Cell Analysis

High efficiency methods for the analysis of cells are making far deeper insights into processes within cell biology possible, and are thereby laying the foundation for many medical and biotechnology applications. Our cell analysis department offers a wide range of methods for the cultivation and analysis of primary cells and cell lines. Cell culture laboratories equipped with state-of-the-art technology and microscopes and with biosafety level S1 or S2 permit work to be done with blood and many other biological cell specimens, among other activities. We develop customer-specific methods in accordance with your individual requirements and specifications, and will help you with your preclinical research projects, as well as pharmaceutical or medical product testing.

Dynamic Blood Compatibility Tests

© Fraunhofer IZI-BB

Stent mit Halterungsvorrichtung und Einweg-Probenbehältnis. Unsere innovativen Testsysteme zur Bestimmung der Hämokompatitbilität kardiovaskulärer Implantate ermöglichen Untersuchungen unter sehr kontrollierten Strömungsbedingungen und erlauben so die Analyse von scherratenabhängigen Reaktionen des Blutes.

Over the course of the development of biocompatible implant surfaces, cell culture-based testing systems are a key diagnostic instrument to allow the interaction of the new materials with living tissue to be assessed with little effort. In the case of cardiovascular implants, flow-dependent reactions, such as in the coagulation system, present particular challenges for the test environment, as it is necessary to factor in parameters such as specimen geometry, flow rates and flow conditions.

The objective of the project currently in progress is the development of fluidic test stands that allow the in-vitro evaluation of the hemocompatibility of coatings for cardiovascular implants, as well as the hemocompatibility of entire implant modules, both efficiently and in a parallelized process under controlled test conditions (e.g. flow, media composition, etc.) and at lower material costs than previously.

Analysis of Chemotaxis in Microfluidic Systems

Analysis of chemotaxis in microfluidic systems
© Fraunhofer IZI-BB

Phase contrast image of the migration of HFF1 cells in concentration gradients with the corresponding trajectories plotted. Using optical fluorescence methods, changes to the cytoskeleton during the formation of lamellipodia can be monitored dynamically. Scale bar: 50 µm.

Chemotaxis refers to the directional migration of cells in concentration gradients of a stimulating substance, and plays a key role in many important biological processes such as embryonic development, immune response or cancer. An understanding of the fundamental molecular mechanisms is essential for the development of new active substances that are used for these processes. Unfortunately, classic chemotaxis assays do not allow a sufficient level of control to be exercised over the experimental framework conditions for the study of chemotaxis. To overcome these limitations, we use microfluidic systems that allow extremely stable concentration gradients to be produced, and that allow the migration of the stimulated cells to be dynamically recorded for hours. The gradients this involves are generated under laminar flow conditions by means of diffusion between two parallel subflows. Varying the flow speeds allows the rise in the gradient to be modified, and allows it to be positioned at different positions in the microfluidic channel. This ensures that the location and the time of stimulation of cells with soluble factors can be varied with a high degree of flexibility, and can be adapted to the respective test conditions.

Calcium Signals in Single Cells

Calcium Signals in Single Cells
© Fraunhofer IZI-BB

Creating a specific contact on one individual T-cell using a functionalized microparticle in a microchannel. The increase in the intracellular Ca2+ concentration triggered by binding the cell to the particle surface was measured using a calcium-sensitive fluorescent dye.

The interaction between cells and their environment is an effective mechanism for controlling cellular states in vivo. To decode the signal transduction processes that this involves, defined events along the cellular signal cascade must be determined, and the interrelation with each other must be explained. Ensemble measurements do not allow this to be achieved, as the averaging of biological data always constitutes a disregard for the variability of the responsiveness of individual cells, and therefore delivers ambiguous results. Only a multiparameter analysis at single cell level can provide the decisive information that is indispensable for a detailed understanding of cellular signal paths. Our Working Group develops techniques and methods that allow the micro-environment of individual cells to be systematically manipulated, which, in turn, makes it possible to expose the cells to soluble or surface-bound stimuli both individually and in a highly controlled manner. The cellular signal transduction processes that this triggers are analyzed on different time-based levels. This allows biological processes such as intercellular communication, or the differentiation of cells, to be studied very precisely and in reproducible environmental conditions.

Analysis of Differentiation Processes and »Artificial Stem Cell Niches«

stem cells
© Fraunhofer IZI-BB

Stem cells differentiated into a neuronal phenotype in a microfluidic system. Extensions of neural cells spread out from a dense cell cluster radially. Detection of neuronal cells by means of β-III-tubulin (green) and actin (red).

The current state of knowledge has shown that the differentiation of stem cells in the organism is predominantly controlled by their micro-environment. Other types of cells, as well as extracellular proteins, play a key role in this. Changes to this so-called »niche« are used to give the stem cell a signal to lie dormant, for example, or to multiply or differentiate.

Unfortunately, the observation of dependencies like this is technically difficult, as work is not being done with a flat layer of cells in culture. Instead, an attempt must be made to track, to microscope, to stain and to manipulate individual cells in a growing embryo or in a fully grown organism instead, and this without exerting any unwanted influence on them. This is, at times, performed on simple organisms such as C. elegans (nematodes) and D. melanogaster (fruit flies). However, the problems when working on complex systems, particularly humans, are insurmountable.

We are developing approaches that will allow the stem cell »niche« to be artificially reproduced and be exported for examination under a microscope. This will allow the behavior of individual stem cells to be studied in their physiological environment, and allow valuable insights into principles and possibilities of influencing stem cell differentiation to be obtained. A distant objective of this approach is the controlled differentiation and preparation of individual cells in chip format.


  • Establishing functional cell assays (e.g. proliferation, cytotoxicity, chemotaxis, neurite growth, stem cell differentiation, intracellular calcium, intracellular pH, etc.)
  • High-end optical microscopy (e.g. high-sensitivity fluorescence measurements, time-resolved fluorescence microscopy of living cell systems, etc.)
  • Expression analysis by means of immunostaining and western blots
  • Detection and quantification of cellular and proteinogenic blood components


  • Confocal scanning laser microscope (Zeiss LSM510)
  • Fully automated fluorescence microscope with specimen stages temperature-controlled by a climatic unit for long-term observation of living cells (Olympus Cell^R)
  • Transmitted and reflected light microscopy with bright field, phase contrast, fluorescence, polarization and total reflection modes (TIRFM)
  • Flow cytometer
  • 200 m² fully equipped cell cultivation facility, blood work station, S1 and S2 laboratories

  • Tel Aviv University, OMNI Group
  • University Hospital Regensburg
  • University Hospital Tübingen

  • Habaza M, Kirschbaum M, Guernth-Marschner C, Dardikman G, Barnea I, Korenstein R, Duschl C, Shaked NT. Rapid 3D Refractive-Index Imaging of Live Cells in Suspension without Labeling Using Dielectrophoretic Cell Rotation. Adv. Sci. (2017), 4, 1600205
  • Kirschbaum M, Jaeger MS, Duschl C. Measurement of surface-mediated Ca2+ transients on the single-cell level in a microfluidic Lab-on-a-Chip environment. Methods Mol Biol. (2015);1272:247-56
  • Schreml S, Meier RJ, Kirschbaum M et al. Luminescent Dual Sensors Reveal Extracellular pH-Gradients and Hypoxia on Chronic Wounds That Disrupt Epidermal Repair. Theranostics. (2014), 4, S. 721-735.
  • Renner A, Jaeger MS, Lankenau A, Duschl C. Position-dependent chemotactic response of slowly migrating cells in sigmoidal concentration profiles. Appl Phys A. (2013), 112(3), 637-645.
  • Kirschbaum M, Jaeger MS, Duschl C. Correlating short-term Ca2+ responses with long-term protein expression after activation of single T cells. Lab Chip. (2009), 9, 3517-3525.
  • Kirschbaum M, Jaeger MS, Schenkel T, Breinig T, Meyerhans A, Duschl C. T cell activation on a single-cell level in dielectrophoresis-based microfluidic devices. J Chromatogr A. (2008), 1202, 83–89.