Central Facility for Microscopy

Light microscopy and electron microscopy are excellent high resolution tools to investigate the adhesion and invasion mechanisms of pathogenic bacteria. High resolution electron microscopy permits to examine and unravel pathogenicity mechanisms on a morphological basis.ZEIM offers equipment and highly sophisticated expertise for the preparation and observation of biological samples.

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Our Expertise

The facility provides access to several fluorescence microscopes (FM), confocal microscopes (CLSM), two transmission electron microscopes (TEM), and a high-resolution field emission scanning electron microscope (FESEM) in addition to the peripheral preparation equipment.

The ZEIM team cooperates with the customer to establish a tailored preparation protocol and imaging technique/s to select the appropriate methodology for each research project. ZEIM has a portfolio of different methods available for preparing biological or material samples for light and electron microscopy. 

The outstanding expertise in the preparation of biological samples for high quality imaging is a key strength of our EM service. The morphological analysis from new isolated microorganisms and bacteriophages is another. Furthermore, ZEIM offers to perform infection experiments with pathogenic bacteria on cell lines with subsequent preparation of samples, image acquisition and followed by analysis for publications. 

We provide support and assistance for imaging with a fluorescence or confocal microscope and a tailored training to the customers’ needs. Besides classical fluorescence labeling studies, double immuno labeling for discriminating between surface adhesion and intracellular uptake of bacterial pathogens are well-established methods in our facility, which can be provided on demand. 

Transmission Electron Microscopy (TEM)

Besides negative-staining for bacteria, bacteriophages or vesicles, representing a rather fast method in EM, a portfolio of different embedding schemes are available. This includes low temperature embedding and high pressure freezing with freeze substitution and subsequent analysis of samples in ultrathin sections via TEM. ZEIM has also experience in performing immuno cytochemical stainings for detecting pathogenicity factors with the help of antibodies and gold nanoparticles in eukaryotic cells or bacteria.


  • Transmission electron microscope Zeiss Libra120 Plus EFTEM
  • Transmission electron microscope Zeiss TEM910
  • Ultramicrotome Reichert Ultracut S, 2x
  • High Pressure Freezer Leica EM-Pact 1
  • Freeze substitution Leica EM AFS, Reichert-Jung CS Auto
  • Coating Unit Bal-Tec MED 020

    Field Emission Scanning Electron Microscopy (FESEM)

    For high-resolution FESEM studies standard protocols have been established which should result in a first satisfying preparation of samples to be investigated. This way infection processes and surface structures can be precisely visualized. However, new preparation methods will be customized and established if needed for special experiments. Similar to TEM, FESEM can be coupled with immuno cytometry to select your targets of interest.


    • Field emission scanning electron microscope Zeiss Merlin with Atlas, STEM Detector, EsB-Detector for material contrast, Shuttle&Find for CLEM (correlative light- and electron microscopy), Oxford EDX Aztec with X-Max Detector
    • Critical-Point Drying Leica EM  CPD300, Bal-Tec CPD 030
    • Sputter Coater Bal-Tec SCD 500

    Fluorescence (FM) and confocal laser-scanning microscopy (CLSM)

    FM/CLSM offer the possibilities to visualize selectively stained compartments of your cells. Thereby staining is achieved by various means including fluorescent dyes, fluorescent proteins or fluorescently labeled antibodies. The big advantage towards EM: You can visualize both live and fixed specimen. In case of three-dimensional structures CLSM is the microscope of choice since it allows acquiring optical sections, which can be reconstructed to 3D volumes afterwards with according software, which is available in ZEIM. 


    • Zeiss Axio Imager A2
    • Zeiss Axio Imager A1
    • Zeiss Axio Observer Z1
    • Zeiss Imager Z2
    • Zeiss Axiovert 100
    • Zeiss Axiovert 200M
    • Leica SP5 upright confocal laser-scanning microscope 
    • Leica SP5 inverse confocal laser-scanning microscope

    Transmission Electron Microscopy

    Fluorescence Microscopy

    Field Emission Scanning Electron Microscopy


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