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
Novel functional imaging modality requiring co-registration with anatomical information for in vivo imaging.
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We use 3D imaging and optical mapping to analyze the cardiac conduction system and its development in mice.
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Using high-resolution imaging and geometric morphology, we study the relation between brain anatomy and capability of flying in birds.
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Achievements
It was identified new binding sites for the calmodulin (CaM) and S100A1, located in the very distal part of the TRPM4 N-terminus.
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Langerhans islets' volume measurements using optical projection tomography and the Fakir method
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Magnetic resonance and computed tomography study of avian brain compartments' volumes measured by our Fakir probe revealed sexual dimorpism in pheasant brains.
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A review article on confocal stereology comprising innovative methods invented at the Department of Biomathematics
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Publications
Novotný; T. - Eckhardt; Adam - Doubková; Martina - Knitlová; Jarmila - Vondrášek; David - Vanaskova; E. - Ošťádal; M. - Uhlík; J. - Bačáková; Lucie - Musílková; Jana
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The possible role of hypoxia in the affected tissue of relapsed clubfoot
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Scientific Reports. 2022; 12(1)); 4462
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IF = 4.996
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Ďúranová; H. - Valková; V. - Olexiková; L. - Radochová; Barbora - Balazi; A. - Chrenek; P. - Vašíček; J.
Rabbit Endothelial Progenitor Cells Derived From Peripheral Blood and Bone Marrow: An Ultrastructural Comparative Study
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Microscopy and Microanalysis. 2022; 28(3); 756-766
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IF = 4.099
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Bačáková; Lucie - Novotná; Katarína - Hadraba; Daniel - Musílková; Jana - Slepička; P. - Beran; M.
Influence of Biomimetically Mineralized Collagen Scaffolds on Bone Cell Proliferation and Immune Activation
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Polymers. 2022; 14(3)); 602
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IF = 4.967
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Abbondanza; Alice - Bas; Irina Ribeiro - Modrák; Martin - Čapek; Martin - Minich; Jessica - Tyshkevich; Alexandra - Naser; Shahed - Rangotis; Revan - Houdek; Pavel - Sumová; Alena - Dumas; S. - Bernard; V. - Janíčková; Helena
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Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors
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Journal of Neuroscience. 2022; 42(13); 2786-2803
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IF = 6.709
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Umek; N. - Janáček; Jiří - Cvetko; E. - Eržen; I.
Horizontal deformation of skeletal muscle thick sections visualised by confocal microscopy
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Journal of Microscopy. 2021; 282(2); 113-122
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IF = 1.952
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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
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Applied Sciences-Basel. 2021; 11(14)); 6535
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IF = 2.838
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Lopot; F. - Dub; M. - Flek; J. - Hadraba; Daniel - Havlíček; M. - Kučera; L. - Štoček; O. - Veselý; T. - Janáček; Jiří
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Gearbox Mechanical Efficiency Determination by Strain Gauges Direct Application
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Applied Sciences-Basel. 2021; 11(23)); 11150
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IF = 2.838
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Knitlová; Jarmila - Doubková; Martina - Plencner; Martin - Vondrášek; David - Eckhardt; Adam - Ošťádal; M. - Musílková; Jana - Bačáková; Lucie - Novotný; T.
Minoxidil decreases collagen I deposition and tissue-like contraction in clubfoot-derived cells: a way to improve conservative treatment of relapsed clubfoot?
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Connective Tissue Research. 2021; 62(5); 554-569
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IF = 3.342
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Jerman; A. - Janáček; Jiří - Snoj; Ž. - Umek; N.
QUANTIFICATION OF THE INTERVENTIONAL APPROACHES INTO THE PTERYGOPALATINE FOSSA BY SOLID ANGLES USING VIRTUAL REALITY
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Image Analysis and Stereology. 2021; 40(2); 63-69
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IF = 0.683
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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
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Accelerated in vitro recellularization of decellularized porcine pericardium for cardiovascular grafts
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Biomedical Materials. 2021; 16(2)); 025024
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IF = 4.103
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TRH-R-eGFP protein in HEK293 cells
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