Facility for Advanced Imaging and Microscopy

Facility for Advanced Imaging and Microscopy

High-end light and electron microscopes, and cutting-edge imaging software and analysis tools

The Facility for Advanced Imaging and Microscopy (FAIM) supports FMI scientists and collaborators with cutting-edge light and electron microscopy, high-content screening, and image analysis.

Our goal is to provide expertise, high-end instrumentation, and technical support to researchers in the institute, so they can focus on their biological questions. We therefore:

  • Provide access to state-of-the-art acquisition systems and analysis workstations.
  • Maintain instruments and workstations to ensure quality and efficiency.
  • Advise and train scientists to ensure optimal usage of our hardware and software.
  • Develop workflows for data acquisition, analysis and storage.
  • Interact with other institutes to benefit from the know-how among the Swiss, European and worldwide networks of microscopy and imaging.

Light microscopy (LM)
Light microscopes are available for a variety of purposes, e.g.: analyze and quantify molecular and cellular dynamics, (co-)localize labels, measure molecular interactions and concentrations. Our microscopes can accommodate a diversity of samples, especially living specimens. We offer a very large palette of imaging modalities, from wide-field imaging to single-point and spinning-disk confocal, structured illumination, TIRF, slide scanning and 2-photon/NLO imaging. Expertise is available on any aspect of the entire process of experiment design, sample preparation and image acquisition.

Electron microscopy (EM)
We provide EM support for biological samples using transmission electron microscopy (TEM) for 2D ultrastructure or immunolabelling, and serial block-face scanning electron microscopy (SEM) for 3D tissue volumes. We are offering service and training to FMI researchers ranging from sample preparation to image analysis. Since 2016, we are sharing an EM facility with Novartis on the St Johann Campus that provides cutting-edge EM to researchers from academia and industry.

High content screening (HCS)
We offer complete support for HCS projects: from assay development and upscaling to image and data analysis. As HCS involves a new mindset to plan experiments, we are involved in the projects from the conception down to the data analysis and statistics. We offer access to instruments enabling the automation of both sample preparation and imaging, providing user training and service. As part of the HCS project lifecycle, we offer tools for visualizing, processing and exploring large imaging datasetsOur special area of expertise is automated culture and imaging of complicated 3D model systems.

Image & data analysis
Acquisition at the microscope is just the first step to address biological questions. The acquired data must then be visualized and carefully analyzed to prove or reject the working hypotheses. Various software tools exist for visualization and generic quantification, but dedicated customized solutions are frequently needed for more complex analyses. We provide continuous training on tools and theory, offer advice and support for image analysis questions, and we develop customized solutions for advanced image analysis workflows, either as stand-alone software tools or plug-ins for the existing software packages, that specifically address our users' questions.

Laurent Gelman: Platform head, FAIM

Suppinger S, Zinner M, Aizarani N, Lukonin I, Ortiz R, Azzi C, Stadler MB, Vianello S, Palla G, Kohler H, Mayran A, Lutolf MP, Liberali P (2023) Multimodal characterization of murine gastruloid development.

Cell Stem Cell. 2023 Jun 1;30(6):867-884.e11

Munz M, Bharioke A, Kosche G, Moreno-Juan V, Brignall A, Rodrigues TM, Graff-Meyer A, Ulmer T, Haeuselmann S, Pavlinic D, Ledergerber N, Gross-Scherf B, Rózsa B, Krol J, Picelli S, Cowan CS, Roska B (2023) Pyramidal neurons form active, transient, multilayered circuits perturbed by autism-associated mutations at the inception of neocortex.

Cell. 2023 Apr 27;186(9):1930-1949.e31

Meeuse MWM, Hauser YP, Nahar S, Smith AAT, Braun K, Azzi C, Rempfler M, Großhans H (2023) C. elegans molting requires rhythmic accumulation of the Grainyhead/LSF transcription factor GRH-1.

EMBO J. 2023 Feb 15;42(4):e111895

Ballmer D, Tardat M, Ortiz R, Graff-Meyer A, Ozonov EA, Genoud C, Peters AH, Fanourgakis G (2023) HP1 proteins regulate nucleolar structure and function by secluding pericentromeric constitutive heterochromatin.

Nucleic Acids Res. 2023 Jan 11;51(1):117-143

Mach P, Kos PI, Zhan Y, Cramard J, Gaudin S, Tünnermann J, Marchi E, Eglinger J, Zuin J, Kryzhanovska M, Smallwood S, Gelman L, Roth G, Nora EP, Tiana G, Giorgetti L (2022) Cohesin and CTCF control the dynamics of chromosome folding.

Nat Genet. 2022 Dec;54(12):1907-1918

Nörpel J, Cavadini S, Schenk AD, Graff-Meyer A, Hess D, Seebacher J, Chao JA, Bhaskar V. (2021) Structure of the human C9orf72-SMCR8 complex reveals a multivalent protein interaction architecture.

PLoS Biol. 2021 Jul 23;19(7):e3001344

Eichenberger BT, Zhan Y, Rempfler M, Giorgetti L, Chao JA (2021) deepBlink: threshold-independent detection and localization of diffraction-limited spots.

Nucleic Acids Res. 2021 Jul 21;49(13):7292-7297

Yang Q, Xue SL, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo E, Liberali P (2021) Cell fate coordinates mechano-osmotic forces in intestinal crypt formation.

Nat Cell Biol. 2021 Jul;23(7):733-744

Bhaskar V, Desogus J, Graff-Meyer A, Schenk AD, Cavadini S, Chao JA (2021) Dynamic association of human Ebp1 with the ribosome.

RNA. 2021 Apr;27(4):411-419

Mateju D, Eichenberger B, Voigt F, Eglinger J, Roth G, Chao JA (2020) Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules

Cell. 2020 Dec 23;183(7):1801-1812.e13

Zinner M, Lukonin I, Liberali P (2020) Design principles of tissue organisation: How single cells coordinate across scales.

Curr Opin Cell Biol. 2020 Dec;67:37-45

Lukonin I, Serra D, Challet Meylan L, Volkmann K, Baaten J, Zhao R, Meeusen S, Colman K, Maurer F, Stadler MB, Jenkins J, Liberali P (2020) Phenotypic landscape of intestinal organoid regeneration

Nature. 2020 Oct;586(7828):275-280

Meeuse MW, Hauser YP, Morales Moya LJ, Hendriks GJ, Eglinger J, Bogaarts G, Tsiairis C, Großhans H (2020) Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans

Mol Syst Biol. 2020 Jul;16(7):e9498

Liu Z, Tardat M, Gill ME, Royo H, Thierry R, Ozonov EA, Peters AH (2020) SUMOylated PRC1 controls histone H3.3 deposition and genome integrity of embryonic heterochromatin

EMBO J. 2020 Jul 1;39(13):e103697

Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH (2020) Mechanisms of OCT4-SOX2 motif readout on nucleosomes

Science. 2020 Jun 26;368(6498):1460-1465

Bhaskar V, Graff-Meyer A, Schenk AD, Cavadini S, von Loeffelholz O, Natchiar SK, Artus-Revel CG, Hotz HR, Bretones G, Klaholz BP, Chao JA (2020) Dynamics of uS19 C-Terminal Tail during the Translation Elongation Cycle in Human Ribosomes

Cell Rep. 2020 Apr 7;31(1):107473

Mayer D, Stadler MB, Rittirsch M, Hess D, Lukonin I, Winzi M, Smith A, Buchholz F, Betschinger J (2020) Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2

EMBO J. 2020 Jan 15;39(2):e102591

Voigt F, Eglinger J, Chao JA (2019) Quantification of mRNA Turnover in Living Cells: A Pipeline for TREAT Data Analysis.

Methods Mol Biol. 2019;2038:75-88

Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH (2019) Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation

Mol Cell. 2019 Aug 8;75(3):483-497.e9

Voigt F, Gerbracht JV, Boehm V, Horvathova I, Eglinger J, Chao JA, Gehring NH (2019) Detection and quantification of RNA decay intermediates using XRN1-resistant reporter transcripts

Nat Protoc. 2019 May;14(5):1603-1633

Serra D, Mayr U, Boni A, Lukonin I, Rempfler M, Challet Meylan L, Stadler MB, Strnad P, Papasaikas P, Vischi D, Waldt A, Roma G, Liberali P (2019) Self-organization and symmetry breaking in intestinal organoid development

Nature. 2019 May;569(7754):66-72

Saito M, Hess D, Eglinger J, Fritsch AW, Kreysing M, Weinert BT, Choudhary C, Matthias P (2019) Acetylation of intrinsically disordered regions regulates phase separation

Nat Chem Biol. 2019 Jan;15(1):51-61

Genoud C, Titze B, Graff-Meyer A, Friedrich RW (2018) Fast Homogeneous En Bloc Staining of Large Tissue Samples for Volume Electron Microscopy.

Front Neuroanat. 2018;12:76

Titze B, Genoud C, Friedrich RW (2018) SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy. Front Neural Circuits

Front Neural Circuits. 2018;12:54

Miyasaka N, Wanner AA, Li J, Mack-Bucher J, Genoud C, Yoshihara Y, Friedrich RW (2018) Functional development of the olfactory system in zebrafish

Mech Dev. 2013 Jun-Aug;130(6-8):336-46

Voigt F, Zhang H, Cui XA, Triebold D, Liu AX, Eglinger J, Lee ES, Chao JA, Palazzo AF (2017) Single-Molecule Quantification of Translation-Dependent Association of mRNAs with the Endoplasmic Reticulum.

Cell Rep. 2017 Dec 26;21(13):3740-3753

Voigt F, Eglinger J, Chao JA (2017) Detection of the First Round of Translation: The TRICK Assay.

Methods Mol Biol. 2018;1649:373-384

Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, Eglinger J, Stadler MB, Giorgetti L, Chao JA (2017) The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells

Mol Cell. 2017 Nov 2;68(3):615-625.e9

Xue G, Kohler R, Tang F, Hynx D, Wang Y, Orso F, Prêtre V, Ritschard R, Hirschmann P, Cron P, Roloff T, Dummer R, Mandalà M, Bichet S, Genoud C, Meyer AG, Muraro MG, Spagnoli GC, Taverna D, Rüegg C, Merghoub T, Massi D, Tang H, Levesque MP, Dirnhofer S, Zippelius A, Hemmings BA, Wicki A (2017) mTORC1/autophagy-regulated MerTK in mutant BRAFV600 melanoma with acquired resistance to BRAF inhibition

Oncotarget. 2017 Sep 19;8(41):69204-69218

Hauer MH, Seeber A, Singh V, Thierry R, Sack R, Amitai A, Kryzhanovska M, Eglinger J, Holcman D, Owen-Hughes T, Gasser SM (2017) Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

Nat Struct Mol Biol. 2017 Feb;24(2):99-107


Platform/Service Head

In current position since 2010
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After gaining an Engineering degree in Biochemistry and a MSc in Immunology in Paris, Laurent did his PhD in Molecular Biology at the Institut Pasteur in Lille and the IGBMC in Strasbourg, where he also did postdoctoral research on in vitro transcription assays. He then moved to the University of Lausanne, where he used advanced microscopy techniques to study gene regulation in living cells.

Technical/Research associates

In current position since 2022
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In current position since 2021
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Google scholar


After gaining a MSc in Computer Science with a focus on computer vision, Tim-Oliver did his PhD in Machine Learning-based image restoration and segmentation methods at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden.

Since 2021 he works as Machine Learning Expert for bioimage analysis in the Facility for Advanced Imaging and Microscopy at the Friedrich Miescher Institute for Biomedical Research. Tim-Oliver has a strong background in Image Analysis, Computer Vision, Machine Learning and Software Development. As part of his daily work, he develops open-source software packages for reproducible and scaling biomedical image analysis.


PhD in Computer Science, Technische Universität Dresden, Germany
MSc in Computer Science, University of Konstanz, Germany
BSc in Computer Science, University of Konstanz, Germany

In current position since 2015
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In current position since 2020
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In current position since 2022
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In current position since 2020
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Google scholar


Laure is trained in biology, with a focus in molecular and cell biology. Her interest in microscopy deepened during her postdoctoral work on cell migration and cell division, and since 2012 she works as a specialist in light microscopy.

• 2018-2020: Senior Light Microscopy specialist at the Light Microscope Facility, MPI-CBG, Dresden, Germany
• 2012-2018: Light Microscopy specialist at the Core Facility for Integrated Microscopy, University of Copenhagen, Denmark
• 2009-2011: Post-doc at EMBL, Heidelberg, Germany
• 2005-2009: Post-doc at Karolinska Institute, Stockholm, Sweden.



• Ph.D. in Life Sciences, University of Lausanne, Switzerland
• M.Sc. in Biology and Health, University of Montpellier, France
• B.Sc. in Biology, University of Lille and University of Burgundy in Dijon, France

In current position since 2022
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In current position since 2020
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In current position since 2003
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Platform/Service Head

Christel Genoud (2008-2020, Platform head, electron microscopy)
Patrick Schwarb (2005-2011, Head image analysis facility)
Jens Rietdorf (2005-2010, Head light microscopy facility)
Thierry Laroche (2004-2005, Head light microscopy facility)

Postdoctoral fellows

Stefan Wacha (2007-2008, Postdoctoral fellow)

Technical/Research associates

Ilya Lukonin (2019-2021, Research associate, platform)
Markus Rempfler (2020-2021, Imaging analysis programmer)
Benjamin Titze (2019-2021, Imaging analysis programmer)
Steven Bourke (2010-2020, Research associate, platform)
Georg Kempf (2019-2020, Research associate, platform)
Ursula Sauder (2017-2020, Technical/Research associate)
Katrin Volkmann (2015-2018, Research associate, platform)
Raphael Thierry (2012-2018, Imaging software programmer)
Tabea Hugenschmidt (2011-2015, Technical/Research associate)
Moritz Kirschmann (2013-2014, Research associate, platform)
Aaron Ponti (2007-2012, Imaging software programmer)
Cihan Cetin (2008-2009, Imaging software programmer)
Genevieve Dardier (2008, Imaging software programmer)


Chi Ho Wai (2019, Undergraduate)
Franziska Kaesler (2019, Undergraduate)
Hacene Nebri (2017, Undergraduate)

Visiting scientists

Jiri Tyc (2020, Visiting scientist)
Jean-Rene Galarneau (2010, Visiting scientist)
Asheesh Gulati (2006-2008, Visiting scientist)
Mario Emmenlauer (2008, Visiting scientist)
Alessandra Griffa (2007-2008, Visiting scientist)

Biography of Laurent Gelman


PhD in Molecular Biology, Institut Pasteur, Lille & IGBMC, Strasbourg
MSc in Immunology, Institut Pasteur, Paris
Engineering degree in Biochemistry, Institut National Agronomique Paris-Grignon, Paris

Positions held

Co-Head of FAIM
Scientific staff at FAIM and Head of LM, FMI
Maitre-Assistant, University of Lausanne
Post-doctoral studies IGBMC, Strasbourg