Electron Microscopy

Vlada Filimonenko

Facility leader

Vlada Filimonenko
LocationIMG – building F
1st floor – rooms 1.60, 1.52
basement – rooms 01.155.1, 01.150, 01.152, 01.153, 01.154, 01.151
Phone+420 241 063 153
DocumentsHow to properly acknowledge the core facility in publications


The Electron Microscopy core facility provides expertise and cutting edge equipment for a broad range of biological sample preparation and ultrastructural imaging techniques. The core facility deals with various biological samples: human and animal cell cultures, plant and animal tissues, worms, microorganisms, lipid micelles. The sample preparation techniques include routine chemical fixation and resin embedding, cryofixation using high-pressure freezing technique, freeze-substitution, plunge-freezing, cryosectioning, and immunolabeling, including simultaneous detection of multiple targets by our self-developed methods.

High-pressure freezing machines, two automatic freeze-substitution machines, freeze-fracture and replica making device, cryo-ultramicrotomes, Leica EM GP2 for automated plunge-freezing, as well as additional wet lab equipment are available. The core facility is equipped with two transmission electron microscopes (TEM) installed in November 2019 – a standard instrument for routine observation and an advanced 200 kV instrument providing the possibility of high-resolution TEM, STEM, 3D electron tomography, cryo-electron microscopy and EDS elemental analysis and mapping.

Our team has a long expertise in the development and optimization of sample preparation techniques for electron microscopy. We have optimized the cryofixation of cultured cells and sample processing after cryofixation, developed a completely new system for simultaneous immunolabeling of five molecular targets, a special technique for combination of 3D pre-embedding immunolabeling and 2D on-section immunolabeling to provide more possibilities for spatial analysis of biological processes. Currently we are working on development of a free online tool for quantification of immunolabeling in electron microscopy. We also collaborate with the companies developing instrumentation for electron microscopy to contribute in development of sample preparation for various modes of microscopic analysis.

We provide open access for our technologies and expertise via Czech BioImaging and Euro BioImaging infrastructures. As the spectrum of approaches and workflows in electron microscopy is very wide, we help the users to select an appropriate technique and to plan the whole experiment. The sample preparation and image acquisition can be done fully by facility staff or we can provide sufficient training and initial support for independent use of the technologies and equipment. We organize a yearly one-week practical course of transmission electron microscopy in life sciences for beginners and intermediate users.

The Electron Microscopy core facility associated to the IMG Microscopy Centre is part of the IMG Czech-BioImaging node and Prague Euro-BioImaging node.

czech bio-imaging logo


Financial Support

The Electron Microscopy core facility is supported from the program for large research infrastructures of the Ministry of Education, Youth and Sports within the project – National Infrastructure for Biological and Medical Imaging (Czech-BioImaging – LM 2018129).

The modernization of equipment was supported by OP RDE (CZ.02.1.01/0.0/0.0/16_013/0001775 – Modernization and support of research activities of the national infrastructure for biological and medical imaging Czech-BioImaging).

Additional information about group