English Intern
  • super-resolution image of microtubules (Manish Singh, Institut Pasteur, France)
Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging

Zimmer Lab / Chair of High resolution optical microscopy

We are pleased that we were able to attract Prof. Christophe Zimmer as part of the Bavarian Distinguished Professorship Programme (Spitzenprofessurenprogramm, High Tech Agenda Bayern). He will start his work at the Rudolf Virchow Center in January 2024:

Future research

Our new interdisciplinary laboratory will combine advanced imaging and artificial intelligence (AI) to push back technical barriers to life science research and directly address key biomedical questions.

We will initially focus on two main projects:

  • High throughput super-resolution imaging and AI for drug discovery: Diseases such as cancer or those caused by antibiotic-resistant bacteria urgently call for new drugs. However, the pipelines delivering drug molecules with new modes of action are drying up. High-throughput imaging of cells exposed to large chemical libraries has been successful at identifying new drug candidates but requires labor-intensive and time-consuming follow up assays to identify drug targets. We aim to speed up phenotypic drug discovery by using experimental and computational methods to predict drug targets from imaging data alone. This project combines high throughput and adaptive super-resolution imaging with deep learning-based image analysis. It is based on a close collaboration with teams of microbiologists at Institut Pasteur, Paris and elsewhere.
  • Live cell nanoscopy through AI: A holy grail in biological research is to characterize the structure and dynamics of molecular structures within cells at the best possible spatial and temporal resolution. Super-resolution microscopy based on single molecule localization (SMLM) can now reach nanometric scales or better, but requires extremely long acquisition times. Consequently, live cell super-resolution imaging remains mostly out of reach, preventing the detailed analysis of molecular dynamics. We are pursuing approaches based on state-of-the-art AI (deep learning) methods to speed up SMLM imaging with the goal of enabling molecular-scale resolution imaging at high temporal resolution in live cells. Achieving this goal will open the door to a better understanding of fundamental processes of cellular life and pathologies, from cytoskeletal dynamics to mitochondrial reorganization and chromatin organization.

Job opportunities!

If you are interested in joining our lab and you have a strong background in microscopy, AI, biophysics, cell biology, microbiology or related fields, please see our current job announcements here.

We also have an opening for a junior group leader position in microbiology. Please see the details here.

Recent Publications

Isnard P, Vergnaud P, Garbay S, Jamme M, Eloudzeri M, Karras A, Anglicheau D, Galantine V, Jalal Eddine A, Gosset C, Pourcine F, Zarhrate M, Gibier JB, Rensen E, Pietropaoli S, Barba-Spaeth G, Duong-Van-Huyen JP, Molina TJ, Mueller F, Zimmer C, Pontoglio M, Terzi F, Rabant M, , A specific molecular signature in SARS-CoV-2-infected kidney biopsies., JCI Insight 2023 Mar; 8(5): .

Sabaté T, Lelandais B, Bertrand E, Zimmer C, , Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging., Nucleic Acids Res 2023 Feb; (): .

Krentzel D, Shorte SL, Zimmer C, , Deep learning in image-based phenotypic drug discovery., Trends Cell Biol 2023 Jan; (): .

Ouyang W, Bai J, Singh MK, Leterrier C, Barthelemy P, Barnett SFH, Klein T, Sauer M, Kanchanawong P, Bourg N, Cohen MM, Lelandais B, Zimmer C, , ShareLoc – an open platform for sharing localization microscopy data., Nat Methods 2022 Oct; (): .

Imbert A, Ouyang W, Safieddine A, Coleno E, Zimmer C, Bertrand E, Walter T, Mueller F, , FISH-quant v2: a scalable and modular tool for smFISH image analysis., RNA 2022 06; 28(6): 786-795.

Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, Sommer S, Isnard P, Rabant M, Gibier JB, Terzi F, Simon-Loriere E, Rameix-Welti MA, Pierron G, Barba-Spaeth G, Zimmer C, , Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH., Life Sci Alliance 2022 Apr; 5(4): .

Nunes Vicente F, Lelek M, Tinevez JY, Tran QD, Pehau-Arnaudet G, Zimmer C, Etienne-Manneville S, Giannone G, Leduc C, , Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging., Sci Adv 2022 Feb; 8(8): eabm2696.

Sabate T, Zimmer C, Bertrand E, , Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells., Methods Mol Biol 2022 ; 2532(): 275-290.

Link to all publications

starting 2024 W3 Professor, Rudolf Virchow Center, University of Würzburg, Germany
since 2021 Professor, Institut Pasteur, Paris, France
2020 – 2023   Director of the Computational Biology department, Institut Pasteur, France
2015 – 2016 Visiting Scholar, University of California at Berkeley, USA
2012021 Research Director, Institut Pasteur, France
2009 Habilitation to direct research (HDR), University Paris 11, France
since 2008 Head of Imaging and Modeling Unit, Institut Pasteur
2003 – 2007 Staff scientist, Institut Pasteur, Paris, France
2000 – 2002 Postdoctoral researcher, Institut Pasteur, Paris, France
1998 – 2000 Assistant research geophysicist, Space Physics Group, University of California Los Angeles, USA
1997 PhD, Astrophysics and Space Techniques, University Paris 7, France