Training Example: Bruker Spatial Biology (formerly NanoString Technologies, Inc.) – Review the Data, Give Your Score & Compare to the Real AI Evaluation

[H1] The most complete, high-fidelity ecosystem that is available today

[IMG: Head-on view of nCounter Pro Analysis System]

[H2] nCounter® Analysis System

Highly robust single or multiomics bulk analysis for rapid biomarker discovery and development
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[IMG: GeoMx® Digital Spatial Profiler for Spatial Biology]

[H2] GeoMx® Digital Spatial Profiler

Unmatched discovery multiomics to profile from cells to tissue structures for spatial breakthroughs at scale
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[IMG: CosMx™ Single-cell Imaging Platform for Spatial Biology]

[H2] CosMx® Spatial Molecular Imager

High sensitivity, subcellular imaging of the whole transcriptome for complete pathway-level spatial insights
Learn more

[H2] CellScape™ XR Precise Spatial Proteomics

Flexible subcellular proteomics for rapid and quantitative spatial phenotyping
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[H2] PaintScape™ Spatial 3D Genome+

High precision, multiplexed direct visualization of the 3D genome
Learn More

The CosMx® SMI and decoder probes are not offered and/or delivered to the Federal Republic of Germany for use in the Federal Republic of Germany for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof in a method used in fluorescence in situ hybridization for detecting a plurality of analytes in a sample without the consent of the President and Fellows of Harvard College (Harvard Corporation) as owner of the German part of EP 2 794 928 B1. The use for the detection of cellular RNA, messenger RNA, microRNA, ribosomal RNA and any combinations thereof is prohibited without the consent of the President and Fellows of Harvard College (Harvard Corporation).

[H2] Featured Events & Webinars

View Calendar

[H4] Webinar

[H3] From AtoMx® tissue exploration to spatial conversations to open-source insights
Feb 12, 2026 | 8:00 am – 9:00 am PST

[H4]

[H3] Expanding the Frontiers of Spatial Biology: Best-in-Class Solutions for Every Layer of Biology
Mar 3, 2026 | 12:08 am – 9:00 am PST

[H4] Webinar

[H3] A New Era for nCounter: Introducing Simple, Scalable, Bulk Multiomics
Mar 4, 2026 | 8:00 am – 9:00 am PST

CosMx WTX

[H2] Unmatched same-cell whole transcriptome and multiomics for complete pathway-level spatial insights

Order Today

[H2] Deciphering the Complexity of Biology

“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.”

[IMG: Portrait of Dr. Kolar.]

Dr. Grant Kolar
Director, Research Microscopy and Histology Core, St. Louis University School of Medicine

“The CosMx SMI complemented our efforts to generate organ atlases of the healthy human system together with our partners of the Human Cell Atlas project. It allowed us to visualize single-cell reference maps directly in organs. The scale of 1000-plex gene panel with image-guided cell segmentation makes the CosMx SMI, a unique platform for spatial genomics!”

[IMG: Portrait of Holger Heyn]

Dr. Holger Heyn
Team Leader, Single Cell Genomics Group, CNAG, Spain

“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.”

[IMG: Portrait of Nigel Jamieson]

Dr. Nigel B Jamieson
Professor of Surgery, University of Glasgow, UK

“The Bruker Spatial Biology cancer panels, in general, and the Breast Cancer 360 Panel, in particular, in combination with the outstanding analytical tools developed by Bruker Spatial Biology, provide straightforward, informatically-rich tools for characterization of the functional genomic landscape of breast cancer.”

[IMG: Dr. Aubrey Thompson]

E. Aubrey Thompson, PhD
Professor of Cancer Biology, Mayo Clinic

“There is a big movement underway to study the microenvironments of cancers in different organs because it is known that immunotherapy doesn’t work the same across different cancer types. GeoMx will be the key to us to understand those mechanisms. It will be able to see things we only dreamed about—it will be revolutionary”

[IMG: Nina Radosevic]

Nina Radosevic, MD
Surgical & Molecular Pathologist / Cell Biologist, Associate Research ProfessorUniversity Clermont Auvergne, INSERM, Centre Jean Perrin

“We plan on utilizing the nCounter PanCancer IO 360 Gene Expression Panel as we move on to Digital Spatial Profiling with the GeoMx system to generate some of our gene signatures and explore new regions of interest.”

[IMG: Troy McEachron]

Troy McEachron, PhD
Assistant Professor of Research, University of Southern California

“The deciding factor in obtaining the GeoMx DSP was its ability to look at both transcriptomic and proteomic information.”

[IMG: Peter O’Toole]

Peter O’Toole, PhD
Director of the Bioscience Technology Facility, University of York

“nCounter allowed us to use flash-frozen paraffin embedded tissues that were a few years old, as well as didn’t have necessarily the best quality RNA, and still get really great data from it.”

Emily Schwarz
Ohio State University

“The GeoMx DSP is a workhorse in the lab for hypothesis testing… Complementing the single-neuron resolution of GeoMx, we rely on the CosMx SMI to achieve true subcellular spatial analyses and uncover cell-cell interactions… Bruker Spatial Biology’s consistent advancements in panel development and plexity provide us with the confidence that they will continue empowering neuroscientists to explore complex questions.”

Miranda Orr, PhD
Assistant Professor, Gerontology and Geriatric Medicine, Wake Forest School of Medicine

Accelerate scientific insights from discovery through translational research 

[H2] 7,000 Publications and counting

Browse the vast and growing catalog of peer-reviewed research from oncology 
to biomarker discovery enabled by Bruker Spatial Biology technologies.

View Publications

Careers

[H2]
Become a Part of the Spatial Biology Revolution

“I have really enjoyed becoming a part of the company and teaching our customers more about the technologies Bruker Spatial Biology offers and how to apply them to push their research forward.”
Amanda Mason
Field Applications Scientist

View Careers

[IMG: Amansa Mason smiling outdoors]

“Bruker Spatial Biology is a uniquely innovative place to work, as we get to do far more exciting and cutting-edge science than most companies our size. We experience the thrill of building technologies alongside the satisfaction that comes from participating in research advancing patient care for a broad range of disease areas.”
Erin Piazza
Senior Bioinformatics Scientist

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[IMG: Erin Piazza]

“At Bruker Spatial Biology I have a great opportunity to work with outstanding engineers and be part of the leading edge of gene expression instrumentation.”
Edgar Ali Lazcano Romano
Quality Control Engineer III

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[IMG: Edgar]

[IMG: Amansa Mason smiling outdoors]

[IMG: Erin Piazza]

[IMG: Edgar]

CosMx® Human Whole Transcriptome Panel

Blog Post
Accurate Cell Segmentation: The Critical Foundation of Spatial Biology

Blog Post
Key Considerations in High-Fidelity Spatial Transcriptomics with CosMx® SMI

Blog Post
Why Transcriptomics Matters: Understanding the Value of High-Resolution Spatial Molecular Imaging

Blog Post
How CosMx SMI Enables Next-Generation Spatially Resolved Cell Assays with Subcellular Resolution

Home » Product Roadmap
[H2] Introducing CellScape™ XR, the Highest Performing Spatial Proteomics Ecosystem Delivering Best-in-Class Data Fidelity, Robustness and Flexibility
Human FFPE intestinal biopsy stained on CellScape XR
CellScape XR is the next generation of Bruker’s precise spatial proteomics platform. CellScape XR combines major advancements across the instrumentation, software, and the assay ecosystem to deliver best-in-class data quality, dramatically expand available markers, more than double throughput, with further improved robustness and flexibility. This includes improvements in optics and imaging chamber design, which combined with EpicIF™ technology, enables rapid whole-slide signal removal between staining cycles within seconds. The launch also includes expanded VistaPlex™ multiplex assay kits, building on hardware improvements that enable use of a broader range of fluorophore conjugated antibodies, and PowerOMX™ data engine for improved data processing. The significantly expanded menu of VistaPlex assay kits is comprised of primary fluorescently labelled antibodies for robust assay performance. With Bruker’s proprietary EpicIF technology, fluorescence signal from any organic fluorophore can be removed, enabling users to customize VistaPlex panels with a wide range of directly conjugated antibodies. As an add-on to the VistaPlex kits, Bruker will offer a new universal antibody labeling capability, VistaFlex™, developed in collaboration with Proteintech® Group, enabling use of virtually any IHC-validated unlabeled antibody on the market without the need for antibody stripping, thus broadening assay design freedom and opening access to a wider range of protein targets and application‑specific antibodies.
Pre‑orders are open now, and commercial shipments of CellScape XR are expected this summer.
Learn More
[H2] High Precision, Multiplexed Direct Visualization of the 3D Genome with PaintScape™
PaintScape in situ single cell chromosome traces from the 419-plex ChromoPaint HuCL PanChromo MPX panel
PaintScape is a first and only high precision platform enabling multiplexed, direct visualization of the 3D genome in situ in single cells. PaintScape enables the unprecedented study of genome organization and structure, allowing researchers to visualize chromosomal organization and investigate how spatial genome structural variations influence gene dysregulation and disease biology. At AGBT 2026, Bruker presented first-of-its-kind 3D genome visualization on both cell lines and intact fresh frozen (FF) tissue using the PainScape platform. In addition, Bruker will launch two new panels for the PaintScape platform, including the ChromoPaint™ HuCL PanChromo MPX panel, a 419-plex panel designed for genome wide in situ visualization of chromosomal organization in human cell lines. Lastly, Bruker announced the OncoPaint™ Oncogenic Pathway Panel that will be available later this year, a 1000+-plex modular panel designed to combine genome wide chromosome painting with painting of select cancer pathway associated gene regions in increased genomic resolution.
Pre-orders are open now, and commercial shipments of the PaintScape platform are expected to begin this spring.
Learn More
[H2] CosMx® SMI Extends Complete Spatial Biology Approach to miRNA, TCR, and Mouse Whole Transcriptome
CosMx Same-Cell Multiomics with CosMx WTX (left) and protein (right) from human lung tissue
Bruker’s CosMx Spatial Molecular Imager (SMI) delivers the most complete single-cell and subcellular spatial transcriptomic view of human biology through multiomic imaging of the whole transcriptome (WTX) plus 64+ proteins from a single FFPE or FF tissue section. Bruker now extends their complete biology approach to mouse research by announcing development of the CosMx Mouse Whole Transcriptome (WTX) assay. The mouse WTX assay will be available for both FFPE and FF tissues with early access through Bruker’s Technology Access Program this spring and full commercial availability later this year. Bruker also unveiled plans for commercial high-plex spatial miRNA and T-Cell Receptor (TCR) assays at subcellular resolution. The new miRNA assay will enable researchers to jointly interrogate mRNA, protein, and miRNA from the same cell, delivering a more complete multiomic view of gene regulation, post-transcriptional control, and cell state transitions. The TCR assay for the study of variable–diversity–joining mRNA expression will provide a new layer of in-depth immune biology in addition to whole transcriptome imaging.
Learn More
[H2] AtoMx® SIP Leverages Complete Biology Layers for Image-First Experience, AI-Ready Data, and 3D Cell Segmentation
AtoMx Spatial Discovery: “Image-first” and conversational data analytics
Bruker’s AtoMx Spatial Informatics Platform (SIP), designed to accelerate study-level insights from CosMx SMI data, now introduces a spatial discovery mode for rapid image-based exploration of subcellular and single-cell whole transcriptome data. This new experience pre-calculates spatial insights as well as prepares data exports for conversational large language models (LLM). Applying LLMs to the comprehensive data of CosMx SMI results in richer and higher quality LLM outputs than would be possible with any other commercial spatial assay and platform, giving researchers the most complete interactive experience for biological understanding. Bruker also introduced 3D AI cell segmentation models to AtoMx SIP, extending their best-in-class definition of single-cell boundaries for accurate RNA transcript assignment in space. This advancement addresses long-standing limitations of other platforms and cell segmentation algorithms that do not account for biologically overlapping cells in tissue sections.
Learn More
[H2] GeoMx® Discovery Proteome Atlas Showcases Unmatched Spatial Biomarker Discovery at Scale with Whole Transcriptome and 1200+ Protein Targets
Bruker’s GeoMx Digital Spatial Profiler (DSP) enables large-cohort interrogation of the whole transcriptome and the Discovery Proteome Atlas (DPA), a spatial assay profiling more than 1,200 protein targets. At AGBT 2026, researchers presented applications ranging from oncology to neuroscience, demonstrating how GeoMx DSP opens the possibilities for spatial biomarker discovery at scale. Bruker additionally introduced a cross-platform GeoMx DPA and CellScape XR workflow from the same tissue section that presents an unprecedented opportunity for spatial protein biomarker discovery to subsequent validation and translational studies.
Learn More
[H2] nCounter® Extends Leadership in Gene Expression Analysis with New Multiomics Capabilities
nCounter is now multiomic! With the power to measure RNA and protein from the same sample on a single platform and within one streamlined workflow, the nCounter Analysis System is more capable than ever. To complement this advancement, Bruker Spatial Biology has introduced the nCounter Data Analysis Pipeline—a user‑friendly desktop solution designed for rapid, publication‑ready insights. From raw data to high‑quality outputs in minutes, it brings simplicity and speed to multiomic data analysis.
Learn More
[H2] Sign up for product updates
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[H2] Related Resources

Event
AGBT 2026

Brochure/eBook
CellScape™ Brochure

Brochure/eBook
GeoMx DSP – Brochure

Brochure/eBook
CosMx® SMI – Brochure

Home » Products » CosMx Spatial Molecular Imager » CosMx® Same-Cell Multiomics
[H2] CosMx Same-Cell Multiomics with RNA and Protein for Unlimited Spatial Exploration
Discovery begins with high-fidelity, unbiased data. With the launch of CosMx Same-Cell Multiomics, researchers can now interrogate RNA and protein in and around each cell in their tissue, unlocking a deeper understanding of cellular function with spatial context.
The CosMx SMI Same-Cell Multiomics workflow is the only solution to enable detection of over 19,000 RNA and 72 proteins, all within the same FFPE tissue section. This high-fidelity spatial multiomics platform delivers whole transcriptome and high-plex protein data at subcellular resolution, allowing scientists to move beyond inferring biology from cell types to directly making biological insights using a pathway-centered approach.
[IMG: Fluorescent tissue image with CosMx protein markers, with inset zoomed in to show whole-transcriptome with single-cell resolution]

[H2] How It Works

Make your spatial research multiomic with the new CosMx Same-Cell Multiomics protocol. Enhance your transcriptomic findings with protein-based context and phenotypic information, orthogonally validate biomarkers in the same cell, and refine your cell types using integrated analysis methods.

01:

[H3] Validated and Ready-to-Use
Start your spatial multiomics experiments with confidence. Our rigorously validated RNA assays and protein assays ensure reproducibility and reliability from day one.

02:

[H3] Expand Discovery with Customized Antibodies
Push beyond the standard. Customize with up to 8 additional antibodies to tailor your assays to your unique research.

03:

[H3] Flexible with a Variety of RNA Assays
Your research, your way. CosMx Same-Cell Multiomics adapts to your RNA plex needs, with a choice of 1K, 6K, or over 19K assay panels, giving you the flexibility to design experiments without compromise.

04:

[H3] Simplified Workflow with Removable Flow Cell Coverslip
Experience a streamlined process with our new removable flow cell coverslip, making sample handling and workflow management easier than ever.

[H2] Featured Solutions for CosMx Same-Cell Multiomics
Add any Human CosMx RNA Assay to the CosMx Human IO Protein Assay, and customize with up to 8 additional protein targets.
[IMG: Schematic displaying CosMx Human IO Protein Assay plus any choice of Human RNA Assays to achieve CosMx Same-Cell Multiomics]

[H2] Applications

CELL PHENOTYPING

Gene/Protein Correlation

TISSUE CONTEXT

CELL PHENOTYPING

[H2] Identify cell types and states with greater accuracy by combining transcriptomic profiles with protein expression in the same cell.

Gene/Protein Correlation

[H2] Confirm candidate biomarkers directly in tissue by aligning protein detection with RNA expression at subcellular resolution.

Protein Layer
RNA Layer

TISSUE CONTEXT

[H2] Map cellular heterogeneity and cell-cell interactions within their native environment by analyzing RNA and protein together within intact tissue.

This image shows extracellular components of tissue (e.g. Fibronectin in yellow) provided by the protein layer of information.

[H2] Request a Quote
Contact our helpful experts and we’ll be in touch soon.

[H2] Related Resources

CosMx SMI – Single-Cell Imaging

Poster
Whole Transcriptome Single Cell Spatial Imaging of Tumor vs Normal Tissue Microarray

[H2] Related Products

CosMx Spatial Molecular Imager

CosMx Human Whole Transcriptome Panel

CosMx Protein Assays

Home » Resources » Spatial Informatics Hub

See Also:

GeoScript Hub

AtoMx® SIP

[H2] Spatial Biology Informatics play a crucial role in advancing our understanding of data from spatial biology platforms.
By developing the computational tools, we are able to extract valuable insights from the wealth of spatially resolved biological data generated by modern technologies. ​
Our experts in Spatial Informatics here at NanoString have designed and implemented methodologies that can handle the unique challenges posed by spatial data, such as the need to account for tissue heterogeneity, spatial interactions, cell typing, and accurate localization of biological molecules. These methods enable scientists like yourself to uncover spatial patterns, identify novel cell types and functionalities, discover molecular interactions, and gain a deeper understanding of how biology functions within its spatial context. Welcome to the Spatial Informatics Hub: home of all things Spatial Informatics.​
[H2] Open-Source Tools for Spatial Biology
Open-source software tools play a vital role in advancing biological discovery by providing researchers with access to the latest technologies (or “latest from NSTG”) at NanoString by promoting collaboration & transparency, improving reproducibility, and encouraging innovation. By making open-source packages freely available to all researchers, we make sure everyone has access to the latest tools and technologies to carry out research. We’re dedicated to help accelerate our researchers time to discovery​.
The latest open-source packages for CosMx® SMI and GeoMx® DSP are featured here, with even more available on GeoScript Hub for GeoMx DSP data analysis. Explore the packages below to see our latest releases.​

CosMx SMI

AtoMx Custom Modules

GeoMx DSP

Prebuilt Solutions

CosMx SMI

[H2] Open-Source CosMx SMI Packages

[H3] InsituType
This package offers superior accuracy and efficiency in cell typing for spatial single-cell transcriptomics that makes it an effective package to use with complex tissues.
Get started
[H3] InsituCor
InsituCor provides one answer to one of the biggest conundrums in CosMx analysis, “where do I look?”, by returning modules of spatially correlated genes.
Get started

AtoMx Custom Modules

[H2] AtoMx Custom Modules

[H3] Export Data
The custom export modules are recommended if you wish to export data directly to your own AWS S3 bucket or if you wish to customize the export (e.g., edit the export script).
Get started
[H3] RNA QC Plot
The CosMx SMI RNA QC Plot module reads in the output of the Quality Control (RNA) module from the AtoMx SIP cloud platform and creates flowcell-level summaries, including violin plots and a csv with the summarized QC data.
Get started

GeoMx DSP

[H2] Open-Source GeoMx Packages

[H3] SpatialOmicsOverlay Package
This package overlays gene counts, segment annotations, pathway scores, cell type proportions, among other annotations on GeoMx images.
Get started
[H3] Volcano Plot
The Labeled Volcano Plot DSP DA script creates publication-ready labeled volcano plots based on the
researchers’ input and statistical study results. The script also creates a table of tagged genes.
Get started
[H3] SpatialDecon
v1.3 updated October 2022 This script was designed for data from GeoMx high-plex RNA assays, such as the Cancer Transcriptome Atlas and Whole Transcriptome Atlas.
Get started
[H3] TCR Diversity
This script was designed for data from GeoMx DSP NGS assays (Whole Transcriptome Atlas or Cancer Transcriptome Atlas) with TCR Profiling Add-on.
Get started
More on the GeoScript Hub »

Prebuilt Solutions

[H2] Prebuilt Informatics Solutions

Designed with researchers of all backgrounds in mind, we’ve built AtoMx® SIP to simplify spatial bioinformatics and data management to allow data analysis and visualization anytime, anywhere. ​
AtoMx SIP is a no-code informatics solution that allows researchers to analyze spatial multiomics data with NanoString developed best in class analysis modules and provides the flexibility to allow researchers with computational backgrounds to create custom analysis pipelines and scripts. Let us simplify your spatial informatics and data infrastructure so that you can focus on your research.​
For current GeoMx DSP users who prefer to analyze their GeoMx DSP data on-instrument, DSPDA (DSP Data Analysis Suite), offers researchers the ability to use pre​…
Learn About AtoMx Learn about GeoMx Analysis

[H2] CosMx SMI Data Export
The CosMx DA Export module exports the TileDB array, Seurat object, and (optionally) raw, decoded files such as morphology images and per-FOV transcripts. Data is exported per-study.
The Flat File Export module exports flat files which are more readily used with open source tools utilizing functions like Seurat’s Load Nanostring. It does not include images, raw decoded data files, or data objects, and is intended to supplement the CosMx DA Export module. Data from a study is exported per flow cell.

DA Export Download

Flat File Export Download

DA Export Download

[H2] DA Export Module

Download DA Export Module
Resources: Vignette | Setup Instructions

Flat File Export Download

[H2] Flat File Export Module

Download Flat File Export Module
Resources: Vignette | Setup Instructions

[H2] AtoMx RNA QC Plot Custom Module
The CosMx SMI RNA QC Plot module reads in the output of the Quality Control (RNA) module from the AtoMx SIP cloud platform and creates flowcell-level summaries, including violin plots and a csv with the summarized QC data. To access the QC plots and results csv file, click the image icon on the successfully executed RNA QC Plot module in the Pipeline Structure panel.

Download

Download

[H2] Download

Download the RNA QC Plot Custom Module
Resources: Setup Instructions

[H2] CosMx SMI InsituCor
One of the biggest conundrums in CosMx analysis is, “where do I look?” InsituCor provides one answer to this question, returning modules of spatially correlated genes. When genes are correlated across the space of a tissue, it suggests they regulate each other, or are jointly regulated by some underlying factor. We find that modules output by InsituCor are enriched for interesting biology worthy of precious human attention.

Download

Poster

Download

[H2] Download

Download the InsituCor Package
Resources: Vignette Preprint Manuscript

Poster

[H2] Poster

Learn how the InSituCor algorithm discards trivial correlations, exposing gene sets worth attention, in the AACR 2024 poster, “InSituCor: Uncovering gene co-regulation networks in spatial transcriptomics data”
Download Poster

[H2] CosMx SMI InsituType
This module offers superior accuracy and efficiency in cell typing for spatial single-cell transcriptomics that makes it an effective package to use with complex tissues. ​

Download

Download

[H2] Download

Download the InsituType Custom Module
Resources: Vignette Preprint Manuscript