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.
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 May 12;: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 Apr 23
Schenk AD, Cavadini S, Thomä NH, Genoud C (2020) Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE.J Chem Inf Model. 2020 Apr 10
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
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 CircuitsFront 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
Tardat M, Albert M, Kunzmann R, Liu Z, Kaustov L, Thierry R, Duan S, Brykczynska U, Arrowsmith CH, Peters AH (2015) Cbx2 targets PRC1 to constitutive heterochromatin in mouse zygotes in a parent-of-origin-dependent manner.Mol Cell. 2015 Apr 2;58(1):157-71
Oberti D, Biasini A, Kirschmann MA, Genoud C, Stunnenberg R, Shimada Y, Bühler M (2015) Dicer and Hsp104 function in a negative feedback loop to confer robustness to environmental stress.Cell Rep. 2015 Jan 6;10(1):47-61
Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B (2014) miRNAs 182 and 183 are necessary to maintain adult cone photoreceptor outer segments and visual function.Neuron. 2014 Aug 6;83(3):586-600
Consultant / Contractors
Biography of Laurent Gelman
Biography of Christel Genoud
Software and Tools
Test - Not in use for now