Francesco Pampaloni

+49 (69) 798 42544
+49 (69) 798 42546
Room number: 
Curriculum vitae: 
Since 2010Goethe University of Frankfurt, Buchmann Institute of Molecular Life Sciences (BMLS) Staff scientist.
2008European Molecular Biology Laboratory (EMBL Heidelberg), Cell Biology and Biophysics Unit. Staff scientist.
2003‑2008European Molecular Biology Laboratory (EMBL Heidelberg), Cell Biology and Biophysics Unit, Light Microscopy Group (PI Dr. Ernst H. K. Stelzer). Postdoctoral fellow.
2002-2003Forschungszentrum Jülich, IBI-1, postdoctoral fellow in the Jörg Enderlein's Single Molecule Spectroscopy group.
2002PhD (Dr. rer nat.) with excellence (summa cum laude). Thesis: “Force sensing and surface analysis with optically trapped microprobes”
1998‑2002Graduate student - University of Regensburg (Germany), Dept. of Analytical Chemistry and Forschungszentrum Jülich, IBI-1. Advisor Prof. Joerg Enderlein.
1997Graduation in Physical Chemistry with excellence (110/110 e lode), University of Florence, Dept. of Physical Chemistry. Advisor Prof. Piero Baglioni.
1996Erasmus exchange undergraduate student - Karl-August University of Heidelberg (Germany), Institute of Physical Chemistry, Dept. of Biophysical Chemistry (Director Prof. Juergen Wolfrum).
1991‑1997BSc and MSc student in Chemistry, University of Florence, Italy

Biographical sketch - I graduated with a degree in physical chemistry from the University of Florence, Italy, and in 2002 I obtained my Ph.D. from the Analytical Chemistry Department of University of Regensburg, Germany, with a thesis on optical trapping. Following a postdoctoral position at the Research Center Juelich, Germany, in 2003 I joined the European Molecular Biology Laboratory (EMBL) in Heidelberg as a postdoc in the group of Ernst Stelzer, one of the top advanced microscopy groups worldwide. In 2009 I was appointed staff scientist at EMBL. Since 2010 I am staff scientist with permanent position at the Buchmann Institut for Molecular Life Sciences (BMLS) of the Goethe University Frankfurt.


Research focus and future perspectives - 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.

Figure 1 - The organizing factors leading to a functional organoid.

Multicellular spheroids (aka microtissues, Figure 2) have several advantages over other types of 3D cultures.  In cellular spheroids cells spontaneously aggregate and form tissue-like cell-cell contacts.  No exogenous scaffold or extra-cellular matrix are needed [1].  Cellular spheroids are well suitable for drug screenings [2].  A large-scale production of spheroids with standardized properties is possible with commercially available multi-well plates (,  However, tumor cell lines or immortalized cell lines are usually employed to form cellular spheroids.  This reduces the physiological relevance of spheroid-based assays.  Primary cells are a better alternative to cell lines.  Primary cells are isolated from healthy or pathological tissue biopsies.  Spheroids formed with primary hepatocytes develop bile canaliculi and show a liver-like drug metabolism.  Liver spheroids are employed for toxicity screening (  Spheroids formed from primary tumor cells isolated from patients are employed in the clinics to personalize chemotherapy (  However, the drawbacks of primary cells are the time-consuming isolation procedure, high cost, limited availability, and short-timed viability.

Figure 2 - A breast cancer cell spheroid imaged with Light sheet-based Fluorescence Microscopy (LSFM). With LSFM it is possible to image large three-dimensional cultures in 3D at high resolution (data and graphic art by Christian Mattheyer, Francesco Pampaloni, Daniel von Wangenheim and Ernst H.K. Stelzer. From

A cell source alternative to both immortalized cell lines and primary cells is required to the large-scale production of standardized tissue-specific spheroids.  Induced pluripotent stem cells (iPSC) could represent an unlimited source of tissue-specific, disease-specific, and patient-specific cells.  Somatic cells are reprogrammed to iPSC by the transfection of master transcription factors, such as Sox2 and Oct4.  Cerebral tissue, retina, ear sensory epithelium, gut epithelium, and liver organoids have been generated with iPSC-spheroids in the last three years [3-8].  These high-impact works show that 3D cell cultures are essential to differentiate iPSC to a tissue.  In future, assays will be conducted on differentiated iPSC spheroids, which specifically reproduce the target organ, disease, or even individual genotypic traits [9].  Based on that, we anticipate that iPSC-based spheroids will revolutionize the field of cell-based drug screening.

1.    Pampaloni, F., E.H. Stelzer, and A. Masotti, Three-dimensional tissue models for drug discovery and toxicology. Recent Pat Biotechnol, 2009. 3(2): p. 103-17.
2.    Friedrich, J., et al., Spheroid-based drug screen: considerations and practical approach. Nat Protoc, 2009. 4(3): p. 309-24.
3.    Lancaster, M.A., et al., Cerebral organoids model human brain development and microcephaly. Nature, 2013. 501(7467): p. 373-9.
4.    Sato, T. and H. Clevers, Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications. Science, 2013. 340(6137): p. 1190-4.
5.    Koehler, K.R., et al., Generation of inner ear sensory epithelia from pluripotent stem cells in 3D culture. Nature, 2013.
6.    Eiraku, M., et al., Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature, 2011. 472(7341): p. 51-6.
7.    Gonzalez-Cordero, A., et al., Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina. Nature biotechnology, 2013.
8.    Takebe, T., et al., Vascularized and functional human liver from an iPSC-derived organ bud transplant. Nature, 2013. 499(7459): p. 481-4.
9.    Sasai, Y., Next-generation regenerative medicine: organogenesis from stem cells in 3D culture. Cell Stem Cell, 2013. 12(5): p. 520-30.


Imaging MDCK Cysts with a Single (Selective) Plane Illumination Microscope. Swoger, J; Pampaloni, F; Stelzer, EH; Cold Spring Harb Protoc, 2014 PubMed

Imaging cellular spheroids with a single (selective) plane illumination microscope. Swoger, J; Pampaloni, F; Stelzer, EH; Cold Spring Harb Protoc, 2014 PubMed

Light-sheet-based fluorescence microscopy for three-dimensional imaging of biological samples. Swoger, J; Pampaloni, F; Stelzer, EH; Cold Spring Harb Protoc, 2014 PubMed

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME. Godoy, P; Hewitt, NJ; Albrecht, U; Andersen, ME; Ansari, N; Bhattacharya, S; Bode, JG; Bolleyn, J; Borner, C; Böttger, J; Braeuning, A; Budinsky, RA; Burkhardt, B; Cameron, NR; Camussi, G; Cho, CS; Choi, YJ; Craig Rowlands, J; Dahmen, U; Damm, G; Dirsch, O; Donato, MT; Dong, J; Dooley, S; Drasdo, D; Eakins, R; Ferreira, KS; Fonsato, V; Fraczek, J; Gebhardt, R; Gibson, A; Glanemann, M; Goldring, CE; Gómez-Lechón, MJ; Groothuis, GM; Gustavsson, L; Guyot, C; Hallifax, D; Hammad, S; Hayward, A; Häussinger, D; Hellerbrand, C; Hewitt, P; Hoehme, S; Holzhütter, HG; Houston, JB; Hrach, J; Ito, K; Jaeschke, H; Keitel, V; Kelm, JM; Kevin Park, B; Kordes, C; Kullak-Ublick, GA; LeCluyse, EL; Lu, P; Luebke-Wheeler, J; Lutz, A; Maltman, DJ; Matz-Soja, M; McMullen, P; Merfort, I; Messner, S; Meyer, C; Mwinyi, J; Naisbitt, DJ; Nussler, AK; Olinga, P; Pampaloni, F; Pi, J; Pluta, L; Przyborski, SA; Ramachandran, A; Rogiers, V; Rowe, C; Schelcher, C; Schmich, K; Schwarz, M; Singh, B; Stelzer, EH; Stieger, B; Stöber, R; Sugiyama, Y; Tetta, C; Thasler, WE; Vanhaecke, T; Vinken, M; Weiss, TS; Widera, A; Woods, CG; Xu, JJ; Yarborough, KM; Hengstler, JG; Arch Toxicol, 2013 Aug PubMed

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

Time-resolved confocal scanning device for ultrasensitive fluorescence detection. Böhmer M; Pampaloni F; Wahl M; Rahn HJ; Erdmann R; Enderlein J; Rev. Sci. Instrum. 72, 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), 90-99 (1999)