Electron Microscopy

  • To see what no one has seen before!
  • To see what no one has seen before!
  • To see what no one has seen before!
  • To see what no one has seen before!

The Electron Microscopy Facility (EM) offers a variety of preparation techniques for biological samples of diverse origin. We examine the complex architecture of macromolecules, cells and tissues at nanometer resolution using state-of-the-art conventional and cryo-techniques for specimen preparation and visualization. Whether you are interested in quick sample screening or high resolution 2D or 3D imaging, we can help. Furthermore, we provide the processing of purified molecules for conventional and cryo-electron microscopy as well sample preparation for scanning electron microscopy.


    Sample Preparation Techniques

    Sample Preparation Techniques

    Depending on your question and sample we offer a variety of different preparation techniques to ensure optimal preservation of your specimen:

    • Preparation for scanning electron microscopy to study surface structures
    • Negative Staining for rapid visualization of macromolecules, proteins, viruses, organelles or bacteria.
    • Conventional chemical fixation for tissue samples and cell monolayers.
    • High pressure freezing and freeze substitution for superior cellular preservation of cells and tissues.
    • Rotary Shadowing for high contrast examination of protein complexes.
    • Freeze fracturing and etching for visualization of surfaces, membranes and the inside of membranous compartment.
    • Immersion freezing (“cryo plunge freezing”) for best possible preservation of small samples close to their native state.
    • Tokuyasu as a method for cryo-sectioning in combination with immunogold labeling.
    • Immunolabeling to locate structures of interest.
    • Ultramicrotomy: ultra-thin sectioning of resin embedded samples.

    Imaging Techniques

    Imaging Techniques

    We offer the following imaging techniques to study your samples:

    • Scanning Electron Microscopy (SEM) to visualise the surface topology of samples
    • Transmission Electron Microscopy (TEM) to examine the ultrastructure
      • Conventional 2D Electron Microscopy
      • Tomography - 3D Electron Microscopy
      • Correlative microscopy
        • Cryo-electron microscopy/tomography




    We can visualize the following structures:

    • Molecules (RNA, DNA, proteins, lipids)
    • Complexes (liposomes, emulsions, small synthetic structures)
    • Viruses
    • Bacteria
    • Organelles
    • Eukaryotic cells (fungi, plants, animals)
    • Tissues
    • Surface structures

    Training and Infrastructure usage

    Training and Infrastructure usage

    Infrastructure users are trained on a comprehensive set of equipment for sample preparation and visualization of biological specimens at nanometer resolution. All of our instruments - from basic sample preparation equipment to our most sophisticated electron microscopes - are available to users. We further support our users in planning, execution and interpretation of all EM-related experiments.

    For any questions please contact Thomas Heuser.



    The FEI Morgagni 268D is a robust and easy-to-use 100 kV TEM equipped with a 11 megapixel CCD camera. The microscope has a high specimen throughput and it is tailored for routine applications in the multiuser environment of the facility.

    It is being used for:

    • Negative staining samples
    • Rotary shadowing samples
    • Ultrathin sections
    • Immunolabelling


    You can find it in room 4.73.01 (phone: + 43 (1) 7962324 - 7124) and it is reservable via our EM reservation system.


    • Tungsten filament emitter
    • 100 kV (operated at 80 kV)
    • 11 megapixel CCD camera (Morada from Olympus-SIS)


    • Morgagni software (version 3.0)
    • iTEM (version 5.0)


    The 300 kV TEM FEI Tecnai F30 Helium "Polara", unique in Austria and equipped with the most advanced imaging systems, was funded by a Vienna Spot of Excellence grant and became fully operational at the beginning of 2008. We operate the Polara in cooperation with IMBA and IMP.

    It is being used for:

    • Negative staining samples
    • Cryo samples
    • Tomography
    • Analytical EM (EELS)

    You can find it in room 4.59.02 (phone: + 43 (1) 790 44 - 4267) and it is reservable via our EM reservation system.


    • FEG
    • 300 kV
    • Cartridge system with up to 6 cartridges that can be loaded at once
    • Rotation cartridges for double-tilt tomography
    • 24 h LN2 cooling system (optional: cooling at liquid Helium temperature) Pre-GIF Gatan Ultrascan 4000
    • GIF 2002 with 2k CCD


    • Tecnai software (version 3.1)
    • Digital Micrograph (version 3.9)
    • MoniTEM:monitoring system
    • SerialEM (version 3.x): Acquisition of tilt series for electron tomography; grid mapping
    • Leginon: automated collection of images for single particle analysis


    The IMP is currently recruting a new group leader in cryo-EM:

    Tecnai G2 20

    The FEI Tecnai G2 20, a 200 kV TEM, is the third member of our FEI microscope family next to the FEI Morgagni 268D and the FEI Tecnai F30 Helium "Polara". The T20 is equipped with an Eagle 4k HS camera and can be used for routine applications as well as for tomography of room temperature samples.

    It is being used for:

    • Negative staining samples
    • Rotary shadowing
    • Tomography of room temperature samples

    With the help of the IMBA/IMP workshop, we built a new dual-axis-tomography holder for our T20 electron microscope. This holder allows to visualize the 3D structure of resin embedded samples at room temperature in higher quality and higher resolution.

    You can find it in room 4.55. and it is reservable via our EM reservation system.


    LaB6 filament emitter

    • Operated at 80 and 200 kV
    • Eagle 4k HS CCD camera
    • Magnetic field compensation system


    SerialEM (version 3.x): Acquisition of tilt series for electron tomography; grid mapping

    Leica EM GP

    The VBCF EM Facility also operates a Leica EM GP grid plunger. This instrument was developed by Leica Microsystems in cooperation with Günter Resch and can be used for the vitrification of suspended samples like viruses, proteins and cellular components as well as adherent cells for cryo-TEM and cryo electron tomography. The machine plunge freezes samples on grids into a secondary cryogen such as liquid ethane which then allows a direct transfer into a cryo electron microscope. Besides biological specimen, this instrument can be used for industrial emulsions.

    For optimal and reproducible results the grid plunger provides different options. One important consideration in this context is the environmental humidity which should be around 99%. For that reason the whole procedure, like pipetting the sample onto the grid and the following removal of fluid by blotting with filter paper, occurs in a humidity controlled chamber at a variable temperature between +4°C and +60°C. The blotting is carried out automatically controlled by a photosensor. Furthermore all settings, such as humidity, blotting time, grid position, LN2 level and cryogen temperature are displayed and can be adjusted on a touch-screen control panel.

    As specimen preparation with the Leica EM GP has been proven very successful so far, this instrument has become the standard for preparation of vitrified specimen for cryo electron microscopy in our lab.

    Hitachi TM-1000

    Hitachi Tabletop Scanning Electron Microscope TM-1000

    This is a imaging platform for surface visualization at higher resolution and deeper focus depth than achievable by light microscopy. The image is generated with back-scattered electrons induced by an electron beam of 15 keV.

    Sample preparation is straightforward since it does not require coating with a conductive layer. The biological material might be frozen in liquid nitrogen. Alternatively, it might be chemically fixed and critical point-dried.

    Additional laboratory equipment

    High Vacuum Evaporators and Sputter Coaters :

    • Edwards Auto306 high vacuum evaporator (Room 4.73.03)
    • Bal-Tec MED020 high vacuum evaporator with quartz film thickness monitor for resistance evaporation of metals and carbon and electron gun evaporation of Pt and carbon (Room 4.73.03)
    • BALZERS BAF400 for high vacuum evaporation and freeze etching (Room 4.73.03)
    • Bal-Tec SCD005 sputter coater (Room 4.59.02; 4.73.03)

    High Pressure Freezing and Freeze Substitution :

    • Wohlwend HPF Compact 01 high pressure freezer (Room 4.73.04)
    • Leica EMPact high pressure freezer (Room 4.73.04)
    • 2 Leica AFS A and Leica AFS II automatic freeze substitution devices (Room 4.73.04)

    Sectioning :

    • Leica EM Trim for trimming resin-embedded specimens (Room 4.73.04)
    • Reichert EM Trim
    • Reichert UCS ultramicrotome (Room 4.74.02)
    • Leica UCT ultramicrotome (Room 4.74.02)
    • Leica UCT ultramicrotome with Leica EM FCS cryosetup (Room 4.74.03)
    • Leica VT 1000S Vibratome (Room 4.74.03)
    • Leica RMC, Leica LKB and Leica EM KMR2 glass knife makers (Room 4.74.02)

    Immersion and Slam Freezing :

    • FEI Vitrobot Mark III for controlled vitrification of thin specimens on grids (Room 4.59.02)
    • Manual plunge freezers for vitrification of thin specimens on grids (Room 4.59.02)
    • Leica EM CPC metal mirror freezer (Room 4.59.02)

    Embedding :

    • Leica Tissue Processor for embedding larger amounts of tissue (Room 4.74.03)
    • Electron Microscopy Sciences 820 microwave (Room 4.74.03)

    Scanning electron microscopy :

    • BALZERS CPD030 critical point dryer for scanning electron microscopy (Room 4.73.03)
    • Bal-Tec SCD050 (Room 4.73.03)

    Ancillary equipment :

    • Selutec Tec020 cell incubator (Room 4.73.03)
    • 2 Polymerisation ovens (Room 4.73.04)
    • Double distilled water still (Room 4.73.04)
    • Knauer K-7400 semi-micro osmometer (Room 4.73.04)

    Lightmicroscopes :

    • 2 Leica MZ6 stereo microscopes for specimen preparation (Room 4.73.04)
    • Leica Wild M3Z stereomicroscope (Room 4.73.03)
    • Leica S4E stereomicroscope (Room 4.73.04)

    Resources available at Partner Institutions

    User Information

    Starting a new project

    Here is what we need to know in advance if you want to start a new EM project:

    • What's your scientific question?
    • Which organisms and sample are you working with?
    • Do you have preliminary results?
    • Are there any describing papers about what you want do do?



    Citing the Facility

    If you are using our services or instruments, please acknowledge the EM Facility.

    In case of co-authorship:
    The EM Facility of the Vienna Biocenter Core Facilities GmbH (VBCF) acknowledges funding from the Austrian Federal Ministry of Science, Research & Economy and the City of Vienna.

    For acknowledging services by the EM Facility:
    XXXXXX was performed by the EM Facility of the  Vienna Biocenter Core Facilities GmbH (VBCF), member of Vienna Biocenter (VBC), Austria.

    For acknowledging instrument usage in the EM Facility:
    Samples were prepared / data was recorded at the EM Facility of the  Vienna Biocenter Core Facilities GmbH (VBCF), Austria.

    Your publication will then be listed in the 'publications' part on our website.


    To access protocols you have to login into MyVBCF...



    The structure and DNA-binding properties of Mgm101 from a yeast with a linear mitochondrial genome
    Pevala V., Truban D., Bauer J.A., Košťan J., Kunová N., Bellová J., Brandstetter M., Marini V., Krejčí L., Tomáška L., Nosek J., Kutejová E. (2016)
    Nucl. Acids Res. 44(5): 2227-2239 (abstract)

    An endosomal tether undergoes an entropic collapse to bring vesicles together
    Murray D.H., Jahnel M., Lauer J, Avellaneda M.J., Brouilly N., Cezanne A., Morales-Navarrete H., Perini E.D., Ferguson C., Lupas A.N., Kalaidzidis Y., Parton R.G., Grill S.W., Zerial M. (2016)
    Nature doi:10.1038/nature19326 (abstract)

    Semi-solid fluorinated-DPPC liposomes: Morphological, rheological and thermic properties as well as examination of the influence of a model drug on their skin permeation
    Mahrhauser D.S., Reznicek G., Kotisch H., Brandstetter M., Nagelreiter C., Kwizda K., Valenta C. (2015)
    Volume 486(1–2):350–355 (abstract)

    Size analysis of nanoparticles extracted from W/O emulsions
    Nagelreiter C., Kotisch H., Heuser T., Valenta C. (2015)
    Int J Pharm. 488(1-2):29-32. (abstact)

    Autophagy facilitates secretion and protects against degeneration of the Harderian gland
    Koenig U., Fobker M., Lengauer B., Brandstetter M., Resch G.P., Gröger M., Plenz G., Pammer J., Barresi C., Hartmann C., Rossiter H. (2015)
    Autophagy. 11(2):298-313 (abstract)

    Topical delivery of acetyl hexapeptide-8 from different emulsions: influence of emulsion composition and internal structure
    Hoppel M., Reznicek G., Kählig H., Kotisch H., Resch G.P., Valenta C. (2015)
    Eur J Pharm Sci. 68:27-35 (abstract)

    No evidence for intracellular magnetite in putative vertebrate magnetoreceptors identified by magnetic screening
    Edelman N.B., Fritz T., Nimpf S., Pichler P., Lauwers M., Hickman R.W., Papadaki-Anastasopoulou A., Ushakova L., Heuser T., Resch G.P., Saunders M., Shaw J.A., Keays D.A. (2015)
    Proc Natl Acad Sci U S A112(1):262-7 (abstract)

    A molecular ruler regulates cytoskeletal remodelling by the Rho kinases
    Truebestein L.,  Elsner D.J., Fuchs E., Leonard T.A. (2015)
    Nature Communications 6:10029 (abstract)

    Nuclear Pore Basket Proteins Are Tethered to the Nuclear Envelope and Can Regulate Membrane Curvature
    Mészáros N., Cibulka J., Mendiburo M.J., Romanauska A., Schneider M., Köhler A. (2015)
    Dev Cell. 33(3): 285–298 (abstract)

    Non-catalytic motor domains enable processive movement and functional diversification of the kinesin-14 Kar3
    Mieck C.,  Molodtsov M.I., Drzewicka K., van der Vaart B., Litos G., Schmauss G., Vaziri A., Westermann S. (2015)
    eLife 4:e04489 (abstract)

    New Insights into Cilia and Flagella by Cryo-EM
    Heuser T. (2015)
    Leica Science Lab (link)

    SYBR Green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content
    Schoft V.K. , Chumak N., Bindics J., Slusarz L., Twell D., Köhler C., Tamaru H. (2015)
    Plant Reprod 28(1):61-72 (abstract)

    The ciliary transition zone functions in cell adhesion but is dispensable for axoneme assembly in C. elegans
    Schouteden C., Serwas D., Palfy M., Dammermann A. (2015)
    J Cell Biol. 210(1):35-44  (abstract)

    Ultrastructural analysis of Caenorhabditis elegans cilia
    Serwas D., Dammermann A. (2015)
    Methods Cell Biol. 129:341-67 (abstract)

    A Structural Basis for How Motile Cilia Beat
    Satir P., Heuser T., Sale W.S (2014)
    BioScience 64(12):1073-83 (abstract)

    A dual role for autophagy in a murine model of lung cancer
    Rao S., Tortola L., Perlot T., Wirnsberger G., Novatchkova M., Nitsch R., Sykacek P., Frank L., Schramek D., Komnenovic V., Sigl V., Aumayr K., Schmauss G., Fellner N., Handschuh S., Glösmann M., Pasierbek P., Schlederer M., Resch G.P., Ma Y. (2014)
    Nature Communications 5:3056 (abstract)

    Electron Tomography and Simulation of Baculovirus Actin Comet Tails Support a Tethered Filament Model of Pathogen Propulsion
    Mueller J., Pfanzelter J., Winkler C., Narita A., Le Clainche C., Nemethova M., Carlier M., Maeda Y., Welch M.D., Ohkawa T., Schmeiser C., Resch G.P., Small J.V. (2014)
    PLoS Biology 12(1):e1001765 (abstract)

    Membrane deformation and scission by the HSV-1 nuclear egress complex
    Bigalke J.M., Heuser T., Nicastro D., Heldwein E.E. (2014)
    Nat Commun 5:4131 (abstract)

    Mechanosensing through focal adhesion-anchored intermediate filaments
    Gregor M., Osmanagic-Myers S., Burgstaller G., Wolfram M., Fischer I., Walko G., Resch G.P., Jörgl A., Herrmann H., Wiche G. (2014)
    FASEB J. 28(2):715-29 (abstract)


    Assembly mechanism of Trypanosoma brucei BILBO1, a multidomain cytoskeletal protein
    Vidilaseris K., Shimanovskaya E., Esson H.J., Morriswood B., Dong G. (2014)
    J Biol Chem. 289(34):23870-81 (abstract)

    Characterization of a DNA exit gate in the human cohesin ring
    Huis in ’t Veld P.J., Herzog F., Ladurner R., Davidson I.F., Piric S., Kreidl E., Bhaskara V., Aebersold R., Peters J.M. (2014)
    Science Vol. 346(6212):968-972 (abstract)

    The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells
    Jurkin J., Henkel T., Nielsen A.F., Minnich M., Popow J., Kaufmann T., Heindl K., Hoffmann T., Busslinger M., Martinez J. (2014)
    EMBO J. 33(24):2922-36. (abstract)


    Non-peer reviewed plublications

    Freeze Substitution of Trypanosoma brucei
    Harald K., Schmidt K., Leunissen J., Resch G.P. (2014)
    Leica Science Lab (link)

    Protein-mediated transformation of lipid vesicles into tubular networks
    Simunovic M., Mim C., Marlovic T.C., Resch G., Unger V.M., Voth G.A. (2013)
    Biophys J. 105(3):711-9 (abstract)

    Identification of Arabidopsis Meiotic Cyclins Reveals Functional Diversification among Plant Cyclin Genes
    Bulankova P., Akimcheva S., Fellner N., Riha K. (2013)
    PLoS Genet. 9(5):e1003508 (abstract)

    An Iron-Rich Organelle in the Cuticular Plate of Avian Hair Cells
    Lauwers M., Pichler P., Edelman N.B., Resch G.P., Ushakova L., Salzer M.C., Heyers D., Saunders M., Shaw J., Keays D.A. (2013)
    Current Biology 23(10):924-9 (abstract)


    Epidermal keratinocytes form a functional skin barrier in the absence of Atg7 dependent autophagy
    Rossiter H., König U., Barresi C., Buchberger M., Ghannadan M., Zhang C.F., Mlitz V., Gmeiner R., Sukseree S., Födinger D., Eckhart L., Tschachler E.J. (2013)
    Dermatol Sci. 2013 Jul;71(1):67-75. (abstract)

    Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle
    Pickl-Herk A., Luque D., Vives-Adrián L., Querol-Audí J., Garriga D., Trus B.L., Verdaguer N., Blaas D., Castón J.R. (2013)
    Proc Natl Acad Sci U S A. 110(50):20063-8. (abstract)

    Human rhinovirus subviral a particle binds to lipid membranes over a twofold axis of icosahedral symmetry
    Kumar M., Blaas D. (2013)
    J Virol. 87(20):11309-12. (abstract)

    Viral uncoating is directional: exit of the genomic RNA in a common cold virus starts with the poly-(A) tail at the 3'-end
    Harutyunyan S., Kumar M., Sedivy A., Subirats X., Kowalski H., Köhler G., Blaas D. (2013)
    PLoS Pathog. 9(4):e1003270. (abstract)


    Non-peer reviewed plublications

    Substitutes for Uranyl Acetate in TEM Thin Section Post-Staining
    Fellner N., Brandstetter M., Trimmel K., Resch G.P. (2013)
    Leica Science Lab (link)



    The transcription factor c-Jun protects against sustained hepatic endoplasmic reticulum stress thereby promoting hepatocyte survival
    Fuest M., Willim K., Macnelly S., Fellner N., Resch G.P., Blum H.E., Hasselblatt P. (2012)
    Hepatology 55(2):408-18. (abstract)

    Actin branching in the initiation and maintenance of lamellipodia
    Vinzenz M., Nemethova M., Schur F., Mueller J., Narita A., Urban E., Winkler C., Schmeiser C., Koestler S.A., Rottner K., Resch G.P., Maeda Y., Small J.V. (2012)
    J Cell Sci. 125(Pt 11):2775-85. (abstract)

    Optimisation of multiple W/O/W nanoemulsions for dermal delivery of aciclovir
    Schwarz J.C., Klang V., Karall S., Mahrhauser D., Resch G.P., Valenta C. (2012)
    Int J Pharm 435(1):69-75. (abstract)

    Nanocarriers for dermal drug delivery: Influence of preparation method, carrier type and rheological properties
    Schwarz J.C., Weixelbaum,A., Pagitsch,E., Löw,M., Resch,G.P., Valenta,C. (2012)
    Int J Pharm 437(1-2):83-8. (abstract)


    SAS-6 coiled-coil structure and interaction with SAS-5 suggest a regulatory mechanism in C. elegans centriole assembly
    Qiao R., Cabral G., Lettman M.M., Dammermann A., Dong G. (2012)
    EMBO J. 31(22): 4334–4347. (abstract)


    Thomas Heuser

    Thomas Heuser

    Thomas is the head of the EM Facility. His background is in cryo-electron microscopy, cryo-electron tomography and 3D image processing by sub-tomogram averaging.

    Core Facility Head
    IMBA-GMI / 4.73.02

    Marlene Brandstetter

    Marlene Brandstetter

    Marlene is responsible for projects that involve high pressure freezing and freeze substitution, glycerol spraying/low angle rotary shadowing, negative staining and cryo - ultramicrotomy.

    Electron Microscopy Specialist
    IMBA-GMI / 4.74.04

    Nicole Fellner

    Nicole Fellner

    Nicole is responsible for the conventional chemical fixation, embedding of cells / tissues, the FEI Morgagni transmission electron microscope and the Hitachi tabletop scan. electron microsope.

    Electron Microscopy Specialist
    IMBA-GMI / 4.74.04

    Sonja Jacob

    Sonja Jacob

    Sonja is responsible for projects with electron tomography, image processing, video creation / modelling of the collected data. She has experience in neg. staining / producing support films for grids.

    Electron Microscopy Specialist
    IMBA-GMI / 4.74.04

    Katharina Keuenhof

    Katharina Keuenhof

    IMBA-GMI / 4.74.04

    Harald Kotisch

    Harald Kotisch

    Harald is responsible for the T20 electron microscope, high pressure freezing, freeze substitution and freeze fracturing. He is supporting users in immuno electron microscopy and cryo – microtomy.

    Electron Microscopy Specialist
    IMBA-GMI / 4.74.04

    Günter Resch was responsible for establishing the electron microscopy facility at IMP/IMBA and was also the head of this Facility from 2006 to 2011. Later, he led the transfer of the facility into the CSF, where he was facility head until February 2014. He is an expert in cryo-electron microscopy, electron tomography, negative staining and rotary shadowing. Amongst other things, Günter was in charge of the FEI Tecnai Polara cryo-TEM and he was working on the development of new technologies. He has now moved on to his own company Nexperion, offering software, training, and consulting services for electron microscopy.


    • Wohlwend HPF Compact 01 high pressure freezer (IMBA / Room 4.73.04)
    • Leica EMPact high pressure freezer (IMBA / Room 4.73.04)
    • 2 Leica AFS A and Leica AFS II automatic freeze substitution devices (IMBA / Room 4.73.04)