Imaging Mass Cytometry

Unprecedented insight into the complex and diverse tissue microenvironment

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IMC Summit | October 21, 2021

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Discover the world’s first and most proven approach to high-multiplex imaging and single-cell protein analysis. Experiments performed on the Hyperion™ Imaging System deliver unprecedented insight into the tissue microenvironment with single-cell resolution.

With the Hyperion Imaging System you can:

  • deeply characterize the complex and diverse tissue microenvironment
  • gain unparalleled understanding of the spatial relationships between a multitude of cell types and the role of cell phenotypes in the context of disease
  • further stratify subjects by linking high-plex data to outcome in your clinical studies
  • help uncover novel therapeutic targets through the discovery of new biomarkers
  • gain a better understanding of immunotherapy responses that could ultimately help extend patient lives  

Use Imaging Mass Cytometry™ (IMC™) to generate novel research hypotheses with fewer samples in one scan, employing established CyTOF® technology. Enjoy flexible panel design without panel or antibody limitations or concern about antibody order or label assignment. Eliminate autofluorescence, create compact easy to work with data files and avoid timely and costly cyclic tests.


Hyperion Users

See how your colleagues are using IMC to gain new insights. View Scientist Spotlight

Nature publication shows how IMC was used to reveal COVID-19 lung pathology.

Read the publication
Weill Cornell press release

Rebecca Ihrie, PhD, uses mass cytometry, Imaging Mass Cytometry and machine learning to understand malignant brain tumor biology. Watch the webinar

Learn how Traum et. al. used IMC to analyze immune, viral and structural markers in hepatitis B virus immune pathogenesis. Read the publication
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Imaging data

Key to an improved pipeline: The IMC Cell Segmentation Kit—a new Innovative Solution
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See this selection of webinars to learn how researchers are using IMC in cancer, immunology and infectious disease research. Watch now

No Hyperion Imaging System instrument access? Need IMC data for an upcoming grant? Let the experts in our Therapeutic Insights Services team tailor a project to your needs and budget.
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Celebrating an important milestone!
Over 100 peer-reviewed publications using the Hyperion Imaging System for IMC

Dual mode use offers high-multiplex analysis for tissue samples or cells in solution.
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Important Links

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Single-cell analysis enabled by IMC offered some of the earliest high-multiplex imaging views of cellular phenotypes, relationships and response in complex immune reactions, including those linked to cancer. The technology has led to novel pathology insights and facilitates the assessment of biomarkers and therapeutic treatments.

If you do not have use of a Hyperion Imaging System in your lab or facility, consider working with our expert consultants in the Therapeutic Insights Services team. They will tailor and execute a sample-to-answer project designed to suit your specific needs.

Request more information and sign up to stay informed of new developments and IMC application information

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.

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

Learn how our expert consultants can work with you to tailor and execute a sample-to-answer project designed for your specific needs for single-cell mass cytometry or Imaging Mass Cytometry data.


Therapeutic Insights Services

Experts from the Therapeutic Insights Services team also develop and release novel lab-tested reagents and workflows called Innovative Solutions. Learn more about these helpful applications and the recent release of the IMC Cell Segmentation Kit.


Innovative Solutions

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 100 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.

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Primary IMC Antibodies

New Maxpar Human Conjugated Antibodies for Frozen and FFPE Tissue

The Maxpar catalog of pathologist-verified antibodies for IMC for FFPE tissues has now been expanded with conjugated antibodies for frozen human tissue to offer researchers the ability to characterize a wider range of tissues than before. Maxpar antibodies for frozen tissue support rapid and easier panel development with fewer steps, since antigens are in their native state and epitope retrieval is not required.


New Maxpar Human Immuno-Oncology (IO) IMC Panel Kits

To provide researchers with a rich, insightful understanding of tumor-infiltrating lymphocyte activation and infiltration, T cell activation and tissue architecture across several human cancer types, three new multiplex IO panels are now available:

Maxpar Human Tumor-Infiltrating Lymphocytes IMC™ Panel Kit (9-plex)
Maxpar Human Immune Activation IMC Panel Kit (5-plex)
Maxpar Human Tissue Architecture IMC Panel Kit (6-plex)

A fourth panel, the Maxpar Human Immuno-Oncology IMC Panel Kit (18-plex), combines the three IO panels. Each kit contains pre-sourced, pre-tagged, pathologist-verified antibodies and a nucleic acid stain.

Customize any panel by mixing and matching panel kits or by adding your choice of individual Maxpar antibodies in other available channels for Imaging Mass Cytometry™. The panel kits are designed to jump-start IO panel development easily. Researchers save significant panel development time and cost using these pre-selected panel kits.

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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 v7.0

CyTOF® Software v7.0 offers support for imaging and cell suspension-based sample analysis to Hyperion™ Imaging System and Helios™ system users. The software has the built-in capability to switch sample introduction modes, providing users the flexibility to configure hardware as required.

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CyTOF Software v7.0

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 AI-Powered Phenotyping Software for Multiplexed Images

As high-plex IMC™ data continues to stretch our abilities to interrogate the tumor microenvironment, finding meaningful differences in your data becomes an ever more data-heavy and daunting challenge. The Visiopharm® AI-powered phenotyping module streamlines and automates the analysis workflow of high-dimensional image data. Discover individual cell types and populations, then use the comprehensive set of measurement and visualization tools to find differences between study groups.

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Visiopharm Phenotyping Module Software

Indica Labs Provides Software with Streamlined Analysis for High-Multiplex Data

The Indica Labs Highplex FL HALO® module combines ease of use and scalability with powerful analytics for streamlined biomarker analysis of highly multiplexed Imaging Mass Cytometry™ data. This module is ideally suited for applications in immuno-oncology, where multiple markers are required to characterize distinct immune and tumor cell populations within the tissue. When it is used in conjunction with the Indica Labs Spatial Analysis module, the spatial relationships of these cell populations may be further interrogated. .

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Indica Labs 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


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.