Ernst H.K. Stelzer

+49 (69) 798 42547
+49 (160) 8988 485
+49 (69) 798 42546
Room number: 
Curriculum vitae: 

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

since 2019

Vice-Dean for Research (Forschungsdekan) Fachbereich 15


Vice-Dean for Education (Studiendekan) Fachbereich 15

since 2011Professor in the Life Sciences (FB15, IZN), Goethe-Universität Frankfurt am Main
2009–2019Principal Investigator, Clusters of Excellence Macromolecular Complexes (I & II)
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 managed to work in interdisciplinary environments for more than thirty years.  I have been able to bridge the gaps between physics, optical physics, instrumentation development, molecular cell biology, developmental biology and the mathematical interpretations of experiments in the life sciences.

During my Ph.D. thesis (1983-1987), I worked on confocal transmission, reflection and fluorescence microscopy.  I developed confocal 4Pi fluorescence microscopy during 1990-1993 and introduced orthogonal and multi-lens detection schemes commencing 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.  The applicability in the life sciences guided many of my decisions.

The results of my research were published in more than 270 papers and lead to more than 25 patent applications.  My inventions are used in several instruments.  The most prominent is probably Carl Zeiss’ LSM 5xx/7xx/8xx series of confocal microscopes.  Another 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 their observation by 100-10,000 times compared to e.g. confocal fluorescence microscopes.  Hundreds of groups with more than 1,000 instruments worldwide 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 thirty.  I have trained hundreds of biologists in the appropriate application of cutting edge imaging tools.  More than one hundred young scientists have worked in my laboratory, which resulted in about fourty diploma or master theses and more than twenty Ph.D. theses.  My excellent international reputation is further evident from the more than 350 invited talks (more than 250 since 2000), which include numerous plenary and keynote lectures at international meetings, and a regular reviewing activity for peer-reviewed journals and national as well as international funding bodies. 

I should add that as a group leader at EMBL I have been reviewed very successfully six times and that I left EMBL with a non-terminated rolling tenure contract.  In 1999, I was awarded the Ernst Abbe Lecture by the Royal Microscopical Society.  In 2009, I received the Heidelberg Molecular Life Sciences Price together with Jochen Wittbrodt.  EMBO elected me as a fellow in 2009.  In 2014, I received the Carl Zeiss lecture of the Deutsche Gesellschaft für Zellbiologie, became an Honorary Fellow of the Royal Microscopical Society (Oxford, UK) and was the protagonist, when LSFM became Method of the Year 2014

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 or close-to-natural 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 up 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 nowadays. 

Research Interests and Focus

My research interests cover physics, biophysics, physical biology, biophotonics, biomechanics, 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. by deriving the resolution of optical instruments from the Heisenberg uncertainty principle, by analysing microtubule dynamics, by understanding thermal fluctuations in optical tweezers and optical levitation, which led us to the PFM, and by revealing 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 LSFM have become extremely important.  Since 2001, I have concentrated my career on three-dimensional life sciences and physical biology.

Major contributions to early careers of excellent researchers 

More than one hundred young scientists have worked in my laboratory.  Hence, former postdocs as well as students are now junior (H. Kress, E. Reynaud) or full professors (A. Rohrbach, E.L. Florin, Th. Wohland, P. Hänninen) or work as scientists in Max-Planck-Institutes (2014 Chemistry Nobel Prize Laureate S.W. Hell worked as a postdoc in my laboratory from 1990-1993, S. Grill, J. Huisken), at HHMI Janelia Farm (P.J. Keller, K. Khairy), in Paris (P. Girard) or in Barcelona (J. Swoger, J. Colombelli).


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

Light sheet-based Fluorescence Microscopy 

In Light Sheet-based Fluorescence Microscopy (LSFM), optical sectioning in the excitation process minimizes fluorophore bleaching and phototoxic effects.  This allows biological specimens to survive long-term three-dimensional imaging at high spatiotemporal resolution and along multiple directions.  The two canonic implementations, i.e. Selective/Single Plane Illumination Microscopy (SPIM) and Digital Scanned Laser Light Sheet Microscopy (DSLM), have become indispensable tools in developmental biology, three-dimensional cell biology and plant biology. 

LSFM was the result of developing confocal, 4Pi and Theta fluorescence microscopies for more than twenty years.  It is an excellent example for the achievements of those with an interdisciplinary spirit.  My patents in 1993 and 2003 and my seminal papers in 2004 and 2008 document the intensity and the determination that are necessary.  My further work and the refinements of my technology enable the imaging of live biological samples in close-to-natural conditions for several days, leading to breakthroughs in, among other fields, histopathology and drug development.  The initial work was done at EMBL.  However, many of my former students and postdocs have independently pushed the technology to new levels. 

Short description and impact  

Light sheets 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 microscope, the azimuthally arranged light sheet-based fluorescence microscope (LSFM) uses at least two independently operated lenses for illumination and detection.  A single/selective plane illumination microscope (SPIM) employs a cylindrical lens to generate a light sheet.  A collimated laser beam is focused into the plane of the detection lens along one direction while the other direction remains collimated.  A digital scanned laser light sheet-based fluorescence microscope (DSLM) generates light sheets by moving a focused beam that overlaps with the focal plane of the detection lens.  It relies entirely on cylindrically symmetric optics.  In general, optical sectioning and no phototoxic damage or photo bleaching outside a small volume close to the focal plane are intrinsic properties of LSFM.  It takes advantage of modern camera technologies and can be operated with laser cutters as well as in conjunction with fluorescence correlation spectroscopy (FCS).  We have successfully evaluated the application of structured illumination.  We also designed and implemented a SPIM-based frequency domain fluorescence lifetime imaging setup and developed new scanning schemes based on novel optical arrangements that allow us to take full advantage of very high-resolution light microscopy.  During the past decade, we applied LSFM, e.g. in the investigation of three-dimensional microtubule dynamics, the development of Drosophila melanogaster and Danio rerio embryos as well as many different aspects of three-dimensional cell biology.  During the past four years, we placed a particular emphasis on plant biology, three-dimensional cell biology and emerging model organisms such as Tribolium castaneum. LSFM have been commercialized by several companies. They have become the state-of-the-art instruments in developmental biology, three-dimensional cell biology as well as in plant biology and have generated more than 500 publications and more than 7,000 citations. 

Basic concept 

LSFM has revolutionized fluorescence microscopy.  It is based on an extremely simple and yet ingenious optical arrangement that provides true optical sectioning over an extended field of view.  LSFM refers to a technology that observes a specimen with at least one microscope objective lens whose focal plane is illuminated azimuthally by at least one sheet of light.  In LSFM, only a thin volume wrapped around the focal plane of the detection microscope objective lens is illuminated.  Therefore, endogenous organic molecules or fluorophores in the volumes in front and behind the light sheet do not receive any light and are not subject to photo-damage.  These fluorophores cannot contribute to image blurring by out-of-focus light.  In physical terms, LSFM provides true optical sectioning and an axial resolution.  Three-dimensional image stacks are generated by moving the light sheet and the specimen relative to each other.  Hundreds of planes in different locations along the optical axis of the detection lens are illuminated.  Using cameras, tens to hundreds of images, which consist of millions of picture elements, are recorded every second.  Since the optical sectioning capability of LSFM is provided in its illumination process, it exposes a specimen to up to five orders of magnitude less energy than confocal fluorescence microscopy. 

Light sheets have been known for more than 100 years, but so have light spots. Until lasers became available in 1960 (Maiman TH (1960) Stimulated Optical Radiation in Ruby. Nature, 187(4736):493–494.), neither light spots nor light sheets were diffraction limited. Hence, optically sectioning instruments (I. J. Cox, “Scanning optical fluorescence microscopy,” J. Microsc., vol. 133, no. 2, pp. 149–154, 1984.) could not be built. A confocal fluorescence microscope, which illuminates a specimen sequentially with a diffraction-limited spot of light, can only be operated with a laser. Laser light sheet–based devices, including macroscopes (A. H. Voie, D. H. Burns, and F. A. Spelman, “Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens,” J. Microsc., vol. 170, no. 3, pp. 229–236, 1993 & E. Fuchs, J. Jaffe, R. Long, and F. Azam, “Thin laser light sheet microscope for microbial oceanography,” Opt. Express, vol. 10, no. 2, pp. 145–154, 2002), had been built several times, but their capability to perform at a microscopic level was not known until, starting around 2002, my group (LMG, Light Microscopy Group), then at the European Molecular Biology Laboratory (EMBL) in Heidelberg, described the SPIM. The group applied Light Sheet Microscopes to observe live biological specimens (Huisken, Swoger, Del Bene, Wittbrodt, & Stelzer, 2004), (Keller, Schmidt, Wittbrodt, & Stelzer, 2008), determined its optical properties (Engelbrecht & Stelzer, 2006), evaluated its applicability for multiple-views imaging (Swoger, Huisken, & Stelzer, 2003; Verveer et al., 2007)and assessed its applicability at the molecular level with FLIM/FRET- (Greger, Neetz, Reynaud, & Stelzer, 2011)as well as FCS-SPIM (Wohland, Shi, Sankaran, & Stelzer, 2010). The LMG had systematically evaluated diffraction-limited microscopes with two to four lenses, both in theory and in practice, since the early 1990s, selected papers (Hell & Stelzer, 1992; Huisken, Swoger, & Stelzer, 2007; Lindek & Stelzer, 1996; E.H.K. Stelzer & Lindek, 1994). The impact of LSFM was recognized in 2015, when Nature Methods announced “Light Sheet-based Fluorescence Microscopy” Method of the Year 2014 (Ernst H K Stelzer, 2015).

The past eight years

My move from EMBL to the Goethe University in Frankfurt am Main allowed me to re-consider, to which scientific topics I could contribute.  A major goal of the Physical Biology Group is to pursue experiments in the life sciences under close-to-natural conditions.  Hence, its members favour primary cell lines and try to avoid experiments with cultured cell lines, they favour three-dimensional cell cultures over two-dimensional cell monolayers that are cultivated on hard and flat surfaces and they try to maintain the three-dimensional context of plants, cell clusters, tissues sections and small animal embryos.  In consequence, many specimens are relatively large, optically dense and require advanced methods in terms of preparation, maintenance, visualization, data handling and data analysis.

We apply our LSFM to investigate the development of Arabidopsis thaliana’s root system (Maizel, von Wangenheim, Federici, Haseloff, & Stelzer, 2011).  Close-to-natural growth conditions (e.g. upright position, roots in liquid and leaves in air, maintenance of a 16 hrs / 8 hrs diurnal cycle) are essential for observations lasting multiple days.  We have successfully established a complete plant imaging pipeline.  The careful sample preparation and fluorescence light microscopy under close-to-natural conditions allow us to image large volume elements in plants with subcellular resolution.  Our image processing applications identify cells in three dimensions and as a function of time.  A careful analysis allows us to track nuclei movements over time, to determine when cell divisions occur, to measure the orientation of daughter cells in three dimensions and to generate the complete lineage of all cells (Berson et al., 2014; Lucas et al., 2013; Rosquete et al., 2013; Vermeer et al., 2014; von Wangenheim, Daum, Lohmann, Stelzer, & Maizel, 2014).

Most group members establish and apply tissue and spheroid technologies for both fundamental and applied as well as translational, research.  We develop three-dimensional cultures of cell spheroids for drug and toxicity screening purposes.  We collaborate with industrial partners as well as with academic partners and the University’s Clinics.  Spheroids serve as models for the development of healthy tissues and their maintenance in the living organism but also as models for tumour growth (Francesco Pampaloni, Reynaud, & Stelzer, 2007).  We currently evaluate the therapeutic benefits as well as the toxicity of drug candidates in spheroids by means of conventional fluorescence microscopy as well as LSFM and many different biochemical and molecular biology-based assays (Ansari, Müller, Stelzer, & Pampaloni, 2013; F Pampaloni & Stelzer, 2010; Wenzel et al., 2014).

We established the red flour beetle Tribolium castaneum as an EvoDevo model organism in our group and developed a non-invasive long-time fluorescence live imaging protocol for Tribolium embryos for our LSFMs.  By using a new mounting technique, we became able to observe Tribolium embryogenesis for up to 50 hours along multiple directions, documenting all major embryogenic events such as gastrulation, germ band elongation, germ band retraction and dorsal closure continuously in the same specimen.  The embryo survives the imaging process, develops into an adult and produces fertile progeny.  Our long-term observations allowed us to find correlations between morphogenic processes that happen more than 24 hours apart, for example the serosa scar, a transiently formed structure that links serosa window closure during gastrulation and serosa opening during dorsal closure (F. Strobl, Schmitz, & Stelzer, 2015; F. Strobl & Stelzer, 2016; Frederic Strobl & Stelzer, 2014).

Two further major projects are the development of image processing pipelines and the mathematical modelling of our results.


All references are found via:

Twelve influential publications

Chang BJ, Perez Meza VD, Stelzer EHK(2017) csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm, PNAS 114(19):4869-4874.

von Wangenheim D, Fangerau J, Schmitz A, Smith RS, Leitte H, Stelzer EHK, Maizel A (2016) Rules and Self-Organizing Properties of Post-embryonic Plant Organ Cell Division Patterns, Current Biology 26:1–11.

Strobl F, Schmitz A, Stelzer EHK (2015) Live imaging of Tribolium castaneum embryonic development using light-sheet–based fluorescence microscopy, Nature Protocols, 10:1486.1507.

Stelzer EHK (2015) Light-sheet fluorescence microscopy for quantitative biology, Nature Methods, 12(1):23–27.

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.

Pampaloni F, Reynaud EG, Stelzer EHK (2007) The third dimension bridges the gap between cell culture and live tissue, Nature Reviews Molecular Cell Biology 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, Nature Methods 4:311-313.

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.

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.

Stelzer EHK, Lindek S (1994) Fundamental reduction of the observation volume in far-field light microscopy by detection orthogonal to the illumination axis: confocal theta microscopy, Optics Communications 111:536-547.

Hell S, Stelzer EHK (1992) Properties of a 4Pi confocal fluorescence microscope, Journal of the Optical Society of America A A9(12):2159-2166.

Wijnaendts-van-Resandt RW, Marsmann HJB, Kaplan R, Davoust J, Stelzer EHK, Stricker R (1985) Optical fluorescence microscopy in three dimensions: microtomoscopy, Journal of Microscopy 138:29-34. 


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).