Vladislav Krzyžánek
Institute of Scientific Instruments · Czech Academy of Sciences

Vladislav Krzyžánek, Ph.D.

Senior researcher at the Institute of Scientific Instruments of the Czech Academy of Sciences in Brno, and head of the Microscopy for Biomedicine group. President of the European Microscopy Society for 2024–2028.

krzyzanek@isibrno.cz ORCID ↗ Web of Science ↗ Google Scholar ↗ ResearchGate ↗ LinkedIn ↗ Research group ↗
Research

Primary research

I am a specialist in quantitative electron microscopy, cryo-EM and 4D-STEM imaging, with more than twenty-five years of research experience across Brno University of Technology, the University of Münster and the Institute of Scientific Instruments in Brno. My work bridges instrumentation with quantitative bioimaging: low-dose cryo-EM, phase-contrast, quantitative annular dark-field mass determination, and Monte Carlo simulation of electron–matter interaction.

I am the principal developer of MASDET, for mass determination from dark-field STEM data, and MONCA, for Monte Carlo simulation of electron scattering.

Quantitative imaging by STEM

Mass-thickness measurement by electron scattering, and 4D-STEM.

Low-temperature scanning electron microscopy

Cryo-SEM of hydrated and beam-sensitive specimens.

Correlation of signals in electron microscopy

Combining detection channels for richer, quantitative information.

Career

Positions and education

Professional experience

Education

Community

Roles and service

Positions of service

  • since 2024
    President, European Microscopy SocietyOver 5,500 individual members and 25 national societies across Europe
  • since 2024
    Editorial board, Methods in Microscopy
  • since 2022
    Member of the Board of the Institute of Scientific Instruments of the CAS
  • since 2021
    Member of the Council for International Relations of the CAS
  • 2019 – 2024
    President, Czechoslovak Microscopy Society
  • 2017 – 2021
    Evaluation panel P102, Czech Science FoundationVice-chair 2017–2018, chair 2018–2019Member of discipline committee OK1, 2017–2019
2023
Award for merit in the development of microscopy methods
Czechoslovak Microscopy Society

Society membership

Conference organisation

Funding

Projects and lectures

As principal investigator

  • 2023 – 2025
    Advanced cryo-optofluidic platform for correlative light and electron microscopy (CLEM)
    Czech Science Foundation, GA23-07962S
  • 2021 – 2023
    Quantitative low-energy 4D-STEM imaging of beam-sensitive samples
    Czech Science Foundation, GA21-13541S
  • 2017 – 2019
    Quantitative imaging of beam-sensitive samples using correlative signal detection in a cryo-SEM
    Czech Science Foundation, GA17-15451S
  • 2017 – 2018
    Advanced supporting system for combined cryo and in-situ SEM applications
    Technology Agency of the Czech Republic, TG03010046
  • 2014 – 2016
    Quantitative imaging in SEM with elastically scattered electrons
    Czech Science Foundation, GA14-20012S
  • 2008 – 2011
    Mass measurement by electron scattering: nanoanalytics by high-resolution SEM in the transmission mode
    Deutsche Forschungsgemeinschaft, RE782/11 — principal investigator from 2010
  • 2000 – 2001
    Development of a system for molecular mass determination by field-emission SEM
    NATO Science Fellowship Programme
  • 1999 – 2001
    Analysis of 3D objects with imperfect periodicity
    Czech Science Foundation, GA101/99/D077

Other leading roles

  • 2023 – 2028
    Centre of Advanced Electron and Photonic Optics
    Technology Agency of the Czech Republic, TN02000020 — guarantor of the research theme Electron Optics and Detection
  • 2018 – 2022
    Centre of Electron and Photonic Optics
    Technology Agency of the Czech Republic, TN01000008 — executive manager
  • 2018 – 2021
    Scintillation detectors for special use in SEM
    Ministry of Industry and Trade of the Czech Republic, FV30271 — co-principal investigator

Selected invited and plenary lectures

  • 2025
    Unlocking the Power of SEM: Quantitative Imaging and 4D Diffraction Across Disciplines
    Keynote · EMK 2025 & MSC 2025, Istanbul, Turkey
  • 2025
    Cryogenic Electron Microscopy in Life Sciences and Soft Matter
    Invited · 18th Cryogenics IIR Conference, Prague, Czech Republic
  • 2023
    Quantitative STEM imaging
    Invited · Microscopy 2023, Olomouc, Czech Republic
  • 2014
    Scanning Electron Microscopy for Applications in the Life Sciences
    Plenary · 48th Conference of the Polish Society for Histochemistry and Cytochemistry, Wisła, Poland
Teaching

Teaching and supervision

Doctoral supervision

I currently supervise two doctoral students in Physical Engineering and Nanotechnology at the Faculty of Mechanical Engineering, BUT. I am also a registered doctoral supervisor in Biophysics at the Faculty of Science, Masaryk University, and in Biophysical Chemistry at the Faculty of Chemistry, BUT.

Completed doctorates

  • Kamila Hrubanová (2019) — Scanning electron microscopy and its application to sensitive specimens
  • Radim Skoupý (2020) — Quantitative imaging in the scanning electron microscope
  • Kateřina Mrázová (2026) — Electron microscopy for the analysis of microorganisms of importance in food science and biotechnology

Lecturing in university courses

One lecture per semester in each course, occasionally also supervising student seminar work.

  • Advanced Microscopic Methods — Faculty of Science, Masaryk University, since 2019
  • Practical Introduction to Nanotechnology — Faculty of Chemistry, BUT, since 2015
  • Instrumental and Structural Analysis for Medical Applications — Faculty of Chemistry, BUT, since 2021
  • Molecular biophysics and biophysical methods — University of Münster, 2005–2011

Specialist courses

Lecturer, in some of them also in the practical sessions.

  • Biological Specimens in Electron Microscopes — České Budějovice
  • Advanced Methods of Scanning Electron Microscopy — Prague
  • Electron Microscopy and Raman Spectroscopy for Life Sciences Analysis — Brno
Outputs

Software and protected results

MASDET

Software for mass determination by dark-field electron microscopy. Runs under MATLAB or as a standalone program, and converts annular dark-field images into thickness and mass maps.

Method paper ↗MASDET2 abstract ↗

MONCA

MATLAB package for Monte Carlo simulation of electron scattering in thin specimens, in the range 10–200 keV.

Method abstract ↗

Embedding media resistant to beam damage

Embedding media for electron microscopy with enhanced resistance to electron-beam damage, and a method of specimen preparation. With M. Šlouf, A. Strachota, B. Strachota, E. Pavlova and J. Nebesářová.

Czech patent No. 310708 · granted 2026
Industrial Property Office ↗

Sample temperature control assembly

Assembly for controlling specimen temperature in the electron microscope. With R. Skoupý and K. Hrubanová.

Czech utility model No. 32258
Industrial Property Office ↗
Selected outputs

Selected publications

The complete list is available through ORCID and the ASEP database of the Czech Academy of Sciences.

2026

  1. Sikorova P. et al.: Computational methods for automated center determination in electron diffraction patterns. Journal of Applied Crystallography 59 (2026), 845–857.DOI ↗
  2. Pacasova V.-A. et al.: Effect of PHA on viability and stress resilience in Rhodospirillum rubrum. Journal of Applied Microbiology 137 (2026), lxag147.DOI ↗
  3. Fleuriot-Blitman H. et al.: Gene expression analysis reveals distinct PHB depolymerization mechanisms and broader involvement of the PHB cycle in Rhodospirillum rubrum growing on acetate and fructose. Microbial Cell Factories 25 (2026), 72.DOI ↗

2025

  1. Mrazova K. et al.: Enhanced electron microscopy imaging for a detailed structural study of alginate hydrogel containing the encapsulated cells. Carbohydrate Polymers 368 (2025), 124239.DOI ↗
  2. Cernayova D. et al.: Self-entrapment of Azotobacter vinelandii cultures by gelation of their exopolysaccharides: A way towards next-generation bioinoculants. Carbohydrate Polymers 360 (2025), 123607.DOI ↗
  3. Vanickova E. et al.: Ritual Burials in a Prehistoric Mining Shaft in the Krumlov Forest (Czechia). Archaeological and Anthropological Sciences 17 (2025), 146.DOI ↗
  4. Slouf M. et al.: 4D-STEM-in-SEM: Changing an SEM Microscope to a User-friendly Powder Electron Diffractometer. Microscopy and Microanalysis 31 (2025), ozaf045.DOI ↗
  5. Laznicka T. et al.: Assembly for semi-correlation analysis of samples using cryogenic scanning electron microscopy and cryogenic Raman micro-spectroscopy. Measurement Science and Technology 36 (2025), 055903.DOI ↗
  6. Kroupova Z. et al.: Evaluating stress resilience of cyanobacteria through flow cytometry and fluorescent viability assessment. Folia Microbiologica 70 (2025), 205–223.DOI ↗
  7. Jilek Z. et al.: Simulation Study of Low-Dose 4D-STEM Phase Contrast Techniques at the Nanoscale in SEM. Nanomaterials 15 (2025), 70.DOI ↗

2023

  1. Skoupy R. et al.: Robust Local Thickness Estimation of Sub-Micrometer Specimen by 4D-STEM. Small Methods 7 (2023), 2300258.DOI ↗
  2. Mrazova K. et al.: Low Voltage Transmission Electron Microscopy: A Powerful Tool for Ultrastructural Studying of Cyanobacterial Cells. Microorganisms 11 (2023), 888.DOI ↗
  3. Szabova J. et al.: Liposomal form of erlotinib for local inhalation administration and efficiency of its transport to the lungs. International Journal of Pharmaceutics 634 (2023), 122695.DOI ↗

2022

  1. Vancova M. et al.: Cathodoluminescence imaging of cellular structures labeled with luminescent iridium or rhenium complexes at cryogenic temperatures. Scientific Reports 12 (2022), 13432.DOI ↗
  2. Novackova I. et al.: Combination of Hypotonic Lysis and Application of Detergent for Isolation of Polyhydroxyalkanoates from Extremophiles. Polymers 14 (2022), 1761.DOI ↗
  3. Novackova I. et al.: The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions. International Journal of Biological Macromolecules 206 (2022), 977–989.DOI ↗

2021

  1. Hanzelka P. et al.: Low conductive thermal insulation pad with high mechanical stiffness. International Journal of Refrigeration 132 (2021), 92–99.DOI ↗
  2. Slouf M. et al.: High Resolution Powder Electron Diffraction in Scanning Electron Microscopy. Materials 14 (2021), 7550.DOI ↗
  3. Kourilova X. et al.: Biotechnological Conversion of Grape Pomace to Poly(3-hydroxybutyrate) by Moderately Thermophilic Bacterium Tepidimonas taiwanensis. Bioengineering 8 (2021), 141.DOI ↗
  4. Kourilova X. et al.: The First Insight into Polyhydroxyalkanoates Accumulation in Multi-Extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus. Microorganisms 9 (2021), 909.DOI ↗
  5. Slouf M. et al.: Powder Nano-Beam Diffraction in Scanning Electron Microscope: Fast and Simple Method for Analysis of Nanoparticle Crystal Structure. Nanomaterials 11 (2021), 962.DOI ↗
  6. Kizovsky M. et al.: Raman Microspectroscopic Analysis of Selenium Bioaccumulation by Green Alga Chlorella vulgaris. Biosensors 11 (2021), 115.DOI ↗

2020

  1. Trudicova M. et al.: Multiscale experimental evaluation of agarose-based semi-interpenetrating polymer network hydrogels as materials with tunable rheological and transport performance. Polymers 12 (2020), 2561.DOI ↗
  2. 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.DOI ↗
  3. Skoupy R. et al.: Nanoscale estimation of coating thickness on substrates via standardless BSE detector calibration. Nanomaterials 10 (2020), 332.DOI ↗
  4. 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.DOI ↗
  5. 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.DOI ↗

2019

  1. Skoupy R. et al.: Quantitative STEM imaging of electron beam induced mass loss of epoxy resin sections. Ultramicroscopy 202 (2019), 44–50.DOI ↗
  2. Knotigova 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.DOI ↗
  3. Sedlacek P. et al.: PHA granules help bacterial cells to preserve cell integrity when exposed to sudden osmotic imbalances. New Biotechnology 49 (2019), 129–136.DOI ↗
  4. 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.DOI ↗

2018

  1. 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.DOI ↗
  2. Hrubanova K. et al.: The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm. Micron 110 (2018), 28–35.DOI ↗
  3. Kucera D. et al.: Characterization of the promising poly(3-hydroxybutyrate) producing halophilic bacterium Halomonas halophila. Bioresource Technology 256 (2018), 552–556.DOI ↗
  4. Slouf M. et al.: Relations between morphology and micromechanical properties of alpha, beta and gamma phases of iPP. Polymer Testing 67 (2018), 522–532.DOI ↗

2017

  1. 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.DOI ↗

2016

  1. Resch Y. et al.: Molecular, structural and immunological characterization of Der p 18, a chitinase-like house dust mite allergen. PLoS ONE 11 (2016), e0160641.DOI ↗
  2. Obruca S. et al.: Polyhydroxyalkanoates in bacterial cells – more than just storage materials. Materials Science Forum 851 (2016), 20–25.DOI ↗
  3. Obruca S. et al.: How accumulation of poly(3-hydroxybutyrate) helps bacterial cells to survive freezing. PLoS ONE 11 (2016), e0157778.DOI ↗
  4. Mravec F. et al.: Accumulation of PHA granules in Cupriavidus necator as seen by time-resolved confocal fluorescence microscopy. FEMS Microbiology Letters 363 (2016), fnw094.DOI ↗
  5. Tacke S. et al.: A Versatile High-Vacuum Cryo-transfer System for Cryo-microscopy and Analytics. Biophysical Journal 110 (2016), 758–765.DOI ↗
  6. Voberkova S. et al.: Biofilm formation and extracellular polymeric substances (EPS) production by Bacillus subtilis depending on nutritional conditions in the presence of polyester film. Folia Microbiologica 61 (2016), 91–100.DOI ↗
  7. Bok J. et al.: Measurements of current density distribution in shaped e-beam writers. Microelectronic Engineering 149 (2016), 117–124.DOI ↗

2015

  1. Burdikova Z. et al.: Application of advanced light microscopic techniques to gain deeper insights into cheese matrix physico-chemistry. Dairy Science and Technology 95 (2015), 687–700.DOI ↗
  2. Samek O. et al.: Identification of individual biofilm-forming bacterial cells using Raman tweezers. Journal of Biomedical Optics 20 (2015), 051038.DOI ↗
  3. Banerjee S. et al.: Der p 11 is a Major Allergen for House Dust Mite-Allergic Patients Suffering from Atopic Dermatitis. Journal of Investigative Dermatology 135 (2015), 102–109.DOI ↗
  4. Bok J. et al.: Effect of oxidation annealing on optical properties of YAG:Ce single crystals. Optical Materials 46 (2015), 591–595.DOI ↗

2014

  1. Samek O. et al.: Candida parapsilosis biofilm identification by Raman spectroscopy. International Journal of Molecular Sciences 15 (2014), 23924–23935.DOI ↗
  2. Hajduova J. et al.: Structure of polymeric nanoparticles in surfactant-stabilized aqueous dispersions of high-molar-mass hydrophobic graft copolymers. Colloids and Surfaces A: Physicochemical and Engineering Aspects 456 (2014), 10–17.DOI ↗

2013

  1. Bernatova S. et al.: Following the mechanisms of bacteriostatic versus bactericidal action using Raman spectroscopy. Molecules 18 (2013), 13188–13199.DOI ↗

2012

  1. Groscurth S. et al.: Artificial Forisomes Are Ideal Models of Forisome Assembly and Activity That Allow the Development of Technical Devices. Biomacromolecules 13 (2012), 3076–3086.DOI ↗
  2. Hillebrand A. et al.: Down-Regulation of Small Rubber Particle Protein Expression Affects Integrity of Rubber Particles and Rubber Content in Taraxacum brevicorniculatum. PLoS ONE 7 (2012), e41874.DOI ↗
  3. Porizka P. et al.: Application of laser-induced breakdown spectroscopy to the analysis of algal biomass for industrial biotechnology. Spectrochimica Acta Part B: Atomic Spectroscopy 74–75 (2012), 169–176.DOI ↗
  4. Ernst A.M. et al.: Sieve element occlusion (SEO) genes encode structural phloem proteins involved in wound sealing of the phloem. PNAS 109 (2012), E1980–E1989.DOI ↗

2011

  1. Eissenberg J.C. et al.: Drosophila GGA Model: An Ultimate Gateway to GGA Analysis. Traffic 12 (2011), 1821–1838.DOI ↗
  2. Krzyzanek V. et al.: Polyelectrolyte multilayer capsules: Nanostructure and visualisation of nanopores in the wall. Soft Matter 7 (2011), 7034–7041.DOI ↗
  3. Kouyianou K. et al.: The Chlorosome of Chlorobaculum tepidum: size, mass and protein composition revealed by electron microscopy, dynamic light scattering and mass spectrometry-driven proteomics. PROTEOMICS 11 (2011), 2867–2880.DOI ↗
  4. Pfaff M. et al.: Low-energy electron scattering in carbon-based materials analyzed by scanning transmission electron microscopy and its application to sample thickness determination. Journal of Microscopy 243 (2011), 31–39.DOI ↗
  5. Edlmayr J. et al.: Antibodies induced with recombinant VP1 from Human Rhinovirus exhibit cross-neutralization. European Respiratory Journal 37 (2011), 44–52.DOI ↗

2009

  1. Krzyzanek V. et al.: MASDET — A fast and user-friendly multiplatform software for mass determination by dark-field electron microscopy. Journal of Structural Biology 165 (2009), 78–87.DOI ↗

2007

  1. Grote M. et al.: Bundles of hexagonally arranged tubules in timothy grass pollen: Detection of a novel pollen component using anhydrous fixation and image analysis techniques in transmission electron microscopy. Journal of Microscopy 228 (2007), 34–39.DOI ↗
  2. Krzyzanek V. & Reichelt R.: High-Resolution Scanning Electron Microscope for Mass Determination: Progress in the Development of a New Nanoanalytical Tool. Microscopy & Microanalysis 13 (Suppl. 3) (2007), 80–81.DOI ↗

2002

  1. Smarda J. et al.: S-layers on cell walls of cyanobacteria. Micron 33 (2002), 257–277.DOI ↗

2000

  1. Krzyzanek V.: Analysis of continuously distorted quasi-periodic images: Two-dimensional reconstruction of S layers of cyanobacteria. Optical Engineering 39 (2000), 872–878.DOI ↗

1999

  1. Smajs D. et al.: A comparative study of fine structure of cyanobacterial gas vesicles. Algological Studies 94 (1999), 305–316.Link ↗
  2. Smajs D. et al.: New findings of S layers among Cyanobacteria. Algological Studies 94 (1999), 317–332.Link ↗

1997

  1. Rachel R. et al.: II. Fine structure of S-layers. FEMS Microbiology Reviews 20 (1997), 13–23.DOI ↗
Contact

Get in touch

For scientific collaboration, questions about the methods and software described here, or student projects in the research group, please write.

Institute
Institute of Scientific Instruments of the Czech Academy of Sciences
Address
Kralovopolska 147, CZ-61200 Brno, Czech Republic
Phone
+420 541 514 302
E-mail
krzyzanek@isibrno.cz
ORCID
0000-0002-7996-2979
Microscopy for Biomedicine ↗ Institute website ↗ Scopus ↗ European Microscopy Society ↗