Research Groups


Members of the Physical Biology Group

Prof. Dr. Ernst H.K. Stelzer

Professor & Group Leader
Phone +49 (69) 798-42547
Fax +49 (69) 798-42546


Curriculum Vitae  
2012-2013 Vice-Director Buchmann Institute for Molecular Life Sciences (BMLS)
(Buchmann Institut für die molekularen Lebesnwissenschaften, Frankfurt am Main, Germany)
since 2011 Professor in the Life Sciences (FB15, IZN), Goethe-Universität Frankfurt am Main
since 2009 Principal Investigator, Cluster of Excellence "Macromolecular Complexes"
Goethe-Universität Frankfurt am Main
1989-2011 Scientific Group Leader, EMBL, Heidelberg
- Cell Biology and Biophysics Unit
- Cell Biology Programme
- Physical Instrumentation Programme
1987-1989 Project Leader, EMBL, Heidelberg, Physical Instrumentation Programme
1987 Ph.D. (Dr. rer. nat.), Physics, Ruprecht-Karls-Universität Heidelberg
1986-1987 Postdoc, European Molecular Biology Laboratory (EMBL), Heidelberg
Physical Instrumentation Programme
1983-1986 Ph.D. student, Physics, Ruprecht-Karls-Universität Heidelberg
(Ruperto Carola, Heidelberg University, Germany)
performed in Physical Instrumentation Programme, EMBL, Heidelberg, Germany
1983 Diploma, Physics, Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
(Max-Planck-Institute for Biophysics, Frankfurt am Main, Germany)
1977-1982 Student, Physics, Johann-Wolfgang-Goethe-Universität Frankfurt am Main
(Goethe University Frankfurt am Main, Germany)

My scientific profile is that of a physicist who has managed to work in an interdisciplinary environment for more than twenty-five years. I have been able to bridge the gaps between optical physics, instrumentation development, molecular cell biology and the mathematical interpretations of life sciences experiments. During my Ph.D. thesis (1983-1987) I worked on confocal transmission, reflection and fluorescence microscopy. I developed the confocal 4Pi fluorescence microscope during 1990-1992 and introduced orthogonal and multi-lens detection schemes with confocal theta fluorescence microscopy around 1993. The latter lead to the development of the tetrahedral microscope in 1999, which in turn triggered the development of light sheet-based fluorescence microscopy (LSFM) in 2001.

Some of my other contributions include the optical tweezers based photonic force microscope in 1993 and a novel and very successful approach to laser based cutting devices in 1999. I worked extensively on image processing, databases for volume data sets, theoretical aspects of image formation, optical levitation and optical tweezers and the biophysical properties of microtubules. Applications in the life sciences have guided many of my decisions over the years.

The results of my research were published in more than 220 papers and lead to about 20 patent applications. My inventions are used in several instruments. The most prominent is probably Carl Zeiss' LSM 510/710 series of confocal microscopes. A carefully patented development is the photonic force microscope (PFM), which has been commercialized by JPK (Berlin). The recently developed and patented implementations of LSFM (SPIM and DSLM) reduce the energy load on specimens during observation by 100-10,000 times compared to e.g. confocal fluorescence microscopes. More than sixty groups with more than 100 instruments world-wide have started to apply various LSFM designs in their research.

Since 1989 I have organized more than twelve EMBO sponsored courses on advanced live cell microscopy and participated in at least a further twenty. I have trained hundreds of biologists in the appropriate application of cutting edge imaging tools. More than sixty young scientists have worked in my laboratory, which resulted in about twenty-four diploma or master theses and more than ten Ph.D. theses. My international reputation is further evident from the more than 260 invited talks (more than 160 since 2000), which include numerous plenary lectures at international meetings, and a regular reviewing activity for peer-reviewed journals and national as well as international funding bodies.

As a group leader at EMBL I have been reviewed very successfully six times and left EMBL with a non-terminated rolling tenure contract. In 1999 I was awarded the Ernst Abbe Lecture by the Royal Microscopical Society and in 2009 I received the Heidelberg Molecular Life Sciences Price together with Jochen Wittbrodt. EMBO elected me as a fellow in 2009.

My current vision is to develop and apply instruments as well as specimen preparation techniques that allow me and other scientists to observe and manipulate biological specimens efficiently and with high precision or high resolution. Since the early 1990s it has been my long-term interest to provide a set of tools that foster research in the life sciences under physiologically relevant conditions. In particular, I have developed methods that reduce the energy load on specimens during microscopic observations and provide the means for relaxation-type experiments, which are crucial for all quantitative work. This focus has not only been picked by most of my former students, it is probably fair to say that it has made a substantial impact on the manner in which research in the life sciences is performed.

Research Interests and Focus:

My research interests cover biophysics, physical biology, bio-photonics, bio-mechanics, regenerative medicine, cell and developmental biology and optical physics. The effects of noise and fluctuations in physics and in the life sciences have played a major role in my career. My diploma thesis was concerned with dynamic light scattering. Therefore, I have always been very well acquainted with the basics in signal processing and its applications in the life sciences (FCS, optical tweezers, image processing, etc.). I was, able to apply my insights e.g. to derive the resolution of optical instruments from the Heisenberg uncertainty principle, to analyse microtubule dynamics, to understand thermal fluctuations in optical tweezers and optical levitation, which led us to the PFM, and to reveal aspects of yeast re-production. A major reason for our work on zebra fish embryos was actually to investigate variations among different individuals.

Three-dimensional light microscopy and lately mainly LSFM have become extremely important. For the last ten years I have concentrated my career on three-dimensional life science and physical biology. My move from EMBL to the Goethe University in Frankfurt allowed me to reconsider on which scientific topics I would like to work. A main topic will be three-dimensional cell biology. On one hand, my group develops methods that allow us to grow, maintain, observe and manipulate cell clusters such as cysts, spheroids, tissue sections and small animal model systems. On the other hand we use them to investigate autophagy, sensitivity to specific drugs, variability and angiogenesis. Some of the projects are performed entirely within my group others are part of our collaborations with other PIs (e.g. S. Dimmeler, S. Fulda, I. Dikic, A. Acker-Palmer, A. Frangakis).

Two further major elements are the development of image processing pipelines and the mathematical modelling of our results. Our current work on Arabidopsis is supported by the infrastructure (instrumentation, software, specimen chambers) developed during previous projects, by one Ph.D. student, master students and our close interactions with Dr. Alexis Maizel (Heidelberg) and Prof. Enrico Schleiff (Frankfurt). Their groups and their contacts have been essential and complement my own expertise very well.

Light Sheet-based Fluorescence Microscopy (LSFM, DSLM, SPIM):

Specimens scatter and absorb light, thus, the delivery of the probing light and the collection of the signal light (e.g. fluorescence) become inefficient. Not only fluorophores, but many endogenous biochemical compounds absorb light and suffer degradation of some sort (photo-toxicity), which can induce a malfunction of a specimen. In conventional and confocal fluorescence microscopy, whenever a single plane is observed, the entire specimen is illuminated (Verveer 2007). Recording stacks of images along the optical z-axis thus illuminates the entire specimen once for each plane. Hence, cells are illuminated 10-20 and fish embryos 100-300 times more often than they are observed (Keller 2008). This can be avoided by using light sheets, which are fed into the specimen from the side and overlap with the focal plane of a wide-field fluorescence microscope. In contrast to an epi-fluorescence arrangement, an azimuthal arrangement uses two independently operated lenses for illumination and detection (Stelzer 1994; Huisken 2004).

In general, optical sectioning and no photo-toxic damage or photo-bleaching outside a small volume close to the focal plane are intrinsic properties of light sheet-based fluorescence microscopy (LSFM). It takes advantage of modern camera technologies and can be operated with laser cutters (e.g. Colombelli 2009) as well as in fluorescence correlation spectroscopy (FCS, Wohland 2010). We have also successfully evaluated the application of structured illumination in a single plane illumination microscope (SPIM) (Breuninger et al., 2007) and investigated their performance (Engelbrecht & Stelzer, 2006) both theoretically and practically. We also designed and implemented a wide-field frequency domain fluorescence lifetime imaging (FLIM/FRET) setup. More recently, we implemented incoherent structured illumination in our DSLM (Keller 2010). The intensity modulated light sheets can be generated with dynamic frequencies and can be adapted to the image formation process at various depths in objects of different age.

The development of LSFM draws on many previous developments. In particular, confocal theta fluorescence microscopy, which was originally developed together with Steffen Lindek, played a very important role. About a dozen papers on theta microscopy describe its properties and that of LSFM (single & two-photon, annular/Bessel beams, (a)symmetric arrangements, ...) theoretically as well as practically.

Papers (selection):
Maizel A, von Wangenheim D, Federici F, Haseloff J, Stelzer EHK (2011) High-resolution live imaging of plant growth in near physiological bright conditions using light sheet fluorescence microscopy, Plant J, 68(2):377-385.
Keller PJ, Schmidt AD, Santella A, Khairy K, Bao Z, Wittbrodt J, Stelzer EHK (2010) Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy, Nature Methods, 7(8):637-642.
Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008) Reconstruction of zebrafish early embryonic development by Scanned Light Sheet Microscopy. Science, 322(5904):1065-1069.
Keller PJ, Pampaloni F, Stelzer EHK (2007) Three-dimensional preparation and imaging reveal intrinsic microtubule properties, Nat Methods, 4(10):843-846.
Pampaloni F, Reynaud EG, Stelzer EHK (2007) The third dimension bridges the gap between cell culture and live tissue, Nat Rev MCB, 8(10):839-845.
Verveer PJ, Swoger J, Pampaloni F, Greger K, Marcello M, Stelzer EHK (2007) High-resolution three-dimensional imaging of large specimens with light-sheet based microscopy, Nat Methods, 4:311-313.
Huisken J, Swoger J, Del Bene F, Wittbrodt J, Stelzer EHK (2004) Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science, 305:1007-1009.
Colombelli J, Reynaud EG, Rietdorf J, Pepperkok R, Stelzer EHK (2005) In vivo selective cytoskeleton dynamics quantification induced by pulsed ultraviolet laser nanosurgery. Traffic, 6(12): 1093-1102.
Rohrbach A, Stelzer EHK (2002) Trapping forces, force constants and potential depths for dielectric spheres in the presence of spherical aberrations. Appl Opt, 41(13):2494-2507.
Stelzer EHK (2002) Beyond the diffraction limit? Nature, 417:806-807.
Patents (selection)
Stelzer EHK, Enders S, Huisken J, Lindek S, Swoger J: Mikroskop, Deutsches Patent- und Markenamt, DE 102 57 423, internationalized as PCT/EP 03/05991 (EP 1576404 granted 2011) and US Patent & Trademark Office, US 7,554,725 (granted 2009).
Florin EL, Hörber HJK, Stelzer EHK: Verfahren zur dreidimensionalen Objektabtatstung, Deutsches Patent- und Markenamt, DE 199 39 574 (granted 2010), internationalized as US Patent & Trademark Office, US 6,833,923 (granted 2004).
Stelzer EHK, Lindek S: Konfokales Mikroskop, Deutsches Patent- und Markenamt, DE 196 32 040 (granted 1998), internationalized as PCT/EP 97/03953 (EP 0 859 968 granted 2004) and US Patent & Trademark Office, US 6,064,518 (granted 2000).
Stelzer EHK, Lindek S: Konfokales Mikroskop mit einem Doppelobjektiv-System, Deutsches Patent- und Markenamt, DE 196 29 725 (granted 1997), internationalized as PCT/EP 97/03954 (EP 0 866 993 granted 2004) and US Patent & Trademark Office, US 5,969,854 (granted 1999).
Stelzer EHK, Huisken J: Verfahren und Instrument zur Positionierung und Orientierung kleiner Teilchen in einem Laserstrahl, Deutsches Patent- und Markenamt, DE 100 28 418 (granted 2002).
Stelzer EHK, Lindek S, Stefany T, Swoger J: Kompaktes Einzelobjektiv Theta-Mikroskop, Deutsches Patent- und Markenamt, DE 198 34 279 (granted 2001), internationalized as PCT/EP 99/05372 (EP 1 019 769 granted 2004).
Links & Websites
Bettina Spöth

Administrative Assistant
Phone: +49 (69) 798-42545


Sigrun Becker

Phone: +49 (69) 798-42554

Louise Breideband

PhD Student
Phone: +49 (69) 798-42588

Artimiy Golden

PhD Student
Phone: +49 (69) 798-42542

Mariia Golden

PhD Student
Phone: +49 (69) 798-42552

Levin Hafa

PhD Student

Lotta Hof

PhD Student
Phone: +49 (69) 798-42548

Michael Koch

PhD Student
Phone: +49 (69) 798-42550

Till Moreth

PhD Student
Phone: +49 (0)69 798-42548

Dr. Francesco Pampaloni

Staff Scientist
Phone: +49 (69) 798-42544



Curriculum Vitae  
Since 2010 Goethe University of Frankfurt, Buchmann Institute of Molecular Life Sciences (BMLS) Staff scientist.
2008 European Molecular Biology Laboratory (EMBL Heidelberg), Cell Biology and Biophysics Unit. Staff scientist.
2003-2008 European Molecular Biology Laboratory (EMBL Heidelberg), Cell Biology and Biophysics Unit, Light Microscopy Group (PIs Ernst H. K. Stelzer and Ernst-Ludwig Florin). Postdoctoral fellow.
2002-2003 Forschungszentrum Jülich, IBI-1, postdoctoral fellow in the Jörg Enderlein's Single Molecule Spectroscopy group.
2002 PhD (Dr. rer nat.) with excellence (summa cum laude). Thesis: "Force sensing and surface analysis with optically trapped microprobes"
1998-2002 Graduate student - University of Regensburg (Germany), Dept. of Analytical Chemistry and Forschungszentrum Jülich, IBI-1. Advisor Prof. Joerg Enderlein.
1997 Graduation in Physical Chemistry with excellence (110/110 e lode), University of Florence, Dept. of Physical Chemistry. Advisor Prof. Piero Baglioni.
1996 Erasmus exchange undergraduate student - Karl-August University of Heidelberg (Germany), Institute of Physical Chemistry, Dept. of Biophysical Chemistry (Director Prof. Juergen Wolfrum).
1991-1997 BSc and MSc student in Chemistry, University of Florence, Italy

Research focus I am interested in how the cellular microenvironment and architecture regulate cell physiology and tissue development. I am pursuing a cross-disciplinary approach comprising Light Sheet-based Fluorescence Microscopy and 3D cell cultures in order to elucidate these processes. 3D cell cultures aim to reproduce the function of a real tissue, both healthy and pathological. This is achieved by stimulating the cells with the mechanical and biochemical cues that are characteristic of the original tissue. The rationale is not three-dimensionality per se, but rather the generation of physiologically meaningful tissue models through the manipulation of the cellular microenvironment (Figure 1). In vitro tissue models are of great interest for both biotechnology and clinical research. The bio-pharmaceutical industry is seeking reliable cell-based platforms for drug discovery and toxicity screening. Tumor biologists and oncologists need realistic models for a patient-oriented diagnosis and therapy. Stem-cell specialists require in vitro niches for the expansion and differentiation of stem cells.

Book chapters and other publications

Polyethylenimine bioconjugates for Imaging and DNA delivery in vivo. Masotti A; Pampaloni, F; Methods in Molceular Biology: Bioconjugation Protocols, 2nd Ed, Humana Press

Light-sheet-based fluorescence microscopy (LSFM, SPIM) for imaging in three-dimensional developmental and multi-cellular biology. Swoger, J; Pampaloni, F; Stelzer, EHK; Imaging in Developmental Biology, vol. 1, chapter 48, Cold Spring Harbor Laboratory Press

Biomimetic and bioinspired self-assembled peptide nanostructures. Pampaloni, F; Masotti, A; Nanomaterials for the Life Sciences, vol. 7 (Bio-mimetic and Bio-inspired Nanomaterials for Life Sciences), C. Kumar editor, Wiley-VHC, chapter 5, pages 151-210, 2010

Three-dimensional cell cultures in toxicology. Pampaloni, F; Stelzer, EHK; Biotechnology and Genetic Engineering Reviews, chapter 26, pages 129-150, 2009

Live cell imaging in physiologically relevant environments:3D-squared. Pampaloni, F; Keller, PJ; Marcello, M; Reynaud, EG; Schmidt, A; Centanin, L; Wittbrodt, J; Stelzer, EHK; Advance Live Cell Imaging. Special edition of G.I.T. Imaging & Microscopy, GIT Verlag, 2008


New Operator Approach for Deriving Elegant and Standard Hermite-Gaussian and Laguerre-Gaussian Laser Modes. Enderlein, J; Pampaloni, F; JOSA A, chapter 21, pages 1553-1558, 2004

Time-resolved confocal scanning device for ultrasensitive fluorescence detection. Böhmer, M; Pampaloni, F; Wahl, M; Rahn, HJ; Erdmann, R; Enderlein, J; Rev. Sci. Instrum., chapter 72, pages 4145-4152, 2001

Optical tweezers as a tool to study molecular interactions at surfaces. Zahn, M; Kurzbuch, D; Pampaloni, F; Seeger, S; Proc. SPIE 3604 (optical diagnostics of living cells), pages 90-99, 1999



High-resolution deep imaging of live cellular spheroids with light-sheet-based fluorescence microscopy. Pampaloni, F; Ansari, N; Stelzer, EH; Cell Tissue Res, 2013 Apr PubMed

Quantitative 3D cell-based assay performed with cellular spheroids and fluorescence microscopy. Ansari, N; Müller, S; Stelzer, EH; Pampaloni, F; Methods Cell Biol, 2013 PubMed

Fluorescence-based sensors to monitor localization and functions of linear and K63-linked ubiquitin chains in cells. van Wijk, SJ; Fiskin, E; Putyrski, M; Pampaloni, F; Hou, J; Wild, P; Kensche, T; Grecco, HE; Bastiaens, P; Dikic, I; Mol Cell, 2012 Sep PubMed

Polyethylenimine bioconjugates for imaging and DNA delivery in vivo. Masotti, A; Pampaloni, F; Methods Mol Biol, 2011 PubMed

Madin-Darby canine kidney cells are increased in aerobic glycolysis when cultured on flat and stiff collagen-coated surfaces rather than in physiological 3-D cultures. Pampaloni, F; Stelzer, EH; Leicht, S; Marcello, M; Proteomics, 2010 Oct PubMed

Extracting the mechanical properties of microtubules from thermal fluctuation measurements on an attached tracer particle. Taute, KM; Pampaloni, F; Florin, EL; Methods Cell Biol, 2010 PubMed

Three-dimensional cell cultures in toxicology. Pampaloni, F; Stelzer, E; Biotechnol Genet Eng Rev, 2010 PubMed

Three-dimensional tissue models for drug discovery and toxicology. Pampaloni, F; Stelzer, EH; Masotti, A; Recent Pat Biotechnol, 2009 PubMed

Three-dimensional microtubule behavior in Xenopus egg extracts reveals four dynamic states and state-dependent elastic properties. Keller, PJ; Pampaloni, F; Lattanzi, G; Stelzer, EH; Biophys J, 2008 Aug PubMed

Microtubule architecture: inspiration for novel carbon nanotube-based biomimetic materials. Pampaloni, F; Florin, EL; Trends Biotechnol, 2008 Jun PubMed

Microtubule dynamics depart from the wormlike chain model. Taute, KM; Pampaloni, F; Frey, E; Florin, EL; Phys Rev Lett, 2008 Jan PubMed

Three-dimensional preparation and imaging reveal intrinsic microtubule properties. Keller, PJ; Pampaloni, F; Stelzer, EH; Nat Methods, 2007 Oct PubMed

The third dimension bridges the gap between cell culture and live tissue. Pampaloni, F; Reynaud, EG; Stelzer, EH; Nat Rev Mol Cell Biol, 2007 Oct PubMed

High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy. Verveer, PJ; Swoger, J; Pampaloni, F; Greger, K; Marcello, M; Stelzer, EH; Nat Methods, 2007 Apr PubMed

Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length. Pampaloni, F; Lattanzi, G; Jonás, A; Surrey, T; Frey, E; Florin, EL; Proc Natl Acad Sci U S A, 2006 Jul PubMed

Life sciences require the third dimension. Keller, PJ; Pampaloni, F; Stelzer, EH; Curr Opin Cell Biol, 2006 Feb PubMed

Unified operator approach for deriving Hermite-Gaussian and Laguerre-Gaussian laser modes. Enderlein, J; Pampaloni, F; J Opt Soc Am A Opt Image Sci Vis, 2004 Aug PubMed

The signal flow and motor response controling chemotaxis of sea urchin sperm. Kaupp, UB; Solzin, J; Hildebrand, E; Brown, JE; Helbig, A; Hagen, V; Beyermann, M; Pampaloni, F; Weyand, I; Nat Cell Biol, 2003 Feb PubMed

Sven Plath

Technical Assistant
Phone: +49 (0)69 798-42553

Fabian Reinisch

PhD Student
Phone: +49 (0)69 798-42540

Ryan Sarkar

PhD Student
Phone: +49 (69) 798-42588

Heinz Schewe

Chief technician of the CMP-Microscopy Center
Phone: +49 (0)69-798-42557

Curriculum vitae  
since 2012 Staff member of the Frankfurt Center for Advanced Light Microscopy (FCAM), head Prof. Dr. Ernst H.K. Stelzer, and chief technician of the CMP-Mikroskospiezentrum.
1998-2012 Laboratory assistant at the faculty of Biology of the Goethe University Frankfurt am Main.
Advisory activities and technical care of confocal laser scanning microscopes and till 2006 of a transmission electron microscope.
1986-1996 Scientific assistant at the Medical School Hannover in the Dept. of Cell Biology and Electron Microscopy, head Prof. Dr. Enrico Reale. Technical care of several transmission and scanning electron microscopes, and in cooperation with Prof. Dr. Siegfried Boseck, University of Bremen, image structure analyses of electron micrographs by means of light optical diffraction.
1985-1986 Division manager for New Technologies in industrial art at the chamber of handicrafts Münster.
1984 Attendance of a computer tutorial for university graduates at the Nixdorf-Computer GmbH in Münster.
1982 Diploma, Physics Dept. of Electron Microscopy, Diploma thesis: "Konvergente Elektronenbeugung – HOLZ- und FOLZ-Beugungsdiagramme". Advisor Prof. Dr. Ludwig Reimer.
1975-1982 Student in Physics, Westfälische-Wilhelms-University Münster, Germany

Dr. Frederic Strobl

Phone: +49 (69) 798-42551

since 2012 PhD Student in Biology
Physical Biology Group, BMLS, CEF (Prof. Dr. Ernst Stelzer)
Goethe University Frankfurt am Main
2011-2012 Diploma in Cell and Development Biology
Thesis title "The TWEAK/FN14 Axis in Fibrotic Disease"
Heart Development and Regeneration Group (Dr. Felix Engel)
Goethe University Frankfurt am Main and
Max Planck Institute for Heart and Lung Research (Bad Nauheim)
2006–2012 Diploma Student in Biology
Goethe University Frankfurt am Main