Facility for Advanced Imaging and Microscopy

Platform News

Jan 2, 2019
Pushing the boundaries of the visible

Facility for Advanced Imaging and Microscopy

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

The microscopy and imaging core facility supports FMI scientists and collaborators for high-end light and electron microscopy, high-content screening, and image analysis.

Our main goals are to:

  • Provide access to high-end acquisition and analysis workstations.
  • Maintain instruments and workstations to ensure quality and efficiency.
  • Train scientists to make sure hardware and software are used at the highest possible level.
  • Develop workflows for big-data analysis and storage.
  • Connect with other institutes to make usage of the know-how among the Swiss, European and worldwide network 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 variety of samples, especially living specimen. 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 (cell or tissue) going to 2D classic transmission electron microscopy (TEM) for ultrastructure or immunolabelling investigations to 3D volume scanning electron microscopy (SEM) for connectomic. Dedicated to support FMI research groups, we are providing service and training from sample preparation to image analysis. Together with the FMI and Novartis structural EM team we are sharing since 2016 an EM facility that provides cutting-edge EM to a broad researchers community from academia and industry.

High content screening (HCS)
We offer support for HCS from assay development to image and data analysis. As HCS involves a new mindset to plan experiences, we are involved in the projects from the conception to the image analysis.

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. Commercial software packages exist for visualization and generic quantification, but dedicated customized tools are needed for more complex analyses. Our task is thus to develop analysis modules, either as stand-alone tools or plug-ins for the commercial software, that specifically address our users' questions, and to offer continuous training on all our solutions.

Laurent Gelman: Platform head, FAIM

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

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

Curr Opin Cell Biol. 2020 Sep 1;67:37-45

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

Karmakar K, Narita Y, Fadok J, Ducret S, Loche A, Kitazawa T, Genoud C, Di Meglio T, Thierry R, Bacelo J, Lüthi A, Rijli FM (2017) Hox2 Genes Are Required for Tonotopic Map Precision and Sound Discrimination in the Mouse Auditory Brainstem.

Cell Rep. 2017 Jan 3;18(1):185-197

Seeber A, Hegnauer AM, Hustedt N, Deshpande I, Poli J, Eglinger J, Pasero P, Gut H, Shinohara M, Hopfner KP, Shimada K, Gasser SM (2016) RPA Mediates Recruitment of MRX to Forks and Double-Strand Breaks to Hold Sister Chromatids Together.

Mol Cell. 2016 Dec 1;64(5):951-966

Wanner AA, Genoud C, Friedrich RW (2016) 3-dimensional electron microscopic imaging of the zebrafish olfactory bulb and dense reconstruction of neurons.

Sci Data. 2016 Nov 8;3:160100

Titze B, Genoud C (2016) Volume scanning electron microscopy for imaging biological ultrastructure.

Biol Cell. 2016 Nov;108(11):307-323

Wanner AA, Genoud C, Masudi T, Siksou L, Friedrich RW (2016) Dense EM-based reconstruction of the interglomerular projectome in the zebrafish olfactory bulb.

Nat Neurosci. 2016 Jun;19(6):816-25

Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M (2015) H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein.

EMBO J. 2015 Nov 12;34(22):2789-803

Bechara A, Laumonnerie C, Vilain N, Kratochwil CF, Cankovic V, Maiorano NA, Kirschmann MA, Ducret S, Rijli FM (2015) Hoxa2 Selects Barrelette Neuron Identity and Connectivity in the Mouse Somatosensory Brainstem.

Cell Rep. 2015 Oct 27;13(4):783-797

Wanner AA, Kirschmann MA, Genoud C (2015) Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience.

J Microsc. 2015 Aug;259(2):137-42

Genoud C, Houades V, Kraftsik R, Welker E, Giaume C (2015) Proximity of excitatory synapses and astroglial gap junctions in layer IV of the mouse barrel cortex.

Neuroscience. 2015 Apr 16;291:241-9

Stephan R, Goellner B, Moreno E, Frank CA, Hugenschmidt T, Genoud C, Aberle H, Pielage J (2015) Hierarchical microtubule organization controls axon caliber and transport and determines synaptic structure and stability.

Dev Cell. 2015 Apr 6;33(1):5-21


Platform/Service Head

Laurent Gelman (Platform head, FAIM)

Technical/Research associates

Jan Eglinger (Imaging analysis programmer)
Alexandra Graff Meyer (Research associate, platform)
Ilya Lukonin (Research associate, platform)
Laure Plantard (Research associate, platform)
Markus Rempfler (Imaging analysis programmer)
Ursula Sauder (Technical/Research associate)
Benjamin Titze (Imaging analysis programmer)
Sjoerd Van Eeden (IT support specialist)


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

Katrin Volkmann (2015-2018, Postdoctoral fellow)
Stefan Wacha (2007-2008, Postdoctoral fellow)

Technical/Research associates

Steven Bourke (2010-2020, Research associate, platform)
Alexandra Graff Meyer (2014-2020, Research associate, platform)
Georg Kempf (2019-2020, Research associate )
Sandra Muehlhaeusser (2020, Lab manager)
Ursula Sauder (2017-2020, Technical/Research associate)
Markus Rempfler (2018-2019, Imaging analysis programmer)
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)
Jens Rietdorf (2010-2011, Head special applications in microscopy)
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)
Ivan Galimberti (2009, Visiting scientist)
Asheesh Gulati (2006-2008, Visiting scientist)
Mario Emmenlauer (2008, Imaging software programmer)
Alessandra Griffa (2007-2008, Visiting scientist)

Consultant / Contractors

Patrick Schwarb (2012-2014, Consultant)

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

Software and Tools

Test - Not in use for now