamieson
Professor of Surgery, University of Glasgow, UK
“At last count, we have processed 160 samples with the CosMx SMI, including tumor and mouse brain samples. This technology uncovers vital insights into cell biology, enhancing our understanding of both malignant and normal tissues. It is crucial for creating spatial biomarkers and improving patient outcomes. Plus, the equipment and protocols are reliable and user-friendly.”
Dr. Aubrey Thompson
Mayo Clinic Comprehensive Cancer Center, Florida
“The CosMx SMI instrument has become integral to our laboratory’s future direction, and the responsiveness and skill of the customer support for it and the AtoMx SIP has been absolutely fantastic.”
Dr. Grant Kolar
Director, Research Microscopy and Histology Core, St. Louis University School of Medicine
CosMx SMI Research Applications
Explore spatial transcriptomics workflows designed for translational and discovery research across multiple biological systems and disease areas.
Oncology
Characterize tumor heterogeneity, immune infiltration, and biomarker expression at single-cell resolution directly within intact tissue architecture.
Immunology
Access heterogeneity of immune cell population and disease progression at the cellular and sub-cellular level.
Neuroscience
Investigate neuronal organization, spatial gene expression, and cellular interactions in complex brain tissue samples.
Infectious Disease
Investigate host–pathogen interactions, immune responses, and tissue remodeling with high-plex spatial transcriptomics at single-cell resolution.
How does CosMx SMI work?
One spatial molecular imaging platform for high-plex RNA and protein detection, same-cell multiomics, and integrated spatial informatics across FFPE and fresh frozen tissue samples.
Explore CosMx SMI datasets, resources, and insights
Section 7 – Suite Comparison
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| Platform |  nCounterLearn more |  GeoMxLearn more |  CosMxLearn more |  CellScapeLearn more | |
| Why use (primary use case) | Targeted multiomics | Spatial discovery | Spatial multiomics | Spatial proteomics | |
| Applications | Rapid and robust targeted RNA and multiomic expression proven for translational and clinical studies | Early biomarker discovery through high-throughput, cost-effective and high-plex RNA and protein screening | High sensitive subcellular imaging of the whole transcriptome for pathway-level spatial insights | Flexible subcellular proteomics for rapid and quantitative spatial phenotyping | |
| Analyte | miRNA, RNA, protein | RNA, protein | RNA, protein | Protein, RNA | |
| Plex level | 800+ RNA 500+ protein | Targeted RNA assays (up to 2000 targets) Whole transcriptome RNA assays Up to 1200 proteins | Target RNA assays (up to 6000 targets) Whole transcriptome RNA assays Up to 64 proteins | Targeted protein assays (up to 34 targets) Customizable assays up to 20 | |
| Resolution | Bulk | Multicellular (RNA) Single-cell (protein) | Single-cell Subcellular | Single-cell Subcellular | |
| Sample compatibility | FFPE, FF, lysate | FFPE, FF | FFPE, FF | FFPE, FF, cell suspension, lysate | |
| Data readout | nCounter (Direct counting) | NGS, nCounter (Direct counting) | Imaging | Imaging | |
| Analytics | nCounter Data Analytics Pipeline Europa Xp Omics Cloud | AtoMx Spatial Informatics Platform |
Interested in learning more about CosMx SMI for Single-Cell Imaging?
Speak with a spatial biology specialist, request a quote, or explore open spatial biology datasets to accelerate your next discovery.
Section 9 – FAQs
What is CosMx SMI?
CosMx SMI is a high-fidelity spatial molecular imaging platform that enables RNA and protein detection at single-cell and subcellular resolution in FFPE and fresh frozen tissue samples.
What sample types are compatible with CosMx SMI?
CosMx SMI supports formalin-fixed paraffin-embedded (FFPE), fresh frozen tissue samples, organoids and cultured cells enabling flexibility across translational and discovery research workflows.
What RNA assays are available for CosMx SMI?
CosMx Spatial Molecular Imager supports targeted RNA panels up to whole transcriptome workflows, enabling researchers to analyze up to 19,000 RNA targets with spatial context preserved at single-cell and subcellular resolution.
Does CosMx SMI support spatial multiomics?
Yes. CosMx SMI supports same-cell spatial multiomics workflows that enable simultaneous RNA and protein analysis within the same tissue section.
What applications can CosMx SMI support?
CosMx SMI is widely used across oncology, immunology, neuroscience, biomarker discovery, and translational spatial biology research.
What insights can researchers gain from CosMx FFPE datasets?
Researchers can explore cellular heterogeneity, tissue architecture, biomarker expression, immune organization, and pathway-level biology directly within preserved tissue sections.
Does CosMx Spatial Molecular Imager offer grant support for researchers?
Yes. Bruker Spatial Biology provides grant support resources to help researchers incorporate CosMx SMI into funding proposals and spatial biology research applications.
What are the recommended best practices for achieving optimal CosMx® SMI data quality?
CosMx Spatial Molecular Imager best practices include optimizing tissue handling, sample preparation, RNA quality assessment, and workflow execution to maximize sensitivity, spatial resolution, and overall data quality across FFPE and fresh frozen samples.