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

We work with researchers interested in studying the tumor microenvironment, tumor-stromal cells interactions, and the roles of different subpopulations of immune cells in tumor progression and suppression in animal models and cancer patients' samples. 

The laboratory is equipped with a Fluidigm Hyperion Imaging System that performs high-dimensional proteomics analysis of fresh-frozen tissues, tissue microarrays, smeared and formalin-fixed cells, paraffin-embedded tissue. 

Fluidigm Hyperion Imaging System

With this technology, we use metal-labeled antibodies to stain the specimens on glass slides and obtain high-dimensional images of up to 40 protein markers simultaneously. This allows researchers to interrogate the protein markers expression in the nucleus and cytoplasm, as well as on the cell membrane. 

In addition to the tissue slides analysis, the laboratory has implemented this technology for multiplex proteomics characterization of rare circulating tumor cells (CTCs) isolated from cancer patients’ blood samples. This helps to better understand the role of CTCs in the metastatic spread of a disease and to study drug resistance and mutational switchover.  

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


The laboratory has developed and validated the following metal-labeled antibody panels that are available to researchers: 

  • Epithelial to mesenchymal transition markers (EMTs)
  • Metabolic protein markers 
  • Tumor microenvironment  
  • Protein markers targeted to the specific cancer types 
  • Proliferation markers  
  • Cancer stem cell markers 

The Imaging Mass Cytometry Laboratory has established data analysis pipelines:  

  • Cell profiler- histoCAT-based data analysis pipeline from Bodenmiller laboratory  
  • Halo from Indica laboratory  


We work with human and murine sources of fresh-frozen or formalin-fixed, paraffin-embedded tissue samples, smeared cells, rare circulating tumor cells, cell lines and patient-derived primary cultures. 

The laboratory maintains a repository of more than 50 validated metal-labeled antibodies targeted to the EMTs, cancer stem cells, immune cells, and cell metabolism pathways. 

Our expert staff performs metal-label antibody staining, laser ablation of tissue samples and high-dimensional imaging analysis. Our services include: 

  • Metal-label antibody panel design customized for each research project. 
  • Assistance in procurement of commercially available metal-label antibodies. 
  • In-house metal-label antibody conjugation of other antibodies that are not commercially available. 
  • Validation of all the metal-labeled antibodies with known positive and negative control tissue samples or cell lines.


We use fresh-frozen or formalin-fixed, paraffin-embedded tissue sections of 4-5 µm size or smeared cells to stain with up to 40 different metal-labeled antibodies. Different 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 the time-of-flight mass spectrometer where it is resolved based on the atomic mass.

After overlaying all the single isotope signals for every spot for all the laser shots, we generate high dimensional images—achieving spatial and subcellular resolution of tissue samples. 


  • Imaging mass cytometry Description:

    Researchers can request the following services from the Imaging Mass Cytometry Laboratory:  

    • Building the metal-label antibody panel targeted to the project goals  
    • Metal-labeling and validation of in-house conjugated and commercially available metal-label antibodies with known positive and negative control tissue slides.  
    • Staining and acquisition of required number of tissue slides/tissue microarrays.  
    • Sharing raw data from the instrument and assistance with high dimensional data analysis. 

    If you are interested in requesting a service from the Imaging Mass Cytometry Laboratory, please contact Milind Pore or send an email to IMCFNLCR@nih.gov.