Ernst H.K. Stelzer

+49 (69) 798 42547
+49 (170) 6357 168
+49 (69) 798 42546
Room number: 
Curriculum vitae: 

Buchmann Institute for Molecular Life Sciences (BMLS)
Fachbereich Lebenswissenschaften (FB15, IZN)

since 2011Professor in the Life Sciences (FB15, IZN), Goethe-Universität Frankfurt am Main
since 2009Principal Investigator, Cluster of Excellence “Macromolecular Complexes” 
Goethe-Universität Frankfurt am Main
1989–2011Scientific Group Leader, EMBL, Heidelberg
- Cell Biology and Biophysics Unit
- Cell Biology Programme
- Physical Instrumentation Programme
1987–1989Project Leader, EMBL, Heidelberg, Physical Instrumentation Programme
1987Ph.D. (Dr. rer. nat.), Physics, Ruprecht-Karls-Universität Heidelberg
1986–1987Postdoc, European Molecular Biology Laboratory (EMBL), Heidelberg
Physical Instrumentation Programme
1983–1986Ph.D. student, Physics, Ruprecht-Karls-Universität Heidelberg
(Ruperto Carola, Heidelberg University, Germany)
performed in Physical Instrumentation Programme, EMBL, Heidelberg, Germany

Diploma, Physics, Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
(Max-Planck-Institute for Biophysics, Frankfurt am Main, Germany)

1977–1982Student, Physics, Johann-Wolfgang-Goethe-Universität Frankfurt am Main
(Goethe University Frankfurt am Main, Germany)

Scientific Leadership Profile:

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.


Please check other pages on this site for complementary information and approaches to the projects.

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.



All references are found via:

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).