Institute of Physiology CAS

BioImaging Facility


Institute of Physiology CAS
Vídeňská 1083
14220 Praha 4



Daniel Hadraba
Phone: +420 241 062 274

IPHYS BioImaging facility provides access especially to numerous types of confocal microscopes, with a special stress on multiphoton microscopic techniques. Further, optical projection tomography scanners are available as well as μCT/PET scanner enabling imaging of whole animals (mice, rat). Animal facility services are available on site. We cover expertise with image acquisition as well as broad expertise in image analysis, including development of new methods and SW modules (in ImageJ, Amira or Ellipse SW environment) in the field of image processing and analysis, stereology and spatial statistics.

Expertise and support provided to users

1.Image acquisition: confocal microscopy, two-photon microscopy, including fluorescence life time imaging (FLIM) and non-linear techniques based on second harmonic generation (SHG), optical projection microscopy (OPT), optic fibre confocal microscopy, 3D FPALM superresolution microscopy (Euro-BioImaging only) and µCT/PET.

2. Sample preparation including application of clearing techniques for OPT.

3. Handling of laboratory animals for optic fibre confocal microscopy and µCT/PET.

4. Image analysis, stereology, image processing, and 3D reconstructions support including application of deconvolution techniques.

5. Training in microscopic and image analysis methods.

Imaging technologies available

  • Laser Scanning Confocal Microscopy (LSM / CLSM)
  • Spinning Disc Confocal Microscopy (SDCM)
  • Multiphoton Microscopy Systems
  • Fluorescence-Lifetime Imaging Microscopy (FLIM)
  • Fluorescence Resonance Energy Transfer (FRET)
  • Fluorescence Recovery After Photobleaching (FRAP)
  • Non-Linear Microscopy Techniques (e.g. CARS, SHG, THG, SRS)
  • Optic-fiber Confocal Fluorescence Microscopy
  • Optical Projection Tomography (OPT)
  • μPET / CT

Equipment available (technical specification)

Leica SP8 AOBS WLL MP confocal laser scanning microscope with two-photon excitation

Leica SP2 AOBS confocal laser scanning microscope

Leica SPE confocal laser scanning microscope

Bioptonics OPT 3001 optical projection tomography

"Milano" custom-made optical projection tomography

Mauna Kea CellVizio Optic fibre confocal microscopy

Carv II confocal spinning disc microscope

Bruker Albira μCT/PET scanner

3D FPALM superresolution microscopy (only in the framework of Euro-BioImaging)

Research topics directly investigated in the CF

We are engaged in development of new methods in 3D image analysis, stereology, spatial statistics, 3D reconstruction, and studies of variance of stereological methods. Further, we are involved in research projects, concerning above all 3D image analysis, confocal microscopy and stereology, run in cooperation with biologists, e.g., studies of capillary system of the human placenta, rat muscles and brain, bird brain anatomy, conduction system of the heart, extracellular matrix proteins – collagen and elastin, architecture of the spruce needle, structure of the cell compartments, such as nucleus, cytoskeleton and endoplasmic reticulum.

External access to the equipment




Training materials (tutorials, handbooks etc.)



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