Services & Facilities

The Electron Microscopy (EM) Facility provides resources, technology and expertise for studying the ultrastructure of cryo-immobilized and chemically fixed biological samples. Complex projects can be undertaken in collaboration with the facility. We are also developing technologies in electron tomography, correlative light/electron microscopy (CLEM) and scanning electron microscopy (SEM).

As a member of the Biopolis Dresden Imaging Platform (BioDIP), the EM facility is open not only to MPI-CBG scientists but to the Dresden Biopolis.


Sample preparation for electron microscopy

  • Sample preparation for cryo-immobilization (High-pressure freezing, Plunge freezing), or chemical fixation, including microwave processing
  • Sectioning: ultrathin, semi-thin, serial sections, cryo-sections (Tokuyasu)
  • Positive contrasting (pre- or post-embedding) and negative staining
  • Immuno-labelling/staining (as pre-embedding or labeling on plastic- and cryo-sections)

The EM facility has established protocols that maximize the preservation of morphology at the EM level for each of the major model system used at MPI-CBG (cultured cells, C. elegans, Drosophila, mouse, zebrafish ...). Routine immuno-localization techniques for popular antigens such as GFP are also established. However, the best sample fixation and preparation techniques may differ for different antigens and antibodies and thus continuous development is required. We also have protocols for various Light/Electron microscopy correlative approaches.


  • Data acquisition in transmission electron microscopy (TEM), cryoTEM or SEM
  • Electron tomography (3D imaging)
  • Correlative light electron microscopy/tomography (CLEM)
  • Serial block-face scanning electron microscopy (SBF-SEM)

In addition to image acquisition, the EM facility provides data storage and image-processing support (registration, 3D reconstruction, image segmentation).


  • Provision of EM-specified chemicals and supplies for users
  • Support and training in the methods listed in “Service” above and more (e.g. grid preparation…)
  • Access to the state-of-the-art equipment of the facility
  • Training and support in (cryo)ultramicrotome and electron microscope usage
  • Support and assistance in cell morphology, ultrastructure and data interpretation
  • Basic training courses for PhD-students (Dresden International PhD Program)
  • Basic and advanced training in electron tomography (annual international workshop)

Technology development

The EM facility is actively involved in the development of new technologies in EM: In 3-dimensional electron microscopy (3DEM), like can be obtained by electron tomography, the segmentation of structures of interest in the 3D space is a major challenge. We have developed publicly available software and reference EM datasets, for the automatic tracing of microtubules in electron tomography (Weber et al., 2012). This software can be evaluated on our microtubule segmentation portal: We have also been developing new approaches for registration of serial tomography sections. Likewise, the EM facility has been developing multiple correlative light/electron microscopy (CLEM) approaches (Gibson et al., 2014)



  • FEI Titan Halo FEG cryoTEM (300kV) + Gatan Quantum LS GIF & K2-summit direct-detection camera
  • FEI Tecnai F30 FEG TEM (300kV) + Axial Gatan US1000 CCD camera (2k)
  • FEI Tecnai 12 TEM (120kV) + Axial TVIPS CCD camera (2k)
  • FEI Morgagni TEM (100kV) + Side-entry Olympus Morada  CCD Camera (11Mpixels)
  • Electron tomography acquisition software (on Tecnai 12, Titan Halo, Tecnai F30), single particle EPU software (Titan Halo)


  • FEI Magellan 400 SEM + Gatan 3ViewXP2  microtome for SBF-SEM imaging


  • Zeiss Axioplan2 wide-field fluorescence microscope for CLEM, plus access to LM facility (http:// microscopes

Sample preparation

  • Leica UC6/FC6 ultracryomicrotome
  • Leica UCT ultramicrotomes (3 units)
  • Leica Automatic Freeze Substitution units (AFS and AFS2)
  • Leica  EM GP grid plunger
  • Leica EMPACT2/RTS high-pressure freezer
  • Baltec HPM-010 high-pressure freezer
  • Pelco Biowave Pro microwave system for sample preparation
  • Baltec MED-020 high-vacuum coating system (carbon coating and glow discharge)

Image processing

  • 3 dedicated workstations with GPUs for image processing, 3D reconstruction and segmentation