The Imaging Mass Cytometry Laboratory provides cancer researchers with high-dimensional imaging analysis of tumor tissue samples at subcellular resolution. 

In contrast to traditional imaging technologies, such as immunohistochemistry and immunofluorescence, which are capable of staining just two or three protein markers, imaging mass cytometry can simultaneously stain up to 40 protein markers. It is one of the leading technologies in spatial biology and provides compressive and multiparametric analyses of tissue samples at the single-cell level with spatial distribution. Imaging mass cytometry can be used for 3D imaging and can be combined with RNAscope™ technology to simultaneously detect antibody markers and mRNA transcripts.        

We work with intramural staff and extramural nonprofit research organizations interested in studying tumor heterogeneity and interrogating tumor microenvironments, interactions between tumors and stromal cells, and the roles of immune cell subpopulations in tumor progression or suppression in animal models and cancer patient samples.  

Portrait photo

Contact Christine Newkirk, project manager, at for service requests or questions.

Collaboration Opportunities

All investigators with a cancer-focused project are welcome to request a service from the laboratory. 

Mass cytometry image of infiltration of CD8a T cells and Macrophages
Infiltration of CD8a T cells and Macrophages (CD68) in high NOS2 expressing ER-negative Breast Cancer. Clinical sample from Dr. David Wink laboratory.

Mass cytometry image of expression in non small cell lung cancer
Expression of DNA-IR, β-catenin, Vimentin,CD3, and CD20 in Non small Cell Lung Cancer (NSCLC).
Mass cytometry image of PDX mouse models
Identification of CTCs from the PDX mouse models, showing expression of human specific PanCK, EpCAM, E-cadherin, COX2 and β- catenin in CTCs with pool of CD45+ve mouse leukocytes in the background. Pre-Clinical sample from Dr. Esta Sterneck laboratory.

Fluidigm Hyperion Imaging System
Submissions accepted on a rolling basis

Request our services

We provide access to technology for pilot studies, collection of preliminary data, and investigations to complement ongoing research.

Technology to assess tissue microenvironments 

The laboratory is equipped with a Standard BioTools™ Hyperion™+ Imaging System that performs high-dimensional proteomics analyses of formalin-fixed, paraffin-embedded tissue samples; tissue microarrays; fresh-frozen tissues; and smeared cells on glass slides.

We use this technology to stain the specimens with metal-labeled antibodies and obtain high-dimensional images of up to 40 protein markers simultaneously. This allows researchers to interrogate the protein markers’ expression in the nucleus, in the cytoplasm, and on the cell membrane.

Individualized support for investigators 

We work with researchers to design customized metal-labeled antibody panels, validate those panels, and optimize the staining protocols. The Imaging Mass Cytometry Laboratory maintains a state-of-the-art pipeline for quantitative analysis of high-dimensional, single-cell data.

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Imaging mass cytometry laboratory workflow  

To address investigators’ research questions, we develop metal-labeled antibody panels and validate them with positive and negative control tissue slides/tissue microarrays. Once an antibody panel is locked, we use 4–5-µm sections of fresh-frozen or formalin-fixed, paraffin-embedded tissue, or smeared cells, for staining with up to 40 different metal-labeled antibodies. Regions of interest on glass slides are then ablated with a Hyperion™ laser ablation unit using a 1-µm spot size. The content is ionized and transferred to a time-of-flight mass spectrometer, which resolves it based on its atomic mass.

Video file
An end-to-end workflow for multiplexed image processing and analysis. Nat Protoc 18, 3565–3613 (2023). Windhager, J., Zanotelli, V.R.T., Schulz, D. et al.

After overlaying the single isotope signals for every spot for all of the laser shots, we generate high-dimensional images that provide spatial and subcellular resolution of the tissue samples. Raw data from the instrument are shared with the investigator’s laboratory. If required, we also contribute in-data analysis. For high-dimensional data analysis, we implement project-dependent cell segmentation analyzed with the Bodenmiller Lab pipeline.


Our capabilities and specializations

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Up to 40 different metal-labeled antibodies 

The laboratory developed and validated several metal-labeled antibody panels to achieve spatial and subcellular resolution of tissue samples. This resource is available to researchers.

Additional Content
  • Epithelial-to-mesenchymal transition markers (EMTs) 

  • Metabolic protein markers  

  • Tumor microenvironments   

  • Protein markers targeted to specific cancer types  

  • Proliferation markers   

  • Cancer stem cell markers