CosMx Spatial Molecular Imager
Whole transcriptome subcellular imaging with same-cell multiomics
Further, CosMx® Spatial Molecular Imager (SMI) is the only single-cell whole transcriptome spatial platform to provide same-cell spatial multiomics in formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at single cell and subcellular resolution.
Exploring Spatial Transcriptomics
Discover how spatial transcriptomics reveals what genes are expressed, which cells express them, and where they are located.
Introduction to the CosMx SMI Platform
Explore the power of CosMx SMI and see how high-plex single-cell spatial biology can unlock deeper biological insights otherwise missed.
Unlock Same-Cell Multiomics
CosMx SMI Same-Cell Multiomics workflow is the only solution to enable detection imaging of over 19,000 RNA and 64+ proteins, all within the same FFPE tissue section.
What sets CosMx SMI apart?
Best-in-class Sensitivity
Uncover discoveries otherwise missed
Unmatched detection efficiency to deliver the highest number of transcripts and unique genes per cell
Subcellular Whole Transcriptome Imaging
From inferring to projecting complete biological pathways directly onto the tissue
First spatial platform to image the entire protein-encoding transcriptome inside every single cell
Same-Cell Multiomics
Detect over 19,000 RNA and 64+ proteins, all within the same FFPE tissue section
Add another dimension to your data with comprehensive, same-cell RNA and Protein insights
Accurate Cell Segmentation
Resolve overlapping cells and improve single-cell boundary definition in dense tissues
Best-in-class AI algorithms for the most accurate definition of cell boundaries and assignment of transcripts to individual cells
Subcellular Analysis
Preserve the vital link between tissue morphology, RNA, and protein with subcellular resolution
Mapping the intracellular landscape with RNA and protein together at subcellular resolution
Integrated Spatial Informatics Platform
Accelerate study-level spatial data to biological insights
The AtoMx Spatial Informatics Platform is the first comprehensive cloud platform, fully integrated with CosMx SMI, enabling dynamic whole tissue exploration, extending analysis with 3rd party conversational AI, and applying fit-for-purpose open-source pipelines.
Powered by an integrated platform
Instrument
The only spatial imager achieving single-cell whole transcriptome and 64+ proteins with best-in-class sensitivity
Panels & Assays
CosMx RNA and protein panels/assays enable targeted and whole-transcriptome scale spatial discovery.
AtoMx SIP
A unified cloud-native workflow designed to accelerate every stage of spatial data analysis journey.
Trusted by leading researchers in spatial biology
“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
“Spatial context is necessary for training foundation models that truly learn human biology. We have demonstrated that our models exhibit clear scaling laws; as we ingest more high-resolution CosMx data, we see a predictable and powerful increase in the models’ ability to represent complex biology. We are excited to partner with Bruker to scale toward one billion spatially resolved human cells, spanning the breadth of oncology and beyond.”
Ron Alfa, MD, PhD
Co-Founder and CEO of NOETIK
Turning CosMx SMI data into real-world discoveries
Explore spatial transcriptomics workflows 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.
From sample to spatial insights
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.
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.
Explore the CosMx SMI resource library
Find the right platform for your research
| Platform |  CosMxLearn more |  CellScapeLearn more |  GeoMxLearn more |  nCounterLearn more |  PaintScapeLearn more |
| Applications | High fidelity, high sensitivity, subcellular imaging of the whole transcriptome with proteomics for complete pathway-level spatial insights | High fidelity, flexible subcellular proteomics for rapid and quantitative spatial phenotyping | High fidelity, unmatched discovery multiomics to profile from cells to tissue structures for spatial breakthroughs at scale | Rapid and robust targeted RNA and multiomic expression proven for translational and clinical studies | High fidelity, high precision multiplexed direct visualization of spatial organization of the 3D genome |
| Analyte | RNA, protein | Protein, RNA | RNA, protein | miRNA, Protein, RNA | DNA |
| Plex level | 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 | Targeted RNA assays (up to 2000 targets) Whole transcriptome RNA assays Up to 1200 proteins | 800+ RNA 500+ protein | Targetd DNA Assays (419+ targets) |
| Resolution | Single-cell Subcellular | Single-cell Subcellular | Multicellular (RNA) Single-cell (protein) | Bulk | Single-nuclei |
| Sample compatibility | FFPE, FF, organoids, cultured cells | FFPE, FF, cell suspension, lysate | FFPE, FF | FFPE, FF, lysate | Human cell lines, FF tissue (coming soon) |
| Data readout | Imaging | Imaging | NGS, nCounter (Direct counting) | nCounter (Direct counting) | Imaging |
Ready to see what CosMx SMI can do for your research?
Speak with a spatial biology specialist, request a quote, or explore open spatial biology datasets to accelerate your next discovery.
CosMx SMI Frequently Asked Questions
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 more than 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 Bruker Spatial Biology offer CosMx SMI 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.
Please view our CosMx grant resource document for more information.
What are the recommended best practices for achieving optimal CosMx SMI data quality?
CosMx SMI 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.