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