Imaging Methods

Imaging Methods

Mgr. Aleš Benda, Ph.D.

Mgr. Aleš Benda, Ph.D. — Laboratory head

About us

IMCF covers three main areas - Optical (fluorescence) microscopyElectron microscopy and  Flow cytometry. We offer our users training on and access to high end instrumentation, plus we provide consulting services on optimal experimental design, sample preparation, data acquisition, analysis and interpretation of the obtained results. We also organise microscopic courses.


Link to national and international research infrastructures and consortia


IMCF BIOCEV is part of Czech-Bioimaging infrastructure, that provides an open access to a wide range of imaging technologies and expertise to all scientist in the Czech Republic and from abroad by a unified and coordinated logistics approach.  

A part of our running cost for optical and electron microscopy is currently covered from Czech-BioImaging large infrastructure project LM2015062, to get the discounted fee please acknowledge this project as well. Thank you!

Czech-Bioimaging Access Procedure

Application form for CzBI open access


IMCF BIOCEV is part of the Prague node of the Euro-BioImaging infrastructure, that provides open access, services and training to a broad range of state-of-art biological and medical imaging technologies. 

Euro-Bioimaging Access Procedure 

Application form for EUBI open access 



We acknowledge Imaging Methods Core Facility at BIOCEV, institution supported by the MEYS CR (Large RI Project LM2018129 Czech-BioImaging) and ERDF (project No. CZ.02.1.01/0.0/0.0/16_013/0001775) for their support with obtaining imaging data presented in this paper.


We acknowledge the Imaging Methods Core Facility at BIOCEV for their support with obtaining flow cytometry data presented in this paper.


Useful links



We offer services in  Optical (fluorescence) microscopyElectron microscopy and  Flow cytometry with optional help in subsequent data analysis

How to access our services

Information for new users:

  1. Contact us
    • If you want to use our services, do not hesitate to call or email anyone from our team

  2. Meet us for the first time
    • A meeting will be scheduled for you to meet with IMCF staff members. Here we get to discuss your project and see how we can best assist you.
    • Registration to Czech Bioimaging Open Access is part of the first meeting as well. 

  3. Register to booking system
    • In order to keep track of the instrument usage we use booking system. It also allows you to readily manage your reservations. Steps for registration are outlined here.

  4. Attend theoretical and practical training
    • Few of our instruments are simply push button systems, and as such we do our best to help you understand fundamentally how they function so you can make informed decisions. 

  5. Receive a certificate
    • After attending the training on given instrument you get the certification that allows you to use the instrument unsupervised.

  6. Independent measurement
    • Now you can use the instrument on your own. Beware that IMCF staff is here for you, so do not hesitate to ask for help.


Booking system



Optical (fluorescence) microscopy


Electron microscopy


Flow cytometry


Data Analysis


Flow Cytometry



  • Multicolour flow cytometry analysis
  • 5 spatially separated lasers
  • 18 fluorescent detectors
  • Sample loading options:
    • 5ml tubes
    • 96-, 384-well plates

More info

BD FACS Aria Fusion

BD FACS Aria Fusion

  • Fluorescence Activated Cell Sorting
  • 5 spatially separated lasers
  • 18 fluorescent detectors
  • T° control of a sample
  • Sorting on/into device options:
    • Eppendorfs
    • 5ml-, 15ml- tubes
    • 6-, 24-, 48-, 96-, 384-well plates
    • Microscope slides  

More info


Electron Microscopy

FEI Helios NanoLab 660 G3 UC

FEI Helios NanoLab 660 G3 UC

  • FIB-SEM DualBeam microscope
  • High resolution scanning electron microscopy with focus ion beam

More info

Leica EM ACE600 – coating system

Leica EM ACE600 – coating system

  • precise coating of samples foe subsequent examination with an electron microscope
  • glow discharge
  • freeze fracture cryo set

More info

Optical Microscopy

Carl Zeiss LSM 880 NLO

Carl Zeiss LSM 880 NLO

  • Inverted confocal microscope
  • Multiphoton excitation and non-descanned detection with FLIM option
  • Internal spectral detection unit

More info



  • Inverted confocal microscope
  • WLL and internal spectral detection unit
  • FLIM and FCS

More info



  • Inverted widefield microscope
  • TIRF illumination
  • Image splitter
  • SIM super-resolution microscopy
  • STORM super-resolution microscopy

More info




Makki A., Rada P, Žárský V., Kereiche S., Kovacik L., Novotny M., Jores T., Rapaport D., Tachezy J. 2019 Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biology. 17(1):e3000098. doi: 10.1371/journal.pbio.3000098



Bajzikova, M., Kovarova, J., Coelho, A. R. et al.: Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells. Cell Metab (2018).

♯ STED                ♯ Huygens             ♯ confocal       ♯ 2-photon excitation   

Baresova, V., Skopova, V., Souckova, O. et al.: Study of Purinosome Assembly in Cell-based Model Systems with De Novo Purine Synthesis and Salvage Pathway Deficiencies. PLoS One 13, 1-13 (2018).

♯ Huygens      ♯ confocal

Cerychova, R., Bohuslavova, R., Papousek, F et al.: Adverse Effects of Hif1a Mutation and Maternal Diabetes on the Offspring Heart Cardiovas Diabetol 17, 1-16 (2018).

♯ confocal  ♯ SEM

Font-Haro, A. et al.: Expression of TIM-3 on Plasmacytoid Dendritic Cells as a Predictive Biomarker of Decline in HIV-1 RNA Level During ART. Viruses 3, 1-13 (2018).

♯ BD Fortessa

Frolikova, M., Manaskova-Postlerova, P., Cerny, J. et al.: CD9 and CD81 Interactions and their Structural Modelling in Sperm Prior to Fertilization. Intern Journal of Mol Sci 19, 4-17 (2018).

♯ SIM  ♯ confocal      ♯ Huygens

Grzelak, A., Polakova, I., Smahelova, J. el al.: Experimental Combined Immunotherapy of Tumours with Major Histocompatibility Complex Class I Downregulation. Intern Journal of Molec Sci 19, 3693 (2018).

♯ BD Fortessa

Hubackova, S., Davidova, E., Rohlenova, K. et al.: Selective Elimination of Senescent Cells by Mitochondrial Targeting is Regulated by ANT2. Cell Death and Differ, 1-15 (2018).

♯ BD Fortessa

Janovec, V., Aouar, B., Font-Haro, A. et al.: The MEK1/2-ERK Pathway Inhibits Type I IFN Production in Plasmacytoid Dendritic Cells. Front In Immunol 9, 1-16 (2018).

♯ BD Aria       ♯ BD Fortessa

Kazamia, E., Sutak, R., Paz-Yepes, J. et al.: Endocytosis-mediated Siderophore Uptake as a Strategy for Fe Acquisition in Diatoms. Science Advances 4 (2018).

♯ confocal

Kollarova, J., Kostrouchova, M., Benda, A. and Kostrouchova, M.: ALKB-8, a 2-Oxoglutarate-Dependent Dioxygenase and S-Adenosine Methionine-Dependent Methyltransferase Modulates Metabolic Events Linked to Lysosome-Related Organelles and Aging in C. elegans. Folia Biol. (Praha). 64, 46–58 (2018).


Kostrouchova, M., Kostrouchova, V., Yilma, P. et al.: Valproic Acid Decreases the Nuclear Localization of MDT-28, the Nematode Orthologue of MED28. Folia Biologica 64, 1-19 (2018).


Mach, J., Bila, J., Zeniskova, K. et al.: Iron Economy in Naegleria Gruberi Reflects its Metabolic Flexibility. Intern Journal for Parasitol 48, 719-727 (2018).

♯ Huygens      ♯ confocal

Rada, P., Makki, A., Zarsky, V. and Tachezy, J.: Targeting of Tail-Anchored Proteins to Trichomonas Vaginalis Hydrogenosomes. Mol Microbiol (2018).

♯ SIM              ♯ STED           ♯ confocal       ♯ EM chemical fixation

Stafkova, J., Rada, P., Meloni, D. et al.: Dynamic Secretome of Trichomonas Vaginalis : Case Study of β-amylases. Mol & Cell Proteom 17, 304-320 (2018).

♯ SIM             ♯ TEM

Becker, W., Studier, H., Wetzker, C. and Benda, A.: Ultra-fast HPM Detectors Improve NAD(P)H FLIM. Progress in Biomedical Optics and Imaging - Proceedings of SPIE 10498 (2018).

♯ 2-photon excitation ♯ FLIM

Ma, Y., Benda, A., Kwiatek, J. et al.: Time-Resolved Laurdan Fluorescence Reveals Insights into Membrane Viscosity and Hydration Levels. Biophys Journal (2018).

♯ FLIM  ♯ time-resolved GP

Nicovich, P. R., Kwiatek, J. M., Ma, Y. et al.: FSCS Reveals the Complexity of Lipid Domain Dynamics in the Plasma Membrane of Live Cells. Biophys Jour 114, 2855-2864 (2018).


Olsinova, M., Jurkiewicz, P., Kishko, I. et al.: Roughness of transmembrane helices reduces lipid membrane dynamics. iScience 10, 87–97 (2018).


Proksova, P., Lipov, J., Zelenka, J. et al.: Mason-Pfizer Monkey Virus Envelope Glycoprotein Cycling and Its Vesicular Co-Transport with Immature Particles. Viruses 10, 575 (2018).

# spinning disk           # TEM            # widefield

Shestivska, V., Olsinova, M., Sovova, K. et al.: Evaluation of Lipid Peroxidation by the Analysis of Volatile Aldehydes in the Headspace of Synthetic Membranes Using Selected Ion Flow Tube Mass Spectrometry. Rapid Commun in Mass Spectrometry 32, 1617-1628 (2018).

Allolio, C., Magarkar, A., Jurkiewicz, P. et al.: Arginine-rich Cell-penetrating Peptides Induce Membrane Multilamellarity and Subsequently Enter via Formation of a Fusion Pore. PNAS (2018), 201811520.

♯ FIB-SEM     ♯ FLIM

Cermak, V. et al.: RNA-seq of Macrophages of Amoeboid or Mesenchymal Migratory Phenotype Due to Specific Structure of Environment. Sci. Data 5, 1–8 (2018).

Gemperle, J., Dibus, M., Koudelkova, L., Rosel, D. and Brabek, J.: The Interaction of p130Cas with PKN3 Promotes Malignant Growth. Mol. Oncol. 1–26 (2018).

♯ confocal

Koudelkova, L. et al.: Novel FRET-Based Src Biosensor Reveals Mechanisms of Src Activation and Its Dynamics in Focal Adhesions. Cell Chem. Biol. 1–14 (2018).

♯ confocal       ♯ TIRF            ♯ FRET           ♯ FRAP

Siahaan, V. et al.: Kinetically Distinct Phases of Tau on Microtubules Regulate Kinesin Motors and Severing Enzymes. BioRxiv (2018). doi:10.1101/424374


Soldatova, I., Prilepskaja, T., Abrahamyan, L., Forstova, J. and Huerfano, S.: Interaction of the Mouse Polyomavirus Capsid Proteins with Importins is Required for Efficient Import of Viral DNA Into the Cell Nucleus. Viruses 10, 1–22 (2018).

♯ confocal

Tolde, O. et al.: Quantitative Phase Imaging Unravels New Insight Into Dynamics of Mesenchymal and Amoeboid Cancer Cell Invasion. Sci. Rep. 8, 1–13 (2018).

♯ hologpraphy

Agarwal, K. Machan, R. and Prasad, D.K: Non-heuristic Automatic Techniques for Overcoming Low Signal-to-Noise-Ratio bias of Localization Microscopy and Multiple Signal Classification Algorithm. Scientific Repors 8 (1), 2018.

♯ Elyra

Neburkova, J., Sedlak. F., Zackova Suchanova, J. et al.: Inhibitor-GCPII Interaction: Selective and Robust System for Targeting Cancer Cells with Structurally Diverse Nanoparticles. Mol Pharmaceut, 15 (8), 2932 – 2945 (2018).

♯ BD Fortessa


Blecha, J. et al.: Antioxidant Defense in Quiescent Cells Determinates Selectivity of Electron Transport Chain Inhibition-Induced Cell Death. Free Radic Biol Med 112, 253-266 (2017).

♯ 2-photon excitation ♯ confocal       ♯ Huygens

Bohuslavova, R., Cerychova, R., Nepomucka, K. and Pavlinkova, G.: Renal injury is accelerated by global hypoxia-inducible factor 1 alpha deficiency in a mouse model of STZ-induced diabetes. BMC Endocr. Disord. 17, 1–12 (2017).

♯ confocal

Branis, J. et al.: The Role of Focal Adhesion Anchoring Domains of CAS in Mechanotransduction. Sci Rep 7 (2017).

♯ STED           ♯ confocal

Danko, M., Hrdlovic, P., Martinicka, A., Benda, A. and Cigan, M.: Spectral Properties of Ionic Benzotristhiazole Based Donor-Acceptor NLO-phores in Polymer Matrices and their one- and two-photone Cellular Imaging Ability. Photochem Photobiol Sci 16 (2017).

♯ 2-photon excitation   ♯ FLIM

Hornikova, L., Fraiberk, M., Man, P., Janovec, V., Forstova, J.: VP1, the Major Capsid Protein of the Mouse Polyomavirus, Binds Microtubules, Promotes their Acetylation and Block the Host Cell Cycle. FEBS J. 284, 301-323 (2017).

♯ BD Fortessa            ♯ TEM            ♯ confocal

Huerfano, S., Ryabchenko, B., Spanielova, H. and Forstova, J.: Hydrophobic Domains of Mouse Polyomavirus Minor Capsid Proteins Promote Membrane Association and Virus Exit from the ER.  FEBS J 284, 883-902 (2017).

♯ confocal       ♯ TEM

Kellerova, P. and Tachezy, J.: Zootonic Trichomonas Tenas and the New Trichomonad Species, Trichomonas Brixi n.sp., from the Oral Cavities of Dogs and Cats. Int J Parasitol 47, 247-255 (2017).

♯ SIM              ♯ FIB-SEM                 ♯ TEM

Kokavec, J. et al.: The ISWI ATPase Smarca5 (Snf2h) is Required for Proliferation and Differenciation of Hematopoietic Stem and Progenitor Cells. Stem Cells 35, 1614-1623 (2017).

♯ cytometry

Kostrouchova, M. et al.: The Nematode Homologue of Mediator Complex Subunit 28 , F28F8.5, is a Critical Regulator of C. elegans Development. PeerJ 2017 (2017).


Luo, W. et al.: ARHGAP42 is Activated by Src-Mediated Tyrosine Phosphorylation to Promote Cell Motility . J Cell Sci 130, 2382-2393 (2017).

♯ confocal

Novakova, Z. et al.: Novel Monoclonal Antibodies Recognizing Human Prostate-Specific Membrane Antigen (PSMA) as Research and Theranostic Tools. Prostate 77, 749–764 (2017).

♯ BD Fortessa  

Pavlinkova, G. et al.: Transgenerational inheritance of susceptibility to diabetes-induced male subfertility. Sci. Rep. 7, (2017).

♯ confocal

Skultetyova, L. et al.: Human Histone Deacetylase 6 Shows Strong Preference for Tubulin Dimers Over Assebled Microtubules. Sci Rep 7 (2017).


Voleman, L. et al.: Giardia Intestinalis Mitosomes Undergo Synchronised Fission but not Fusion and are Constitutively Associated with the Endoplasmic Reticulum. BMC Biol 15 (2017).

♯ SIM             ♯ widefield     ♯ spinning disk           ♯ Huygens

Zackova Suchanova, N., Neburkova, J., Spanielova, H., Forstova, J. and Cigler, P.: Retargeting Polyomavirus-like Particles to Cancer Cells by Chemical Modification of Capsid Surface. Bioconug Chem. 28, 307-313 (2017).

♯ BD Fortessa            ♯ TEM            ♯ confocal      


 Boukalova, S. et al.: Mitochondrial Targeting of Metformin Enhances its Activity against Pancreatic Cancer. Mol Cancer Ther. 15, 2875-2886 (2016).

♯ BD Fortessa

Dvorakova, M. et al.: Incomplete and Delayed Sox2 Deletion Defines Residual Ear Neurosensory Development and Maintenance. Sci Rep 6, 1-16 (2016).

♯ confocal       ♯ SEM

Jankovicova, J. et al.: Characterization of tetraspanin protein CD81 in mouse spermatozoa and bovine gametes. Reproduction (2016). doi:10.1530/REP-16-0304

♯ confocal       ♯ Huygens

Agarwal, K. & Macháň, R. Multiple signal classification algorithm for super-resolution fluorescence microscopy. Nat. Commun. 7, (2016).

♯ Superresolution microscopy

Benda, A., Aitken, H., Davies, D. S., Whan, R. & Goldsbury, C. STED imaging of tau filaments in Alzheimer’s disease cortical grey matter. J. Struct. Biol. 195, (2016).


Jiang, Y. et al. Time-resolved fluorescence anisotropy study of organic lead halide perovskite. Sol. Energy Mater. Sol. Cells 151, (2016).

Ma, Y., Benda, A., Nicovich, P. R. & Gaus, K. Measuring membrane association and protein diffusion within membranes with supercritical angle fluorescence microscopy. Biomed. Opt. Express 7, (2016).

Macháň, R., Foo, Y. H. & Wohland, T. On the Equivalence of FCS and FRAP: Simultaneous Lipid Membrane Measurements. Biophys. J. 111, 152–161 (2016).

Yavas, S., Macháň, R. & Wohland, T. The Epidermal Growth Factor Receptor Forms Location-Dependent Complexes in Resting Cells. Biophys. J. 111, 2241–2254 (2016).


Mgr. Aleš Benda, Ph.D. Mgr. Aleš Benda, Ph.D.

Aleš Benda, Ph.D.

Head of the facility, optical (fluorescence) microscopy
Mgr. Marie Olšinová, Ph.D Mgr. Marie Olšinová, Ph.D

Marie Olšinová, Ph.D

Optical (fluorescence) microscopy
Ing. Dalibor Pánek, Ph.D. Ing. Dalibor Pánek, Ph.D.

Dalibor Pánek, Ph.D.

Optical (fluorescence) microscopy
Mgr. Irena Krejzová, Ph.D. Mgr. Irena Krejzová, Ph.D.

Irena Krejzová, Ph.D.

Electron microscopy
Mgr. Martin Fraiberk, Ph.D Mgr. Martin Fraiberk, Ph.D

Martin Fraiberk, Ph.D

Electron microscopy
Mgr. Lucia Motlová Mgr. Lucia Motlová

Lucia Motlová

Electron microscopy
Bc. Lenka Backová Bc. Lenka Backová

Lenka Backová

Data analysis
Mgr. Ján Sabó Mgr. Ján Sabó

Ján Sabó

Optical (fluorescence) microscopy
Mgr. Libuše Vaněčková Mgr. Libuše Vaněčková

Libuše Vaněčková

Administration support
Ing. Galina Kislik Ing. Galina Kislik

Galina Kislik

Flow Cytometry – on maternity leave
Mgr. Markéta Dalecká Mgr. Markéta Dalecká

Markéta Dalecká

Electron microscopy – on maternity leave
Ing. Petra Prokšová-Grznárová, Ph.D. Ing. Petra Prokšová-Grznárová, Ph.D.

Petra Prokšová-Grznárová, Ph.D.

Flow cytometry and Optical (fluorescence) microscopy - on maternity leave