Available technologies/expertise

Czech-BioImaging offers access to a wide range of biological and medical imaging technologies:


To search a concrete imaging technology and its availability within Czech-BioImaging infrastructure, please use our searching tool:

Overview of available technologies

Advanced light microscopy

Optical microscopy; macroscopic imaging of whole tissue or animal imaging; multiphoton deep penetration intravital imaging for obtaining 3D structure of thick specimens, tissues and live animals; high-throughput automated and semi-automated microscopy allowing statistical analysis of large amount of cells as well as their functional characteristics; high speed cell sorting providing the possibility for the isolation of the precisely defined cells, which can be used in further biological and biochemical assays, as well as for the statistical analysis of cellular responses; fast live cell imaging; long term live cell imaging for continuous observation to track slow or delayed cellular responses; combined physiological and optical imaging for a correlative study between cell and tissue activity and structure; non-invasive multi-modality imaging covering the scale from subcellular ultrastructures to the small animals; optical microscopy combined with simultaneous recording of electrical signals and/or electrical stimulations; small animal preclinical imaging; multimodal imaging of the particular animal; calibration of light microscopy systems; automated microscopy for acquisition of histology databases or genetic screens based on the expression of marker genes; imaging of plant systems; advanced incoherent holographic microscopy and robotic environment for quantitative evaluation of cell behavior.

Fluorescence microscopy 

Laser scanning confocal microscopy allowing sensitive spectrally-separated multichannel image acquisition, fast in vivo scanning, and optical sectioning of the live and fixed animal and plant specimens and thus giving access to 4D information about biological samples; high-end spinning disc microscopy with high sensitivity and spatiotemporal resolution allowing fast image acquisition with minimal photobleaching; functional imaging (FRET, FRAP, photoactivation) monitoring the microenvironment changes and molecular interactions in live cells and tissues with submicrometer spatial resolution and down to microsecond time resolution; fluorescence life time imaging (FLIM) and non-linear techniques based on second harmonic generation (SHG) - with unique image analysis support including development of custom-made SW implementation; single plain illumination microscopy (SPIM); 3D FPALM superresolution microscopy; super-sensitive visualizing and quantifying of PPI using FLIM-FRET; TIRF imaging used for cell membrane studies providing detailed insight into the structures located up to few hundreds nanometers from the glass – specimen interface. In vivo tracking of multiple molecules and processes; 3D reconstruction and localization of molecular processes; multimodal holographic microscopy as coherence-controlled holographic microscopy with fluorescence; polychromatic flow cytometry providing sensitive, high speed, multi-parametric fluorescence measurement of the large numbers of particles in the flow of sheath fluid.

Super-resolution 3D imaging

Super-resolution 3D imaging of live and fixed biological specimens, stimulated emission depletion (3D gated STED), super-resolution localization microscopy techniques (PALM, 3D-STORM

Electron microscopy

High-resolution (cryo-) transmission electron microscopy (TEM) with maximal resolution of 0.27 nm (200 kV TEM); low voltage electron microscopy intended for the characterisation of nanoparticles and nanofibers; high resolution (cryo-) scanning electron microscopy (SEM) with focused ion beam (FIB) for biological applications, for the visualization and studying of active pharmaceutical ingredients like hyaluronan chemicals or micelles dedicated for targeted drug delivery, biofilms etc.; 3D electron tomography; electron energy-loss chemical analysis in situ.

Correlative light and electron microscopy

Sample preparation: microdissection; detection of mRNA and proteins using both whole-mount and on-sections techniques; preparation of the constructs of fluorescently labelled proteins in vivo; fluorescent labelling of proteins and DNA using bright synthetic labels; chemical fixation suitable for morphology studies and immunolabeling; resin embedding (LR White, Lowicryls, Epons, Quetols) using own equipment for polymerization from -50 C to +60 C); SEM sample preparation; high-pressure freezing for vitrifying samples up to 200 µm in thickness preventing the formation of crystal ice; automated freeze-substitution minimizing the human factor errors; plunge-freezing producing high-quality vitrified samples for single particle analysis or cryo-tomography research applications; (cryo-) sectioning (50–100 nm) and semi-thick sections for tomography (200–500 nm); multi-immunolabeling of five molecular targets using self-developed detection system; own immunolocalization method combining 3D pre-embedding immunolabeling and 2D on-section immunolabeling to expand the possibilities for analysis of biological processes.

Neuroscience imaging

Two top available research MRI scanners 3T Siemens MAGNETOM Prisma MR scanners, one of the scanners prepared for multinuclear measurement (31P spectroscopy); MR compatible 256-channel HD-EEG system; MR compatible 30-channel EEG/polygraph system + second standalone polygraph system (measurements of breathing, ECG, skin conductance, movement, EMG); system for visual stimulation in MR; computational servers and local data storage.

The two scanners enable for hyperscanning (simultaneous fMRI).

Magnetic resonance

A multinuclear high-field 9.4T 30cm-bore MR system equipped for imaging and spectroscopy of mice, rats and rabbits; a 4.7T 20cm-bore MR imaging system; certified small animal in-vivo imaging facility (mouse, rat, rabbit, pig); small-animal ultrasound scanner Vevo 2100. Expertise in measurement and physiological modeling of perfusion, robust quantitative MR, and MR measurement of diffusion parameters with ensuing analysis of anatomical connectivity.

Magnetic particle imaging (MPI)

Magnetic particle imaging (MPI) combined with MRI resulting in images of tissue and organ components with exceptional positive contrast in any depth and allowing real- time non-toxic monitoring of cells and/or molecules in organism. The combination of micro-CT with PET and SPECT in single device intended for preclinical imaging of small laboratory animals (mice, rats).

Image analysis

Image analysis and development of new methods - development of tailor-made image acquisition methods, image processing and analyzing algorithms for camera-based light microscopy and other types of microscopy; image analysis software allowing highly sensitive and specific fluorescence imaging in living cells via fluorescence intensity decay shape analysis microscopy (FIDSAM); acquisition of 3D cell images using automated confocal spinning-disc microscopy (including live cell imaging); 3D reconstruction of fixed biological specimens with nanometer spatial resolution, stereological methods 3D reconstructions, including development of custom-made SW implementation; analysis of series of images of cell activity dynamics from quantitative phase imaging (QPI).

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