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.
Contact
Laurent Gelman: Platform head, FAIM
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):e3001344Eichenberger 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 1Yang 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):733-744Bhaskar 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):411-419Mateju 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.e13Zinner M, Lukonin I, Liberali P (2020) Design principles of tissue organisation: How single cells coordinate across scales.
Curr Opin Cell Biol. 2020 Dec;67:37-45Lukonin 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):275-280Meeuse 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):e9498Liu 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):e103697Michael 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):1460-1465Bhaskar 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):107473Mayer 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):e102591Voigt F, Eglinger J, Chao JA (2019) Quantification of mRNA Turnover in Living Cells: A Pipeline for TREAT Data Analysis.
Methods Mol Biol. 2019;2038:75-88Rabl 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.e9Voigt 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):1603-1633Serra 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):66-72Saito 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):51-61Genoud 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;12:76Titze B, Genoud C, Friedrich RW (2018) SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy. Front Neural Circuits
Front Neural Circuits. 2018;12:54Miyasaka 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):336-46Voigt 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):3740-3753Voigt F, Eglinger J, Chao JA (2017) Detection of the First Round of Translation: The TRICK Assay.
Methods Mol Biol. 2018;1649:373-384Horvathova 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.e9Xue 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):69204-69218Hauer 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):99-107Karmakar 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):185-197Seeber 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):951-966Wanner 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;3:160100Titze B, Genoud C (2016) Volume scanning electron microscopy for imaging biological ultrastructure.
Biol Cell. 2016 Nov;108(11):307-323Wanner 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
Members
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
After gaining an MSc in Computer Science with a focus on computer vision, Tim-Oliver worked on machine learning solutions for biomedical image analysis at the Max Planck-Institute of Molecular Cell Biology and Genetics. Since 2021 he works as machine learning expert for bioimage analysis.
EducationMSc 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 2019
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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 2020
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In current position since 2003
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