Cytometry Core

Flow & Mass Cytometry Core Facility

The multi-parameter analysis of cells within a heterogeneous sample at the single cell level is one of the most important technology for understanding of biological relationships and mechanisms in the context of health and disease. Key technologies are the analysis of single cells in suspension using flow cytometry or mass cytometry, as well as the analysis of cells in the tissue context using histopathology or imaging mass cytometry.

The Charité | BIH Cytometry Core offers expert service and state-of-the-art equipment for multi-parameter cell analysis and high-speed cell sorting.

A close cooperation with the research groups enables the joint development of new methods, which can then be made available to the users of the core unit. We offer the possibility to generate high-quality reproducible research data by regular maintenance of all instruments and implementation of quality management procedures.

The core facility is open to all scientists (Charité, BIH, other academic research institutions). Project specific resources (personnel and consumables) exceeding the basic funding are covered by usage fees.

Feel free to contact us at any time, we look forward to supporting you with your research projects.

Access & Service Hours

Services and instruments can be accessed via the platform OpenIRIS. A short introduction for getting started in OpenIRIS can be found here. Please also note the userguidelines for the core facility. Details on access to the different technologies can be found in the specific sections.

Project Meeting

We want to make sure that you get the best support for your scientific project. Thus before instruments and services of the core facility can be used, we discuss technical details and your needs for instruments and services in a project meeting.

The project meeting for the different technologies can be requested via OpenIRIS ('Services' - Project Meeting'). During this meeting you will get access to the respective booking calendar ('Scheduler') or service request ('Services') for further bookings.

In preparation of the project meeting we need you to complete the respective registration form for the required technology and upload it with the request for the project meeting.

  • Registration Flow Cytometry (cell sorting and analysis) - download
  • Registration mass cytometry - download
  • Registration imaging cytometry - download


Mass Cytometry (CyTOF/Helios) & Imaging Mass Cytometry (IMC/Hyperion)

  • If you are planning mass cytometric experiments for the first time, please contact us at least three months before the expected start of the experiments, ideally before the first sampling. The preparation and preservation of the samples is a critical factor for mass cytometry and should therefore be discussed in advance.
  • Please also contact us at least 6 weeks before the start of each new project to discuss the technical and timely feasibility of the new project.


Service Hours

Analyzers (flow cytometry) can be used independently 24/7. Instrument training, cell sorting and mass cytometry are offered during the service hours of the core facility. Bookings outside these hours might be scheduled upon request for specific projects.

Monday: 15:00 - 18:00 (CyTOF not available)
Tuesday: 10:00 - 21:00
Wednesday: 10:00 - 21:00
Thursday: 10:00 - 21:00
Friday: 10:00 - 18:00 

Flow Cytometry (Analysis and Cell Sorting)

Flow cytometry allows for the analysis of cells within a heterogeneous sample on single cell level for a multitude of parameters at a high throughput. Cells can also be sorted for further analysis, e.g. in vitro experiments or sequencing. Cell sorting can be performed in bulk or single cells into 96-well plates/384-well plates.

The configuration of the instruments are available in OpenIRIS (login needed) under ‘Details’ of the specific instrument.

Cell Analysis

Analyzers can be used independently after successful completion of the basic training. Analyzers can be booked via OpenIRIS at any time up to 14 days ahead ('Scheduler'). Instrument training is requested via 'Services' - 'Training Flow Cytometry'. The use under supervision/with support is scheduled upon request.

Equipment (Images): FACSCantoll "Thalia", LSRII SORP "Melpomene", MACSQuant "Euterpe"

Cell Sorting

Cell sorting is offered as service (staff-operated). Appointments can be scheduled at any time via OpenIRIS ('Scheduler' - AriaII SORP "Calliope") up to 14 days in advance.

Equipment (Image): FACSAria II SORP "Calliope"

Training - Flow Cytometry

The basic instrument training consists of 4 hands-on sessions. It is offered as a one-by-one training and mandatory to be use the analyzers independently. Instrument training for the different flow cytometers can be requested via OpenIRIS ('Services' - 'Training Flow Cytometry').

In addition to our basic instrument training, we offer training dedicated to special topics, e.g. automatic compensation and the use of quality controls for longitudinal studies. We also offer instrument training for users who will use their own instruments. Please contact us for details.

Mass Cytometry

As in conventional flow cytometry, cells within a heterogeneous sample are analysed on single cell level for a multitude of parameters (Scheme). However, instead of using fluorochrome-labeled antibodies to bind to the antigen of interest and being limited to the number of spectrally resolvable fluorochromes, mass cytometry (CyTOF - cytometry by Time-Of-Flight) uses metal isotope-labeled antibodies that are analyzed by their time-of-flight (TOF). This allows for the analysis of currently >40 parameters per cell and a deep profiling of phenotype and function of cells.

Sample Acquisition

The analysis of samples with mass cytometry is provided as service (staff-operated). Measurement dates are requested via OpenIRIS ('Services' - 'Mass Cytometry - Sample Acquisition') stating the desired date. Before starting an experiment, please wait for the confirmation of the booking by the core facility. The availability of measurement time can vary depending on the number of samples and the type of sample. The start of the measurement may differ from the desired time based on other bookings on the same day. If the desired date is not available, we offer an alternative date.

Imaging Mass Cytometry

Imaging Mass Cytometry (IMC) is an approach for the targeted and epitope-specific multiparameter analysis of tissue sections (Scheme). In contrast to conventional immunohistochemistry or immunofluorescence, this technology allows for the simultaneous detection of >35 specific markers on the tissue by using metal-isotopes and their different masses as analytes. Tissue sections are labeled with epitope-specific, metal isotope conjugated antibodies and the tissue is ablated in 1x1 µm spots by a laser. The ablated material is carried into the mass cytometer, and the metal ion content of each pixel is analyzed by time-of-flight mass spectrometry. The signals are then plotted as a multiparameter image that can be analyzed by any imaging software. For more information about this new technology contact the core facility.

Measurement of tissue samples

IMC is offered as service (staff-operated) or independent usage with assistance. Measurement of tissue sections can be requested via OpenIRIS ('Services' - 'Imaging Mass Cytometry - Sample Acquisition') with a date/deadline and will then be coordinated by the core facility. Longer measurements usually run overnight or over the weekend. Please request measurements as early as possible.

Antibody Conjugation

Antibodies that are labeled with metal isotopes are used for mass cytometry. These labeled antibodies can be obtained from the manufacturer. Alternatively, in particular in the case of antibody-isotope combinations which are not commercially available, purified antibodies can be labeled with the corresponding metal isotope using a conjugation kit. This enables the use of almost all antibodies that are available in purified form. 

We offer the labeling of antibodies using the conjugation kit as a service, but also the provision of reagents for independent labeling. 

The labeling of antibodies can be requested in OpenIRIS ('Services' - 'Mass Cytometry - Antibody Labeling Service').

Tissue Microarrays

Using the Minicore3, tissue punches can be combined to form a tissue microarray (TMA) on one paraffin block (Scheme). The tissue microarray technology enables efficient analysis by placing hundreds of tissue samples on a single slide. This enables an investigation with different in situ methods (e.g. IMC, immunofluorescence) in one pass and under the same standardized conditions.

The Minicore3 can be used independently after instrument training. The training can be requested via OpenIRIS ('Services' - 'Minicore 3 - Tissue Mircroarray Services') and the instrument can booked via 'Scheduler'.