Flow cytometry is a versatile tool to characterize cell types, to determine their activation state on the single cell level, to investigate the cell cycle and also to physically separate cell types from each other, e.g. to further cultivate them, to transplant them or to investigate expression profiles, up to expression investigations of single cells, e.g. by means of RNASeq. The Core Unit Flow Cytometry provides equipment and expertise, so that you can get the best out of your cells.

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Some of the filter elements of the cell sorter FACSAria III. Photo: Uwe Müller

Analysis and sorting of cells by flow cytometry

The Core Unit Flow Cytometry (CUDZ) is located in the S2 laboratories of the Institute of Virology of the Faculty of Veterinary Medicine and has two flow cytometers of the latest generation. The Core Unit is jointly operated by the Institute of Virology, which is responsible for project management in accordance with the Infection Protection Act, the Ordinance on Biological Substances and Genetic Engineering and provides logistical support, and the Institute of Immunology, which is responsible for technical management. It provides interested users from the University of Leipzig, non-university research institutions and companies with equipment and the corresponding know-how in the field of analytical and preparative cytometry. Thus it is possible to analyze and physically sort cells (e.g. for expression analysis or cultivation).

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Evaluation of the recorded data with analysis software such as FACSDiva or FlowJo. Design: Uwe Müller

The developments in the field of fluorochromes and the novel technical possibilities in the field of flow cytometry have opened up new and diverse applications in recent years. A modular system of fluorescence detection makes it possible to react to such innovations by changing the filter composition.

The CUDZ offers a profitable use of these versatile technologies due to the excellent equipment and the trained and specialized personnel. The instrument settings can be adapted to the needs of the respective research project. In addition to the actual measurements, CUDZ's service also includes the consultation of the best antibody panels for a specific problem and support in the preparation of staining protocols.

As the only unit in Leipzig, CUDZ offers the possibility to carry out work under safety level S2. Thus it is possible to work on the devices with infectious material* as long as the pathogens are subject to safety level 2.

Another Core Unit for Flow Cytometry is located at the Interdisciplinary Center for Clinical Research (IZKF) under the direction of Dr. Lösche, with whom we cooperate closely.

For the use of the equipment of the CUDZ the completion of the different forms (depending on the sample material), that you will find in the sidebar, is necessary.

*In this context, please note that the absence of HIV, HBV and HCV must be guaranteed if the human sample material is not inactivated!

Flow cytometers of the CUDZ

The CUDZ has two flow cytometers, one for cell analysis and one for cell sorting. For further information please refer to the following information

LSR-Fortessa - Details in pictures

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The BD LSRFortessa II is currently one of the most powerful analytical flow cytometers available.

The instrument is equipped with five lasers and 18 fluorescence detectors.

Color Wave length Type mW fluorescence detectors
blue 488 nm solid state laser 50 2
red 640 nm diode laser 40 3
yellow-green 561 nm solid state laser 50


violet 405 nm diode laser 50 6
UV 355 nm solid state laser 20 2

Up to twenty parameters (forward and sideways scattered light and 18 fluorescence parameters) can be detected simultaneously.

The BD LSRFortessa can be operated via tubes or a multisampler (HighThroughputSampler, HTS). After instruction by the supervisors, the instrument can be worked on independently. The CUDZ team advises on multi-channel and multi-channel measurements.

Please discuss the exact filter equipment for the fluorochromes to be used with the CUDZ staff when planning your experiments.

The measurement and evaluation software FACSDiVa 6.1.3 runs on a Windows XP computer. License keys can be borrowed from the Core Unit for a short time.

The reservation of the usage dates takes place via an online calendar to which every registered user has access.

FACSAria III - Details in pictures

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The modern high speed cell sorter BD FACSAria III is an adjustment free table sorter system. It is equipped with a closed sorting chamber and five air-cooled lasers with innovative optics for multi-laser excitation.

The sorting setting is fully software controlled and has fully digitized electronics. Due to the simple operation and automatic switch-off of the sorting process in case of malfunctions, it can be operated by the user himself after training.

Four of the five built-in lasers can be used in parallel:

Color wave length Type mW fluorescence detectors
blue 488 nm solid state laser 50 2
red 633 nm HeNE laser 40 3
yellow-green 561 nm solid state laser 50


violet 405 nm diode laser 50 3
nearUV 375 nm solid state laser 7 3

Up to 15 parameters (forward and sideways scattered light and 13 fluorescence parameters) can be detected simultaneously.

Sorting is possible both in tubes and via an Automated Cell Deposition Unit (ACDU). The latter allows sorting directly onto a slide or into a microtiter plate (6, 24, 48, 96 and 384 wells). It is equipped with an aerosol management system, which also enables the sorting of L2/S2 bio-materials.

The external heating/cooling system of the sorter allows the cells to be tempered before and after sorting, which improves cell vitality and colour stability.

Up to 20,000 cells/s can be sorted and four populations can be sorted simultaneously.
It is possible to sort cells and particles sterile.
The measurement and analysis software BD FACSDiva runs on a Windows XP computer.

The usage dates are agreed with the head of CUDZ, Dr. Müller to agree on.

Porträtaufnahme von Uwe Müller

Our user philosophy is help for self-help. We train the users thoroughly so that they can analyze their samples independently. However, we are always available for advice and assistance - especially with questions regarding cell sorting.

Uwe Müller, Technical/Scientific Head CUDZ

Usage concept and application form of the CUDZ

The documents are available in PDF format. If you do not have Adobe Reader installed, you can download and install the software here: Adobe Reader.

Please read the usage concept carefully, it also includes the operating costs per hour. Please note that work on the flow cytometers is only possible after filling out the form. For work with S2 pathogens, the form "Application form for work with S2 pathogens" must also be completed.

Please note that work with S2 pathogens must have been carried out beforehand at the Saxon Ministry for the Environment and Agriculture SMUL must be displayed.


The technical and scientific director PD Dr. Uwe Müller will be happy to answer any further questions you may have regarding implementation and experimental planning:

If you have any questions regarding genetic engineering or infectious diseases, please contact the project manager for genetic engineering, infection control and biochemicals, Prof. Dr. Dr. Thomas Vahlenkamp at vahlenkamp(at)vetmed.uni-leipzig.de or Tel. +49 0341 97-38200.

Other Core Units of the University of Leipzig

Characterization of pathogens (CUMI)

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Flow cytometry unit at IZKF

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