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, X-ray crystallography, 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.

Tools

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 support for techniques going from cryo-EM single particle to large 3D volume for connectomic. Dedicated to support FMI research groups, we are providing service and training from sample preparation to image analysis. Since 2016, we have been working together with the EM team at Novartis, sharing a new EM facility that provides cutting-edge EM to a broad researchers community from academia and industry.

X-Ray crystallography
We provide equipment, expertise and hands-on support to FMI research groups interested in all aspects of modern structural biology ranging from cloning, protein expression and purification, to the final 3D structure and publication of the target protein based on X-ray protein crystallography.

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.

Contact
Laurent Gelman: Platform head, light microscopy
Christel Genoud: Platform head, electron microscopy

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 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

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

Kondo S, Bottos A, Allegood JC, Masson R, Maurer FG, Genoud C, Kaeser P, Huwiler A, Murakami M, Spiegel S, Hynes NE (2014) Memo has a novel role in S1P signaling and is [corrected] crucial for vascular development.

PLoS One. 2014;9(4):e94114

Friedrich RW, Genoud C, Wanner AA (2013) Analyzing the structure and function of neuronal circuits in zebrafish.

Front Neural Circuits. 2013;7:71

Zhuravleva E, Gut H, Hynx D, Marcellin D, Bleck CK, Genoud C, Cron P, Keusch JJ, Dummler B, Esposti MD, Hemmings BA (2012) Acyl coenzyme A thioesterase Them5/Acot15 is involved in cardiolipin remodeling and fatty liver development.

Mol Cell Biol. 2012 Jul;32(14):2685-97

Lai JC, Ponti S, Pan D, Kohler H, Skoda RC, Matthias P, Nagamine Y (2012) The DEAH-box helicase RHAU is an essential gene and critical for mouse hematopoiesis.

Blood. 2012 May 3;119(18):4291-300

Ruediger S, Vittori C, Bednarek E, Genoud C, Strata P, Sacchetti B, Caroni P (2011) Learning-related feedforward inhibitory connectivity growth required for memory precision.

Nature. 2011 May 26;473(7348):514-8

Members

Platform/Service Head

Laurent Gelman (Platform head, light microscopy)
Christel Genoud (Platform head, electron microscopy)

Technical/Research associates

Steven Bourke (Research associate, platform)
Simone Cavadini (Project leader)
Jan Eglinger (Imaging analysis programmer)
Alexandra Graff Meyer (Research associate, platform)
Georg Kempf (Research associate )
Ilya Lukonin (Research associate )
Raphael Ortiz (Imaging analysis programmer)
Markus Rempfler (Imaging analysis programmer)
Ursula Sauder (Technical/Research associate)
Andreas Daniel Schenk (Project leader)
Benjamin Titze (Imaging analysis programmer)

Undergraduates

Chi Ho Wai (Undergraduate)

Alumni

Platform/Service Head

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

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)
Laurent Gelman (2008-2010, Imaging & microscopy facility scientist)
Cihan Cetin (2008-2009, Imaging software programmer)
Genevieve Dardier (2008, Imaging software programmer)

Undergraduates

Franziska Kaesler (2019, Undergraduate)
Hacene Nebri (2017, Undergraduate)

Visiting scientists

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

Education

1996-2000
PhD in Molecular Biology, Institut Pasteur, Lille & IGBMC, Strasbourg
1994
MSc in Immunology, Institut Pasteur, Paris
1993
Engineering degree in Biochemistry, Institut National Agronomique Paris-Grignon, Paris

Positions held

2010-
Co-Head of FAIM
2006-2010
Scientific staff at FAIM and Head of LM, FMI
2002-2006
Maitre-Assistant, University of Lausanne
2000-2002
Post-doctoral studies IGBMC, Strasbourg

 

Biography of Christel Genoud

Education

2001-2006
PhD in Life Science, University of Lausanne, post-grade diploma in Neuroscience
2000
MSc in Biology, University of Lausanne

Positions held

2010-
Co-Head of FAIM
2008-2010
Head of EM, FMI
2006-2008
Product Specialist Gatan

Software and Tools

Test - Not in use for now