Laboratory of Advanced Electron Microscopy

Institute of Scientific Instruments of the Czech Academy of Sciences

About us

The Laboratory of Advanced Electron Microscopy was created by combining several research groups at the Institute of Scientific Institute of CAS:

The main task of the laboratory is to provide basic research and services in the field of advanced electron microscopy techniques with a focus on applications in the fields of biology, chemistry and soft matter.

The main fields

  • cryo-SEM
  • quantitative STEM imaging and analysis
  • Raman microscopy and spectroscopy, including Raman tweezers
  • correlative imaging SEM/cathodoluminescence/Raman microscopy
  • cryo sample preparation for EM


Electron microscopy

  • SEM Magellan 400/L (ThermoFisher)
    • cryo-stage with adapter VCT100 (Leica microsystems) with optional extension to cooling down to -30K using liquid Helium
    • EDX detector Octane (EDAX)
    • CL detector MonoCL4+ (Gatan)
    • CL detector SPARC (Delmic)
  • High-pressure-freezer EM ICE (Leica microsystems)
    • Device enabling cutting-edge method of fixation of biological samples using freezing under high pressure, so-called high-pressure freezing. This type of freezing forms vitrified ice, which, unlike crystalline ice, does not damage the cells and even enables fixation of bigger samples.
  • Freeze-substitution unit EM AFS2 (Leica microsystems)
    • Freeze substitution unit enabling transition of biological samples from cryo to room temperature electron microscopy.
  • Cryo-vacuum chamber ACE600 (Leica microsystems)
    • Cryo sample preparation chamber enabling freeze fracturing and etching together with coating by evaporated carbon or metal sputtering (e.g. Pt, Au, Au/Pd, Cr, W, Ir).
  • Cryo-vacuum chamber BAF060 (Leica microsystems)
    • Cryo sample preparation chamber enabling coating the surface by evaporated C or Pt/C under high vacuum with possibilities of angle tilt and rotation during the evaporation. This method of metal coating offers one of the finest surface treatments for highlighting the ultrastructure of samples.

Raman microscopy

  • inVia (Renishaw)
    • instrument for analysis of microbial cells and their response to external stimuli based on Raman-fingerprint
  • Raman tweezers
    • instrument enabling trapping, sorting and analysis of single cells based on Ramman signal

Virtual 3D tour to laboratories


  • Monikh F.A. et al: Engineered Nanoselenium Supplemented Fish Diet: Toxicity Comparison with Ionic Selenium and Stability against Particle Dissolution, Aggregation and Release. Environmental Science: Nano 7 (2020), 2325-2336.
  • Pernicova I. et al: Introducing the Newly Isolated Bacterium Aneurinibacillus sp. H1 as an Auspicious Thermophilic Producer of Various Polyhydroxyalkanoates (PHA) Copolymers–1. Isolation and Characterization of the Bacterium. Polymers 12 (2020), 1235.
  • Sedlacek P. et al: Introducing the Newly Isolated Bacterium Aneurinibacillus sp. H1 as an Auspicious Thermophilic Producer of Various Polyhydroxyalkanoates (PHA) Copolymers–2. Material Study on the Produced Copolymers. Polymers 12 (2020), 1298.
  • Knötigova P.T. et al: Application of Advanced Microscopic Methods to Study the Interaction of Carboxylated Fluorescent Nanodiamonds with Membrane Structures in THP-1 Cells: Activation of Inflammasome NLRP3 as the Result of Lysosome Destabilization. Molecular Pharmaceutics 16 (2019), 3441-3451.
  • Hrubanova K. et al: The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm. Micron 110 (2018), 28-35.
Quantitative STEM/BSE imaging
  • Skoupy R. et al: Nanoscale estimation of coating thickness on substrates via standardless BSE detector calibration. Nanomaterials 10 (2020), 332.
  • Skoupy R. et al: Quantitative STEM imaging of electron beam induced mass loss of epoxy resin sections. Ultramicroscopy 202 (2019), 44-50.
  • Slouf M. et al: Relations between morphology and micromechanical properties of alpha, beta and gamma phases of iPP. Polymer Testing 67 (2018), 522-532.
Correlative Raman-SEM imaging
  • Sedlacek P. et al: What keeps polyhydroxyalkanoates in bacterial cells amorphous? A derivation from stress exposure experiments. Applied Microbiology and Biotechnology 103 (2019), 1905-1917.
  • Hrubanova K. et al: Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy. Sensors 18 (2018), 4089.
  • Obruca S. et al: The presence of PHB granules in cytoplasm protects non-halophilic bacterial cells against the harmful impact of hypertonic environments. New Biotechnology 39 (2017), 68-80.


Laboratory of advanced electron microscopy
Institute of Scientific Instruments of the CAS
The Czech Academy of Sciences
Královopolská 147
CZ-61264 Brno
Czech Republic

VAT number: CZ68081731

Personal contacts:

  • Tomas Radlicka (head of the laboratory)
    phone: (+420) 541 514 294
  • Vladislav Krzyzanek (electron microscopy)
    phone: (+420) 541 514 302
  • Ota Samek (Raman spectroscopy)
    phone: (+420) 541 514 284