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Laboratory of Biomathematics

Laboratory of Biomathematics

The Laboratory of Biomathematics is active in fields of Bioimaging and Image Analysis.

Bioimaging and Image Analysis

The laboratory conducts research into the 3D microanatomical aspects of physiological phenomena at mesoscopic, microscopic and ultrastructural level. It is engaged in a range of collaborative projects across the campus and beyond. If interested please contact us (


  • Diabetic structural changes in capillary network and connective tissue
  • Quantification of isolated pancreatic islets


  • Development of 3D image analysis and stereological methods including software (employed, e.g., in a volumetric analysis of Langerhans islets from human donors)
  • Microscopic optical-contrasting (label-free) strategies to visualize living cells and tissues

OTHER PROJECTS (selection only)

  • Effects of ionizing radiation on blood capillaries network
  • Effects of elevated CO2 on the photosynthetic apparatus’ performance and  ultrastructure
  • Mechanisms governing the formation of extracellular matrix proteins (collagen and elastin)


  • Laser scanning confocal microscopy
  • Two-photon excitation microscopy
  • Second harmonic generation (SHG) microscopy
  •  ‘White-light‘ laser and hybrid detectors (on Leica TCS SP8 WLL MP microscope)
  • FRAP recording, FRET analysis, FLIM/PLIM recording including λ2 scans 
  • Optical projection tomography (OPT)
  • Selective plane illumination (light sheet) microscopy (SPIM)
  • Phase-, modulation- and interference contrast microscopy


  • Software for 3D image analysis, stereology, spatial statistics and deconvolution (Hyughens)
  • Optical/chemical clearing protocols for OPT and SPIM


The group is part of the Czech BioImaging infrastructure [1] supporting open access to most of its microscopes (listed above), and implicitly also to its expertise. The portfolio includes, among other imaging equipment located at other departments, a Nipkow spinning-disk (“Carv II“) confocal microscope [2].






Vondrášek; David - Hadraba; Daniel - Přibyl; J. - Eckhardt; Adam - Ošťádal; M. - Lopot; F. - Jelen; K. - Doubková; Martina - Knitlová; Jarmila - Novotný; T. - Janáček; Jiří . Microstructural Analysis of Collagenous Structures in Relapsed Clubfoot Tissue . Microscopy and Microanalysis. 2023; 29(1); 265-272 . IF = 2.8 [ASEP] [ doi ]
Habart; D. - Koza; A. - Leontovyč; I. - Kosinová; L. - Berková; Z. - Kříž; J. - Zacharovová; K. - Brinkhof; B. - Cornelissen; D. J. - Magrane; N. - Bittenglová; K. - Čapek; Martin - Valečka; J. - Habartová; Alena - Saudek; F. IsletSwipe; a mobile platform for expert opinion exchange on islet graft images . Islets. 2023; 15(1)); 2189873 . IF = 2.2 [ASEP] [ doi ]
Ojha; Srikant - Přibyl; J. - Klimovič; Š. - Hadraba; Daniel - Jiroušková; Markéta - Gregor; Martin . Measurement of Liver Stiffness using Atomic Force Microscopy Coupled with Polarization Microscopy . Jove-Journal of Visualized Experiments. 2022; 20(185)); e63974 . IF = 1.2 [ASEP] [ doi ]
Novotný; T. - Eckhardt; Adam - Doubková; Martina - Knitlová; Jarmila - Vondrášek; David - Vanaskova; E. - Ošťádal; M. - Uhlík; J. - Bačáková; Lucie - Musílková; Jana . The possible role of hypoxia in the affected tissue of relapsed clubfoot . Scientific Reports. 2022; 12(1)); 4462 . IF = 4.6 [ASEP] [ doi ]
Gregorovičová; M. - Bartoš; M. - Jensen; B. - Janáček; Jiří - Minne; B. - Moravec; J. - Sedmera; David . Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation . Ecology and Evolution. 2022; 12(11)); e9476 . IF = 2.6 [ASEP] [ doi ]

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RNDr. Jiří Janáček, PhD.
Head of the Laboratory
Ing. Martin Čapek, PhD.
Senior Researcher (part-time)
RNDr. Barbora Radochová, PhD.
Senior Researcher
Ing. Mgr. Daniel Hadraba, Ph.D.
Postdoctoral Researcher

Mgr. David Vondrášek


Davide Basello

Research Assistant
Ing. Jitka Čočková
Project Manager