INSTITUTE OF PHYSIOLOGY CAS

The Laboratory of Biomathematics consists of two research groups: (1) Bioimaging and Image Analysis, and (2) Biochemistry of Membrane Receptors. Operating mainly at in situ and in vitro levels, respectively, the two groups complement each other when studying phenomena confined to the cell membrane.

1. Bioimaging and Image Analysis

The group 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

Reconstruction and registration of images acquired by multimodal preclinical imaging methods
The conduction system of developing murine heart

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

Umek; N. - Janáček; Jiří - Cvetko; E. - Eržen; I. Horizontal deformation of skeletal muscle thick sections visualised by confocal microscopy . Journal of Microscopy. 2021; 282(2); 113-122 . IF = 1.758 [ASEP] [ doi ]

Skalický; D. - Koucký; V. - Hadraba; Daniel - Vítězník; M. - Dub; M. - Lopot; F. Detection of Respiratory Phases in a Breath Sound and Their Subsequent Utilization in a Diagnosis . Applied Sciences-Basel. 2021; 11(14)); 6535 . IF = 2.679 [ASEP] [ doi ]

Jerman; A. - Janáček; Jiří - Snoj; Ž. - Umek; N. QUANTIFICATION OF THE INTERVENTIONAL APPROACHES INTO THE PTERYGOPALATINE FOSSA BY SOLID ANGLES USING VIRTUAL REALITY . Image Analysis and Stereology. 2021; 40(2); 63-69 . IF = 0.682 [ASEP] [ doi ]

Filová; Elena - Steinerová; Marie - Trávníčková; Martina - Knitlová; Jarmila - Musílková; Jana - Eckhardt; Adam - Hadraba; Daniel - Matějka; Roman - Pražák; Šimon - Štěpanovská; Jana - Kučerová; Johanka - Riedel; Tomáš - Brynda; Eduard - Lodererová; A. - Honsová; E. - Pirk; J. - Koňařík; M. - Bačáková; Lucie . Accelerated in vitro recellularization of decellularized porcine pericardium for cardiovascular grafts . Biomedical Materials. 2021; 16(2)); 025024 . IF = 3.715 [ASEP] [ doi ]

Čapek; Martin - Blažíková; M. - Novotný; I. - Chmelová; H. - Svoboda; D. - Radochová; Barbora - Janáček; Jiří - Horváth; O. THE WAVELET-BASED DENOISING OF IMAGES IN FIJI; WITH EXAMPLE APPLICATIONS IN STRUCTURED ILLUMINATION MICROSCOPY . Image Analysis and Stereology. 2021; 40(1); 3-16 . IF = 0.682 [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
	MUDr. Petr Karen, CSc. Senior Researcher
	Mgr. David Kala PhD Student
	Michaela Vodičková PhD Student
	Mgr. David Vondrášek Technician
	Mgr. Zuzana Kubínová Technician
	Ing. Jitka Čočková Project Manager
	Petr Zvolánek Research Assistant

Laboratory of Biomathematics