INSTITUTE OF PHYSIOLOGY CAS

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 (jiri.janacek@fgu.cas.cz).

CURRENTLY FUNDED PROJECTS

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

LONG-TERM PROJECTS

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)

IN-HOUSE IMAGING MODALITIES

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

AVAILABLE SOFTWARE AND PROTOCOLS

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

OPEN ACCESS TO EQUIPMENT

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].

[1] http://www.czech-bioimaging.cz/

[2] http://www.fgu.cas.cz/en/articles/529-czech-bioimaging-2016-2019

Projects

Reconstruction and registration of images acquired by multimodal preclinical imaging methods

Novel functional imaging modality requiring co-registration with anatomical information for in vivo imaging. More

Image analysis of biological microscopic data for measurement of fibrous microscopic structures

Modulation of microtubule dynamics by nanosecond electric pulses

Development of the cardiac conduction system in mice

We use 3D imaging and optical mapping to analyze the cardiac conduction system and its development in mice. More

Developmental modularity of the brain in the evolution of bird locomotion

Using high-resolution imaging and geometric morphology, we study the relation between brain anatomy and capability of flying in birds. More

Achievements

Calmodulin and protein S100A1 bind in distal N- terminus of TRPM4 channel

It was identified new binding sites for the calmodulin (CaM) and S100A1, located in the very distal part of the TRPM4 N-terminus. More

International poster award (Innsbruck 2016)

Langerhans islets' volume measurements using optical projection tomography and the Fakir method More

Sexual dimorphism in pheasant brains (Scientific Reports 2015)

Magnetic resonance and computed tomography study of avian brain compartments' volumes measured by our Fakir probe revealed sexual dimorpism in pheasant brains. More

Invited review on confocal stereology (Cell & Tissue Research 2015)

A review article on confocal stereology comprising innovative methods invented at the Department of Biomathematics More

Capillary length estimation (Microscopy & Microanalysis 2013)

Publications

Olejníčková; Veronika - Hamor; P. U. - Janáček; Jiří - Bartoš; M. - Zábrodská; E. - Šaňková; B. - Kvasilová; A. - Kolesová; Hana - Sedmera; David . Development of ventricular trabeculae affects electrical conduction in the early endothermic heart . Developmental Dynamics. 2024; 253(1); 78-90 . IF = 2.5 [ASEP] [ doi ]

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 ]

	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 Technician
	Davide Basello Research Assistant
	Ing. Jitka Čočková Project Manager

Laboratory of Biomathematics