Advanced Light And Electron Microscopy Node Prague CZ

The Czech Advanced Light and Electron Microscopy Multi Modal Multi Sited Node located in Prague and in České Budějovice offers a wide range of state-of-the-art light and electron microscopy equipment and techniques, offered by five closely collaborating core facilities. The Node is also active in organizing training and courses focused on theoretical and practical aspects of basic and advanced microscopy techniques. Light microscopy instrumentation includes microscopy systems that range from multi-functional point and spinning disc confocal microscopes, light-sheet system up to high-end multi-photon and super-resolution microscopy systems. In the area of electron microscopy, the Node provides expertise and cutting edge equipment for a broad range of biological sample preparation and ultrastructural imaging techniques, including some cryo techniques, electron tomography, SBF-SEM, FIB-SEM and CLEM. Broad expertise in experiment design and data acquisition is also complemented by extensive data analysis services.

Specialties and expertise of the Node

The main strength is the wide and deep expertise covering most of light and electron microscopy biological applications, allowed by the complementary nature of collaborating core facilities and more than 25 FTE of expert staff operating more than 45 advanced microscopy systems. In super-resolution imaging all main approaches are covered, including STED, SIM and SMLM, by multiple commercial systems from different manufacturers. Information about molecular dynamics and interactions can be obtained by functional imaging, particularly from spatial-temporal correlation analysis (point, line and image F(C)CS), FRAP, photoactivation, FRET, FLIM or PLIM. Label-free imaging profits from non-linear processes induced by femtosecond NIR lasers and offers method like SHG, THG, autofluorescence FLIM including metabolic imaging and CARS for lipid droplets visualization. Innovative low-toxicity label-free imaging is offered by quantitative phase imaging (QPI). Plants growing in their natural gravity conditions can be directly visualized on the vertical microscope stage of CZ LSM880 with Airyscan. Fast 3D acquisitions are covered by spinning disc and light-sheet systems. CARS, QPI and SIM technologies, offered by Prague Node, are currently undertaking a Proof-of-Concept Study (PCS) to become official EuBI technologies. Users interested in trying out these technologies are highly welcome! In electron microscopy the Node offers complete workflow from sample preparation (room temperature or cryo- methods, immunolocalisation) through various imaging modalities (TEM, SEM, SBF-SEM, FIB-SEM, MICRO-ARRAY TOMOGRAPHY) to data analysis (clustering and colocalization in immunolabeling, 3D visualizations). Targeted CLEM workflows allow 3D ultrastructural imaging of rare structures. Data analysis ranges from commercial software packages (Imaris, Huygens, Amira, NIS-Elements and many more) via custom modified routines for image processing and analysis (for example image reconstruction, registration and segmentation, volume reconstruction and 3D visualization, tracking, colocalization analysis, mathematical modeling and analysis of photokinetic experiments, and more) to new software and modules development in the field of stereology and spatial statistics, FLIM and FCS methods.

Offered Technologies:

ISIDORe is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.

Deconvolution widefield microscopy (DWM)
Laser scanning confocal microscopy (LSCM/CLSM)
Spinning disk confocal microscopy (SDCM)
Structured illumination microscopy (SIM)*
Total internal reflection fluorescence microscopy (TIRF)
Two-photon microscopy (2P)
cryoFM *
Image Scanning microscopy (ISM)
Single Molecula localisation microscopy (SMLM)
Stimulated emission depletion microscopy (STED)
Light-sheet mesoscopic imaging (SPIM or dSLSM)
Optical projection tomography (OPT)
Coherent Raman Anti-stokes Scattering Microscopy (CARS)*
Quantitative Phase Imaging (QPI)*
Polarisation microscopy (PM)
Second/Third Harmonics Generation (SHG/THG)
High throughput microscopy/high content screening (HTM/HCS)
Fluorescence (cross)-correlation spectroscopy (FCS/FCCS)
Fluorescence Resonance Energy Transfer (FRET)
Fluorescence Recovery After Photobleaching (FRAP)
Fluorescence Lifetime Imaging Microscopy (FLIM)
Intravital Microscopy (IVM)
High-speed Imaging *
Phosphorescence Lifetime imaging (PLIM) *
Anisotropy/Polarisation Microscopy
Tissue Clearing (TC)*
TEM of chemical fixed samples (TEM)
TEM of cryo-immobilized samples (TEM cryo samples)*
serial section TEM
EM tomography (ET)
Serial Blockface SEM
Focussed Ion beam SEM (FIB-SEM)
Array tomography
Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM)
Immuno-gold EM on resin sections (resin-EM)
Pre-embedding immunolabelling (pre-embed IL)
Pre-embed CLEM
Post-embed CLEM
Cryo Electron Tomography (Cryo-ET)*
Cryo Transmission Electron Microscopy (Cryo-TEM)*
Cryo Scanning Electron Microscopy (Cryo-SEM)*
Cryo Focussed Ion beam (Cryo-FIB)*
Scanning Electron Microscopy (SEM)
Elemental analysis including EDS in TEM (STEM)*
live-cell CLEM
in vivo optical imaging (OI)
Atomic Force Microscopy (AFM)*
Image Analysis-bio *

Additional services offered by the Node

  • Instruments
  • Technical assistance to run instrument
  • Methodological setup (e.g. design of study protocol and standard operation procedures)
  • Training in infarstructure use
  • Probe preparation
  • Animal facilities
  • Wet lab space
  • Server Space
  • Data processing and analysis
  • Training workstations
  • Training seminar room
  • Housing facilities
  • Biobanking, biological material storage and processing

Instrument highlights

Leica TCS SP8 STED 3X and Abberior Instruments Easy 3D STED, DeltaVision OMX™ V4, Nikon N-SIM & N-STORM, Leica TCS SP8 WLL SMD-FLIM, Leica SP8 AOBS WLL MP, Bruker Ultima IntraVital, Carl Zeiss LSM 880 NLO, Andor Dragonfly 503, Carl Zeiss Lightsheet Z.1, vertical plant-optimized Carl Zeiss LSM880 with Airyscan, TESCAN Q-PHASE, Jeol JEM-F200 “F2” , FEI Helios NanoLab 660 G3 UC Apreo VolumeScope SEM (Thermo Fisher Scientific), JEOL JEM-2100F with GATAN K2 Summit direct detector).

Contact details

The Prague Node is managed by the Institute of Molecular genetics CAS. Please see the respective contacts below:

Administration contact person
Daniela Klimesova:

Strategic representative (representation in the Panel of the Euro-BioImaging Nodes)
Aleš Benda:

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