Imaging Mass Cytometry

Visualize pathology and disease with high-multiplex imaging


Changing the course of how diseases are treated and ultimately cured requires a comprehensive understanding of complex cellular phenotypes and their interrelationships in the spatial context of the tissue microenvironment. Imaging Mass Cytometry™ (IMC™) performed on the Hyperion™ Imaging System using Maxpar® metal-tagged antibodies empowers simultaneous imaging of up to 37 protein markers at a time. Bringing together high-parameter CyTOF® technology with imaging capability, the Hyperion Imaging System enables deep interrogation of tissues and tumors at subcellular resolution to uncover pathology insights, new biomarker correlations and cell interactions.


Hyperion Users Imaging data

Bernd Bodenmiller, inventor of Imaging Mass Cytometry, receives the Human Proteome Organization Clinical and Translational Proteomics Award.          

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See highlights from the 2018 Imaging Mass Cytometry User Group Meeting.       


Denis Schapiro on using the histoCAT™ analytical toolbox to unlock unprecedented biological insights.       

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Watch an immuno-oncology webinar given by Kurt Schalper, MD, PhD, of the Yale Cancer Center.

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Fluidigm announces a co-marketing agreement with Visiopharm® to expand and simplify Imaging Mass Cytometry data analysis.        

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23 peer-reviewed publications for the Hyperion Imaging System


Featured Links

  • Imaging Mass Cytometry publications
  • Imaging Mass Cytometry Seminars and Webinars
  • Application Note: Immuno-Oncology Research with the Hyperion Imaging System
  • List of pathologist-verified Maxpar antibodies for Imaging Mass Cytometry
  • Antibody staining protocol
  • Technical support
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    Hear what researchers are saying about Imaging Mass Cytometry with the Hyperion Imaging System.


    The Complete Hyperion Imaging System

    The Hyperion Imaging System is accompanied by a pathologist-verified Maxpar imaging antibody portfolio and reagents, a software suite for image acquisition and data analysis and experienced Fluidigm service and support. Delivering a comprehensive view from one scan, the Hyperion Imaging System can enable you to deeply profile precious formalin-fixed paraffin-embedded (FFPE) or frozen tissues at subcellular resolution to power your next breakthrough.

    Reagents for the Hyperion Imaging System

    Maxpar Metal-Conjugated Antibodies

    Simplify Imaging Mass Cytometry panel design with pathologist-verified Maxpar antibodies. The Maxpar catalog features more than 80 metal-labeled antibodies and continues to grow rapidly. This initial selection of antibodies focuses on immune and oncology targets to be used with FFPE. Combining the antibodies of interest into a panel is easy using a protocol that provides a common antigen retrieval step. This reduces the time to panel development and significantly expands possibilities for immune system and immuno-oncology research on the Hyperion Imaging System. Design your own custom panel to analyze immunity, cancer progression or cancer immunotherapy research targets.

    See Abs

    Primary IMC Antibodies

    Maxpar Labeling Kits

    With Maxpar metal-labeling kits you can tag IgG clones with your choice of up to 35 metals. Order them individually or as sets, with each kit containing enough material to conjugate 4 antibodies in 100 μg amounts.

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    Maxpar Labeling Kits

    Multimetal Labeling Kits

    The multimetal Maxpar kit contains a total of 40 reactions for conjugating metals to monoclonal antibodies, with up to 10 different metals of your choice (each at 4 reactions).

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    Multimetal Labeling Kits

    Buffers and Solutions

    Maxpar buffers provide optimal and consistent staining conditions for external, cytosolic and nuclear targets.

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    Buffers and Solutions

    Custom Antibody Conjugation

    When your study calls for new antibodies or specific antibody configurations, consult our team of experts for custom conjugation services to tailor your antibody panels for collecting high-impact data. Our custom conjugation services speed you from design to discovery with made-to-order metal labeling for antibodies not currently listed in the Maxpar catalog, or alternative metal tagging for all listed items. Choose from 37 nonoverlapping pure metal tags. Contact your local sales representative for more information.

    The Data Analysis Pipeline

    CyTOF Software v6.7

    The CyTOF v6.7 system control software is designed to be a user-friendly and intuitive for Hyperion Imaging System control, and to provide continuous instrument feedback and diagnostic capabilities to users. This gives users the ability to troubleshoot quickly and effectively as well as to provide the highest quality of data output.


    CyTOF Software v6.7

    Visualize Spatial Context of Multiplex Data in Minutes

    The MCD™ Viewer software that accompanies the Hyperion Imaging System precisely converts the scanned cells and tissues into TIFF images of publication quality. Each image can be spectrally separated to display the expression of each protein. Data for each region of interest can be exported for third-party analysis on software such as histoCAT.


    MCD Viewer Software

    Take an interactive tour that demonstrates the basic data visualization concepts enabled by the MCD Viewer software using a selection of data from a 20-marker lung cancer panel study. This is not an actual demo of the MCD Viewer software.


    Interactive Data Visualization

    “Now that we can measure so many markers simultaneously, for the first time we have the ability to comprehensively study cell types and their signaling and functional state in normal tissue and especially in tumors, and also how they are spatially arranged.”
    —Bernd Bodenmiller, PhD, Assistant Professor, Institute of Molecular Life Sciences, University of Zurich

    histoCAT Software for Computational Imaging Mass Cytometry Analysis

    histoCAT software is an innovative computational IMC analysis toolbox that enables comprehensive analysis of cellular phenotypes and their interrelationships within the spatial context of the tissue microenvironment. Developed in the laboratory of Bernd Bodenmiller at the University of Zurich, histoCAT includes novel algorithms to identify the relationships and “social networks” between cells in healthy and disease states and across experimental cohorts. Under an agreement with the University of Zurich, Fluidigm obtained rights to globally distribute histoCAT along with the Hyperion Imaging System.

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    histoCAT Software

    Visiopharm Offers Phenomap Software for Highly Multiplexed Data Analysis

    Phenomap™ software by Visiopharm simplifies the analysis of high-dimensional images, such as those generated through Imaging Mass Cytometry. Phenomap offers a streamlined and intuitive workflow for simultaneous analysis of up to 255 channels by automatically identifying individual cells and performing cell-based phenotyping. This dedicated software tool available through Visiopharm can be used to perform quantitative measurements and automatically cluster data and generate t-SNE plots to visualize phenotypic relationships.

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    Visiopharm Phenomap Software


    Maximize System Performance with Fluidigm Service, Support and Training

    Boost productivity, control costs and minimize downtime with service plan options that are attractively priced and include regularly scheduled maintenance visits to ensure that your Hyperion Imaging System is kept in peak operating condition.

    Fluidigm Field Application Specialists provide you with a selection of training programs to help you get started so you can begin asking new questions in your own research with the Hyperion Imaging System.


    How Imaging Mass Cytometry Works

    Simultaneously Interrogate Multiple Protein Markers—All from a Single Scan

    The Hyperion Imaging System enables deep profiling of precious samples in a single workflow, thereby eliminating the need for serial sections or sequential staining.

    metal tag spectra

    A New Standard in High-Multiplex Protein Detection

    CyTOF technology offers a new standard for high-multiplex protein detection. In contrast to fluorescence spectra, which have broad peaks that can result in signal overlap, metal tag spectra are based on mass and are detected as discrete peaks of similar intensity for similar protein expression level. Because of the sensitivity of mass cytometry, even neighboring isotopes can be readily resolved. This separation enables the routine use of many more metal tags in multiplex experiments without signal overlap, as compared to fluorescent dyes.

    protein detection

    Protein biomarkers in human lung tissue are visualized at subcellular resolution following precise metal-tag capture from a human lung FFPE tissue sample and detection at 1 Da spectral resolution using proven CyTOF technology. Markers include alpha-smooth muscle action (141PR), high-molecular-weight keratin (144Nd), CD31 (145Nd), beta-catenin (147Sm), vimentin (143Nd), Ki-67 (168Er), CD34 (158Gd), CD3 (170Er), histone H3 (176Yb) and collagen I (169Tm).

    Learn more about Imaging Mass Cytometry applications that use a staining method that follows a workflow similar to traditional IF staining. The method generates comparable results while eliminating issues such as autofluorescence and spectral overlap.


    Equivalence White Paper

    A Simple Four-Step Workflow

    The Imaging Mass Cytometry workflow enables deep profiling of standard FFPE or frozen tissue sections and of fixed cells deposited on glass microscope slides using the Hyperion Imaging System.

    IMC workflow

    “Through the ability of looking at 35 different antigens in a tissue section, their relationship to each other, we can really get new insights about cell heterogeneity—cell interactions—that we weren’t able to even approach before.”
    —Klaus Kaestner, PhD, MS, Thomas and Evelyn Suor Butterworth Professor in Genetics, University of Pennsylvania Perelman School of Medicine

    Simplify Multiplex Panel Design with Pathologist-Verified Maxpar Antibodies

    Metal-tagged pathologist-verified Maxpar antibodies for Imaging Mass Cytometry are designed and optimized for use with the Hyperion Imaging System. These antibodies can be combined using a protocol that provides a common antigen retrieval step to simplify panel design for use with FFPE human tissue sections. Flexibly customize panels using your own antibodies with Maxpar labeling kits or custom conjugation options.


    Antibodies for IMC


    The Hyperion Imaging System provides highly multiplexed data with subcellular spatial resolution for up to 37 protein markers on FFPE or frozen tissues or cell smears. Standard protocols for preparing FFPE or frozen tissue slices can be used for sample prep for use with the system.

    A Common Antibody Retrieval Protocol
    The Maxpar antibody staining protocol for Imaging Mass Cytometry makes it easy to combine multiple metal-labeled antibodies in one step. Metal-tagged pathologist-verified Maxpar antibodies for Imaging Mass Cytometry are designed and optimized for use with the Hyperion Imaging System. These antibodies can be combined using a protocol that provides a common antigen retrieval step to simplify panel design for use with FFPE human tissue sections.


    FFPE Staining Protocol

    Metal-Tagged Reagents

    A precisely directed laser beam focused at 1 µm collects protein markers stained with metal-tagged Maxpar antibodies and directs these metal tags for detection using proven CyTOF technology. A discrete signal from each ionized metal tag is detected based on differences in mass instead of wavelength, at 1 Da resolution. The purity and choice of metal isotopes ensure minimal background noise from signal overlap or endogenous cellular components.

    Developed for use with the Hyperion Imaging System, the 80-plus and ever-growing list of antibodies currently available in our catalog has been optimized to detect defining markers in immuno-oncology pathways and cancer and immune cell populations. Each lot of conjugated antibody is quality control-tested on tissue sections using the Hyperion Imaging System. If a desired antibody is not yet present in our catalog, you can conjugate it yourself using our metal-labeling kits or inquire about our custom conjugation services.

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    Fluidigm Products are for Research Use Only. Not for use in diagnostic procedures.