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Highly multiplexed profiling of single cells and tissues are emerging as essential technologies to decipher complex biological phenotypes in health and disease. Mass cytometry (CyTOF – Cytometry by Time of Flight) and imaging mass cytometry (IMC) allow rapid and efficient multiplexing of isotope-labelled detection reagents for analysis of single-cell solutions or tissue slides. These technologies are revolutionizing our understanding of systemic immune responses.

Mass Cytometry: Comprehensively profile cell phenotypes and functional states using CyTOF technology

Mass cytometry is a novel platform for high-dimensional phenotypic and functional analysis of single-cells. Cellular targets can be labeled with more than 40 metal-tagged antibodies. These are detected and quantified by time of flight (TOF) performed on the Helios CyTOF system with minimal overlap between channels. Data is transformed into FCS files which are compatible with most of Flow Cytometry software but is also ideal for bioinformatics approaches.

Imaging Mass Cytometry: Deeply interrogate cellular phenotypes in the spatial context of the tissue environment; Visualize pathology and disease with high-multiplex imaging

Given the importance of spatial resolution to studies of cellular interplay, 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. Computerized analysis of the generated images involves the segmentation of intact cells, nuclei, or other objects of interest, followed by quantification of the expression level of each of the analyzed markers. The high‐dimensional single‐cell data thus generated can then be addressed using tools similar to those used for high parameter flow cytometry data.


•           Currently up to 50 markers measured simultaneously

•           Additional channels for cell identification and viability

•           Sample barcoding to multiplex up to 20 samples in a single tube

•           Minimal signal overlap, no compensation necessary

•           Low biological background contaminations

•           Beads added to samples allows for data normalization

We support users in project planning, experimental design, panel design, sample preparation, optimization, data acquisition and basic data analysis.

The Freiburg Mass Cytometry Unit utilizes a 3rd generation CyTOF Helios and Hyperion platform. We provide core functionality for collaborative projects, ranging from consultation, reagent conjugation, standardized staining work flows, training and data acquisition to guidance with bioinformatics analysis. Frequently, standardized core panels can be rapidly adapted to individual research needs.

External users are welcome – if interested please contact Saskia Killmer or Marilyn Salvat Lago for further information.

We are supported by the German Research Foundation (DFG) and the Faculty of Medicine, University of Freiburg.


Freiburg Mass Cytometry Unit

Saskia Killmer, Mass Cytometry specialist, technical head

Marilyn Salvat Lago, Mass Cytometry specialist

Prof. Dr. Dr. Bertram Bengsch

Contact information: Please contact us via masscytometry.med2@uniklinik-freiburg.de or +49 761 270-35090.