Electron Microscopy

To see what no one has seen before

Whether you are interested in learning how to do electron microscopy (EM) yourself or prefer us to do EM for you – we can help! We offer a wide variety of preparation and visualization techniques for biological samples ranging from standard methods to cutting-edge cryo-EM for high-resolution 2D or 3D imaging. We also provide a basic scanning EM service to visualize surface structures of biological samples.

Need EM of a biological sample? Want to learn how to do EM yourself? Interested in learning more about our EM services? Contact us or visit our Info Hub

VBCF EM Info Hub

SERVICES

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Electron Microscopy Training
User training at Electron Microscopy Facility

Electron microscopy training and infrastructure usage

Infrastructure users receive thorough training in the techniques/instruments they are interested in. All our instruments - from basic sample preparation equipment to our most sophisticated electron microscopes - are available to users 24/7. We further support our users in planning, execution, and interpretation of all EM-related experiments and regularly organize EM workshops and microscopy training.

Electron Microscopy Facility
From fly heads...
Electron Microscopy Facility
... to organelles.

EM service to visualize biological samples

We can do EM for you and have experience in the visualization of the following samples:

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

 

We are also very interested in establishing protocols for new samples.

Electron Microscopy Facility
Ultra-thin sectioning of resin-embedded samples

Sample preparation techniques

We offer a wide variety of different sample preparation techniques to ensure optimal preservation of your specimen:

  • 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 compartments
  • Plunge freezing (immersion freezing) for cryo-EM (“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
  • Sample preparation for SEM (scanning electron microscopy) to study surface structures
Electron Microscopy Facility
Stunning results from EM imaging techniques

Imaging techniques

We offer the following EM imaging techniques to visualize your samples:

  • Basic Scanning Electron Microscopy (SEM) to visualize the surface topology of samples
  • Transmission Electron Microscopy (TEM) to examine ultrastructure
    • Conventional 2D EM
    • Tomography - 3D EM
    • Cryo-EM (single particle and cryo-electron tomography)
  • Correlative Microscopy

EQUIPMENT

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The 200 kV Thermo Fisher Scientific Glacios is a cryo-TEM for high-throughput sample screening and fully automated data recording. The Glacios is exclusively used for cryo-EM (single particle and cryo-tomography). Watch a time-lapse video of the installation below.

Please click here for more information.

 

The FEI Morgagni 268D is a robust and easy-to-use 100 kV TEM equipped with an Mega View III CCD (Olympus-SIS) camera. The microscope is easy to use and tailored for sample screening and routine visualization of:

  • Negatively-stained samples
  • Rotary-shadowed samples
  • Ultrathin sections
  • Immunolabelled samples

Please click here for more information.

The FEI Tecnai G2 20 (T20) is a 200 kV TEM equipped with an Eagle 4k HS camera and can be used for 2D and 3D (tomography) visualization of:

  • Negatively-stained samples (screening and automated data recording)
  • Rotary-shadowed samples
  • Room temperature tomography of resin-embedded samples

Please click here for more information.

This is a robust and easy-to-use table top scanning electron microscope for visualization of surface properties 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 can be frozen in liquid nitrogen. Alternatively, it can be chemically fixed and critical point-dried.

Additionally, we offer the following equipment and techniques:

  • Immersion and slam freezing
  • High vacuum evaporators and sputter coaters
  • High pressure freezing and freeze substitution
  • Sectioning
  • Embedding
  • Sample preparation for scanning electron microscopy
  • Ancillary equipment
  • Light microscopes

Please click here for more information.

 

Installation of GLACIOS at VBCF Electron Microscopy Facility

VBCF ELECTRON MICROSCOPY TEAM

©Zsolt Marton/VBCF

SCIENTIFIC CONTRIBUTIONS

A rapid freezing method to determine tissue layer thickness in drought-stressed leaves. Zekri MA, Leimhofer C, Drexler N, Lang I. Journal of Microscopy, Vol.297, Issue 3, 316-324 (2025).

Effects of small extracellular vesicles derived from normoxia- and hypoxia-treated prostate cancer cells on the submandibular salivary gland epithelium in vitro. Špilak A, Brachner A, Friedl HP, Klepe A, Nöhammer C, Neuhaus W. Tissue Barrier 13(1):e2347062 (2025)

In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-ET. Klumpe S, Senti KA, Beck F, Sachweh J, Hampoelz B, Ronchi P, Oorschot V, Brandstetter M, Yeroslaviz A, Briggs JAG, Brennecke J, Beck M, Plitzko JM. Cell, Volume 188, Issue 8, 2094-2110.e18, ISSN 0092-8674 (2025).

Comprehensive phenotyping combined with multi-omics of Salmonella Infantis and its H2S negative variant - resolving adaption mechanisms to environmental changes. Drauch V, Palmieri N, Spergser J, Hummel K, Brandstetter M, Kornschober C, Hess M, Hess C. Food Microbiology, Volume 129, ISSN 0740-0020, 104744 (2025).

Conditioning period impacts the morphology and proliferative effect of extracellular vesicles derived from rat adipose tissue derived stromal cell. Borger  A, Haertinger M,  Millesi F, Semmler L, Supper P, Stadlmayr S, Rad A, Radtke C . Journal of  Nanobiotechnology  23, 164 (2025).

Self–entrapment of Azotobacter vinelandii cultures by gelation of their exopolysaccharides: A way towards next–generation bioinoculants,
Carbohydrate Polymers. Černayová D, Súkeník M, Obruča S, Smilek J, Kalina M, Mrázová K, Hrubanová K, Krzyžánek V, Sedláček P. Carbohydrate Polymers, Volume 360, 123607 (2025).

PHLPP2 is a pseudophosphatase that lost activity in the metazoan ancestor. Husremović T, Meier V, Piëch L, Siess KM, Antonioli S, Grishkovskaya I, Kircheva N, Angelova SE, Wenzl K, Brandstätter A, Veis J, Miočić-Stošić F, Anrather D, Hartl M, L. Truebestein L, Cerron-Alvan LM, Leeb M, Žagrović B, Hann S, Bock C, Ogris E, Dudev T, Irwin NAT, Haselbach D, Leonard TA. Proc. Natl. Acad. Sci. U.S.A. 122 (14) e2417218122 (2025).

A conserved role for centriolar satellites in translation of centrosomal and ciliary proteins. Pachinger C, Dobbelaere J, Rumpf-Kienzl C, Raina S, Garcia-Baucells J, Sarantseva M, Brauneis A, Dammermann A. J Cell Biol 224 (8): e202408042 (2025).

ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213.Ahel J, Balci A, Faas V, Grabarczyk DB, Harmo R, Squair DR, Zhang J, Roitinger E, Lamoliatte F, Mathur S, Deszcz L, Bell LE, Lehner A, Williams TL, Sowar H, Meinhart A, Wood NT, Clausen T, Virdee S, Fletcher AJ. Nat Commun. 2025 May 13;16(1):4414 (2025).

Morphological and molecular characterization of Stomachicola muraenesocis Yamaguti, 1934 (Digenea: Hemiuridae) from the daggertooth pike conger Muraenesox cinereus (Forsskål). Ghanei-Motlagh R., Hernández-Orts J.S., Fast M.D., Whyte S.K., El-Matbouli M., Saleh M. Parasitology , Volume 151 , Issue 1 , January 2024 , pp. 24 - 44

Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins. Pultar M, Oesterreicher J, Hartmann J, Weigl M, Diendorfer A,  Schimek K, Schädl B, Heuser T, Brandstetter M, Grillari J, Sykacek P, Hackl M, Holnthoner W. (2024) Journal of Extracellular Biology Vol3, Issue 1, e134 (2024).

Structural basis of human U5 snRNP late biogenesis and recycling.Riabov Bassat D, Visanpattanasin S, Vorländer M.K., Fin L, Phillips AW, Plaschka C. Nat Struct Mol Biol 31,747-751(2024).

Generation of complex bone marrow organoids from human induced pluripotent stem cells.  Frenz-Wiessner S, Fairley SD, Buser M, Goek I, Salewskij K, Jonsson G, Illig D, Putlitz B, Petersheim D, Li Y, Chen P, Kalauz M, Conca R, Sterr M, Geuder J, Mizoguchi Y, Megens RTA, Linder MI, Kotlarz D, Rudelius M, Penninger JM, Marr C, Klein C. Nature Methods 21,868-881(2024).

Dynamic microvilli sculpt bristles at nanometric scale. Ikeda KN, Belevich I, Zelaya-Lainez L, Orel L, Füssl J, Gumulec J, Hellmich C, Jokitalo E, Raible F (2024)  Nat Commun 15, 3733 (2024).

Correlative light and electron microscopy at defined cell cycle stages in a controlled environment. Bragulat-Teixidor H. and Otsuka S. (2024) Methods in Cell Biology Vol 187, 73-97 (2024).

Staying on track - Keeping things running in a high-end scientific imaging core facility. Renaud O, Aulner N, Salles A, Halidi N, Brunstein M, Mallet A, Aumayr K, Terjung S, Levy D, Lippens S, Verbavatz JM, Heuser T, Santarella-Mellwig R, Tinevez JY, Woller T, Botzki A, Cawthorne C, Core4Life Consortium, Munck S. J Microsc Vol 294 Issue 3 276-294 (2024). 

Mechanism for the initiation of spliceosome disassembly. Vorländer MK, Rothe P, Kleifeld J, Cormack ED, Veleti L, Riabov-Bassat D, Fin L, Phillips AW, Cochella L, Plaschka C (2024) Nature 632, 443–450 (2024). 

Docking a flexible basket onto the core of the nuclear pore complex. Stankunas E, Köhler A. (2024) Nat Cell Biol 26, 1504-1519 (2024). 

Tau fibrils evade autophagy by excessive p62 coating and TAX1BP1 exclusion. Ferrari L, Bauer B, Qiu Y, Schuschnig M, Klotz S, Anrather D, Juretschke T, Beli P, Gelpi E, Martens S. Sci. Adv.Vol10,Nr.24, eadm8449 (2024).

The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S. EMBO Rep. 25(7):3137-3159 (2024).

Seipin governs phosphatidic acid homeostasis at the inner nuclear membrane. Romanauska A, Stankunas E, Schuldiner M, Koehler A. Nature Communications 15 10486 (2024).

 

Adeno-Associated Virus-like Particles' Response to pH Changes as Revealed by nES-DMA. Zoratto S, Heuser T, Friedbacher G, Pletzenauer R, Graninger M, Marchetti-Deschmann M, Weiss VU. Viruses. 2023 Jun 13;15(6):1361.

Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Bodrug T, Welsh KA, Bolhuis DL, Paulаkonis E, Martinez-Chacin RC, Liu B, Pinkin N, Bonacci T, Cui L, Xu P, Roscow  O, Amann SJ, Grishkovskaya I, Emanuele MJ, Harrison JS, Steimel JP, Hahn  KM, Zhang W, Zhong ED, Haselbach D, Brown NG. Nat Struct Mol Biol. 2023 Nov;30(11):1663-1674.

Structural evidence for elastic tethers connecting separating chromosomes in crane-fly spermatocytes. Forer A, Otsuka S. Life Sci Alliance. 2023 Aug 17;6(11):e202302303.

Human serum albumin nanoparticles as a versatile vehicle for targeted delivery of antibiotics to combat bacterial infections. Skoll K, Palmetzhofer J, Lummerstorfer M, Anzengruber M, Gabor F, Wirth M. Nanomedicine: Nanotechnology, Biology and Medicine, Volume 50, 2023, 102685, ISSN 1549-9634.

A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans. Dobbelaere J., Su Y. T., Erdi B., Schleiffer A., Dammermann A. The EMBO Journal 2023 e113616.

Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. Hodáková Z., Grishkovskaya I., Brunner L. H., Bolhuis D.L, Belačić K, Schleiffer A., Kotisch H., Brown N.B., Haselbach D. The EMBO Journal 2023 42:e113348.

Archaeosomes facilitate storage and oral delivery of cannabidiol. Sedlmayr V., Horn C., Wurm D.J., Spadiut O., Quehenberger J. International Journal of Pharmaceutics 2023, Volume 645, 2023, 123434, ISSN 0378-5173.

Lipid saturation controls nuclear envelope function. Romanauska A. & Köhler A. Nat Cell Biol 25, 1290–1302 2023.

Morphological Study of PHA Producing Bacteria. Hrubanova K., Sikorova P., Mrázová K., Nebesarova J., Obruca S., Krzyzanek V.  Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Pages 883–884.

Structure and regulation of the myotonic dystrophy kinase-related Cdc42-binding kinase. Truebestein L, Antonioli S, Waltenberger E, Gehin C, Gavin AC, Leonard TA. Structure, 31,435-446.e4.

Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus. Ghanei-Motlagh R, Fast MD, Groman D, Kumar G, Soliman H, El-Matbouli M, Saleh M. Parasites Vectors 16, 182 (2023).

Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Ehrmann JF, Grabarczyk DB, Heinke M, Deszcz L, Kurzbauer R, Hudecz O, Shulkina A, Gogova R, Meinhart A, Versteeg GA, Clausen T. Science. 2023 379(6637):1117-1123.

Extracellular Vesicles and Particles Modulate Proton Secretion in a Model of Human Parietal Cells. Mistlberger-Reiner A, Sterneder S, Reipert S, Wolske S, Somoza V. ACS Omega. 2023 8(2):2213-2226.

Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle, Fadeev E, Carpaneto Bastos C, Hennenfeind JH, Biller SJ, Sher D, Wietz M, Herndl GJ, microLife 2023, 4, uqac025

mRNA recognition and packaging by the human transcription-export complex. Pacheco-Fiallos B, Vorländer MK, Riabov-Bassat D, Fin L, O'Reilly FJ, Ayala FI, Schellhaas U, Rappsilber J, Plaschka C. Nature. 2023 Apr 5. doi: 10.1038/s41586-023-05904-0. Epub ahead of print.

Aerosol delivered irradiated Escherichia coli confers serotype-independent protection and prevents colibacillosis in young chickens. Paudel S, Hess C, Kamal Abdelhamid M, Lyrakis M, Wijewardana V, Thiga Kangethe R, Cattoli G, Hess M. Vaccine. 2023 41(7):1342-1353.

A molecular network of conserved factors keeps ribosomes dormant in the egg. Leesch F, Lorenzo-Orts L, Pribitzer C, Grishkovskaya I, Roehsner J, Chugunova A, Matzinger M, Roitinger E, Belačić K, Kandolf S, Lin TY, Mechtler K, Meinhart A, Haselbach D, Pauli A. Nature. 2023 613(7945):712-720

Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating—Role of Na+ and K+. Real-Hohn A, Groznica M, Kontaxis G, Zhu R, Chaves OA, Vazquez L, Hinterdorfer P, Kowalski H, Blaas D Viruses. 2023; 15(4):1003.

PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Cikes D, Elsayad K, Sezgin E, Koitai E, Torma F, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Miranda ND, Taylor A, Grapentine S, Al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov AV, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. Nat Metab. 2023 5(3):495-515.

Fundamental insights in early-stage inclusion body formation. Kopp J, Bayer B, Slouka C, Striedner G, Dürkop M & Spadiut O (2023) Microbial Biotechnology, 16, 893–900.