Biological Specimens in Electron Microscopes 2025
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Information
Biology Centre of CAS – Institute of Parasitology and Faculty of Science – Institute of Physics and Biophysics, University of South Bohemia, České Budějovice, Czech Republic
This practical course is focused on the advanced methods of biological specimen preparation for electron microscopy. The main goal is to make participants familiar with the theoretical background and the latest practical developments in this field. The programme includes state of the art fixation, including cryo-methods, cutting of ultrathin sections from embedded or frozen samples, methods of negative staining and immunolabeling, specimen preparation for transmission and scanning electron microscopy and methods of specimen preparation for 3D electron microscopy (single particle analysis, electron tomography, array tomography and serial block-face). The results will be evaluated using electron microscopes. The course is limited to 15 participants. It is intended for Master and PhD students, young researchers, technicians, and new EM users. This course is supported by 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)“.
Organizers & Speakers
Marie Vancová
Since 2021, the head of the LEM. Electron microscopy of biological specimens, Sample preparation, Cryo sample preparation, Sectioning, Cryo sectioning, Immunolocalization,
Jana Nebesářová
The former head of LEM. Electron microscopy, Specimen preparation, Sectioning, Biological Imaging
Vladislav Krzyžánek
President of EMS, Electron Microscopy, Biomedical Imaging, STEM imaging, Quantitative imaging
Joshua Lea
Product Scientist at Oxford Instruments WItec, specializing in Raman spectroscopy and RISE microscopy applications. He has experience in developing nanomaterials for sensing and applying Raman spectroscopy for materials characterization.
Louise Hughes
Experienced biological electron microscopist with expertise in biological specimen preparation, 3D electron microscopy, TEM and SEM, SBFSEM, array tomography, electron tomography and data reconstruction. Currently working as a product manager and focused on EDS analytical techniques in life sciences.
Ota Samek
Head of the Biophotonics and Optofluidics group at the Institute of Scientific Instruments of the Czech Academy of Sciences in Brno. His research focuses on the application of Raman spectroscopy and optical tweezers for rapid identification of microorganisms and infection diagnostics.
Jiří Týč
Volume-EM specialist, SBF-SEM, Arry tomography, Confocal microscopy, Bioimaging
Zdeno Gardian
SPA specialist, TEM, SPA, Image processing, Structural biology
Tomáš Bílý
TEM-tomography specialist, Image processing 3D visualization
František Kitzberger
EM-Image processing/segmentation specialist, Volume SEM, Image processing, segmentation, analysis
Programme
23 - 27 June 2025, České Budějovice
| Monday | ||
| Lectures: Introduction to SEM | ||
| 12:45 | Welcome Address | Marie Vancová |
| 13:00 | Principles of Scanning Electron Microscopy | Vladislav Krzyzanek (UPT) |
| 13:45 | Specimen Preparation for SEM | Jana Nebesářová |
| 14:30 | Coffee break | |
| Lectures: SEM-RAMAN-EDS | ||
| 14:45 | Introduction of the new SEM-RAMAN-EDS microscope system | Marie Vancová |
| 15:00 | RAMAN Spectroscopy for the life sciences | Ota Samek (UPT) |
| 15:30 | Combination of SEM and confocal Raman Imaging | Joshua Lea (Oxford Instruments) |
| 16:10 | Introduction to EDS in Life Sciences | Louise Hughes (Oxford Instruments) |
| Tuesday | ||
| Lectures: Volume EM | ||
| 9:00 | Volume EM (SBF-SEM, Array Tomography) and Specimen Preparation | Jiří Týč |
| 10:00 | Introduction to Image Processing and Quantification | František Kitzberger |
| 10:45 | Coffee break | |
| 11:00 | FAIR data | František Vorel |
| 11:30 | Lunch | |
| Practicals: Volume EM | ||
| 12:30-17:00 | ||
| Group 1: Volume EM, SEM Apreo | Jiří Týč | |
| Group 2: Volume EM Image Processing | František Kitzberger | |
| Wednesday | ||
| Lectures: TEM | ||
| 9:00 | Principles of Transmission Electron Microscopy | Tomáš Bílý |
| 10:00 | Specimen Preparation for TEM at Room Temperature | Marie Vancová |
| 10:45 | Coffee Break | |
| 11:00 | Visualization of Macromolecules in TEM, Negative Staining | Zdeno Gardian |
| 11:30 | Electron Tomography | Tomáš Bílý |
| 12:00 | Lunch | |
| Practicals: TEM | ||
| 13:00-17:00 | ||
| Group 1: Basic TEM Operation – JEOL 1400 | Tomáš Bílý | |
| Group 2: Negative Staining, TEM, and SPA – JEOL 2100F | Zdeno Gardian | |
| Thursday | ||
| Lectures: Cryo Methods, Immuno-EM, Sectioning | ||
| 9:00 | Cryo Methods in Sample Preparation | Marie Vancová |
| 9:40 | Immunogold Labeling | Marie Vancová |
| 10:20 | Coffee Break | |
| 10:40 | 10:40 Tokuyasu Method Practical demonstration | Martina Tesařová |
| 11:40 | Lunch | |
| Practicals: Sectioning, Contrasting, Immuno-EM | ||
| 13:00-17:00 | ||
| Group 1: Semithin/Ultrathin Sectioning, Contrasting | Petra Masařová, Jana Kopecká | |
| Group 2: Immunolabeling and TEM | Marie Vancová, Martina Tesařová | |
| Friday | ||
| Practicals: Sectioning, Contrasting, Immuno-EM | ||
| 9:00-12:15 | ||
| Group 1: TEM Grids: Formvar and Carbon Coating, Correlative Approaches, Staining | Petra Masařová, Jana Kopecká, Martina Tesařová | |
| Group 2: High-Pressure Freezing and Freeze Substitution (HPF/FS) | Marie Vancová | |
| Group 3: Cryo-EM Workflow for Protein Visualization | Zdeno Gardian | |
| Group 4: Electron Tomography | Tomáš Bílý | |
| Group 5: SEM Operation | Jiří Týč | |
| Group 6: Image Quantification | František Kitzberger | |
| Group 7: SEM Sample Preparation | Jana Nebesářová | |
| 12:15 | Round Table Discussion and Closing Remarks | |
Registration
Registration Fees:
Academia: up to 2 500 CZK
Industry: up to 10 000 CZK
The course fee will be calculated according to the sessions chosen during the registration. See the registration form for the details. Fee includes admission, the course materials, course dinner and coffee breaks.
Lunches can be ordered extra. (for additional 120,- CZK per day)
For registration click here
Contact: Martina Tesařová (holland@paru.cas.cz)
Venue and accomodation
Venue: Laboratory of Electron Microscopy, Biology Centre CAS, České Budějovice.
Branišovská 31, 370 05, České Budějovice, Czech Republic
(See map below)
How to get to the venue
By public transport:
From the train station of the bus station, go the bus stop located under the Mercury shopping centre and take bus No. 3 in direction Máj – Antonína Barcala and get off at the bus stop Jihočeská Univerzita. Then cross the street to the university campus and from go to the building of the laboratory.
By car:
In case you plan to get here by the car, go to the address: Branisovska 31, 370 05, České Budejovice. You can park your car on the parking lot at the Biology Centre. (ring at the gate and tell that you participate on this course if asked). Other parking possibility is at the recomended accommodation site.
Accommodation
You can arrange your accommodation either in the Penzion U Šípku (contact person: Marie Hloušková, +420 604 375 441, usipku.cb@seznam.cz), or in the Penzion Dvořák (+420 721 810 410, PenzionDvorak@email.cz). Both of the pensions are located within 15 minutes of walk from the venue. For closer information see the map.
