09 – 10 December 2025
Building Da I. IPHYS BIF, Krc Campus, Videnska 1083, Prague
The two-day course consists of lectures and hands-on sessions which will demonstrate basic mechanical testing methods such as atomic force microscopy, indentation test or uniaxial and biaxial tensile test. The tests will be introduced in practical sessions together with their biological and methodological relevance. To relate the mechanical tests to the most significant biomechanical structures such as collagen fibers, elastic fibers or fat, the participants will be taught how to link these mechanical properties and microscopy images. Due to the minimum sample alternations, the images are acquired using label-free techniques, for instance, pSHG, THG or CARS.
18 – 21 November 2025
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
Practical hands-on training on 3D correlative light and electron microscopy combining confocal fluorescence imaging and electron microscopy imaging contain focused ion beam milling (FIB-SEM) and electron tomography (ET).
Light, particularly fluorescence, microscopy offers live-cell compatibility and flexibility in labelling by specific molecular probes. In this way, insight into the function of cells at their native state can be obtained. Electron microscopy, on the hand, provides unmatched spatial resolution. Correlative light and electron microscopy (CLEM) combines the unique information from both techniques in a single image. During the course you will try hands-on a complete CLEM workflow from sample preparation to image processing. The hands-on sessions will be conducted using the state-of-the-art equipment available at IMCF, including high-end fluorescence confocal microscopes, scanning electron microscope (SEM) with focused ion beam (FIB) milling and transmission electron microscope (TEM).
14 – 15 October 2025
Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6
We are pleased to invite you to the annual two-day course ‘Multimodal Light Microscopy Imaging in Plant Research’ organised by the Imaging Facility IEB in Prague, on 14–15 October 2025.
This year, expect a whirlwind of new technologies presented in four parallel hands-on sessions. Look forward to 3D lifetime STED super-resolution microscopy (Mirava from Abberior Instruments); Lattice Lightsheet 7 (Zeiss); Microfluidics on Vertical stage spinning disk; and Image Analysis and Data Presentation.
The invited speakers are Stefanie Weidkamp-Peters (HHU Duesseldorf); Aleš Benda (Biocev Prague); Gero Schötel (Abberior Instruments); and Pavel Krist (Zeiss).
Tailored to experienced users.
Please register by sending an email to ifieb@ueb.cas.cz. The number of participants is limited to 28.
Registration fee – 1000 CZK.
13 – 17 October 2025
Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
The five-day theoretical course with practical demonstrations is devoted to modern light and electron microscopy, and the program is updated every year to reflect the newest trends. The course covers the theoretical background of microscopy as well as fundamental techniques in microscopy, and continues quickly to cutting-edge methods like super-resolution light microscopy, light-sheet microscopy, imaging of whole living organisms, and cryo-electron microscopy.
In the theoretical part, the course will cover the principles of light and electron microscopy, image creation, biological sample preparation recommendations, and will provide a guidance through the principal image processing procedures. The practical part of the course consists of demonstrations in smaller groups at the instruments, covering a wide range of microscopy methods, including Koehler illumination adjustment, widefield fluorescence microscopy, fluorescence macroscopy, confocal scanning and spinning disc microscopy, quantitative phase microscopy, light-sheet microscopy, advanced superresolution microscopy (STED, SIM), transmission electron microscopy, scanning electron microscopy, and cryo-methods of EM sample preparation.
After completing the course, the participant will be able to determine which microscopic technique should be used in order to answer the research question, including the sample preparation and data processing for publication. However, do not expect a detailed technical training on the microscopes or advanced training on sample preparation, super-resolution techniques or electron microscopy, these are part of the more specialized courses which we highly recommend (see course.img.cas.cz for details).
The course is primarily intended for PhD students and young researchers in the biomedical fields. A number of doctoral committees counts this course towards the fulfillment of student’s study obligations.
The course is an introduction to both light and electron microscopy with solid theoretical background extended with many practical presentations. The lectures and also practical sessions are taught by experts and scientists from the field or by product specialists from leading microscopy companies.
23 – 27 June 2025
Laboratory of Electron Microscopy, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31 370 05, České Budějovice
TBD
13 May – 14 May 2025
Light Microscopy Core Facility, Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
This one-day course focuses intensively on image data segmentation and cell tracking using state-of-the-art deep learning methods like StarDist, Cellpose, Omnipose, and MitoSegNet. It demonstrates how segmentation aids in analyzing image-based objects and how tracking applies segmentation to study cells dynamically over time. TrackMate, a plugin in Fiji, integrates StarDist and Cellpose for cell segmentation and tracking. The course also covers the Delta2 framework for tracking dense bacteria populations and explores ZeroCostDL4Mic, a cloud computing framework with advanced deep learning methods for microscopy tasks like segmentation, object detection, and denoising. The course aims to highlight the practicality and user-friendly nature of these deep learning techniques.
Also, a sponsor’s lecture on Apeer.com, Zeiss’s cloud platform, will focus on image processing, including machine and deep learning. At the course’s end, participants can actively practice segmentation and cell measurement using a virtual reality system from the same company.
7 – 9 April 2025
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
The course will focus on basic operations in cryogenic electron microscopy (cryoEM), cryoimaging of vitrified particulate specimens (e.g. microtubules, vesicles, viruses, etc.) and the possibility of correlation with cryogenic fluorescence microscopy (cryoFM). The lectures will cover the theoretical principles of EM/cryoEM and FM/cryoFM. During hands-on sessions, participants will gain practical experience with cryo-sample preparation techniques (Plunge Freezer, High Pressure Freezing) and cryo-imaging using confocal fluorescence microscope and transmission electron microscope. The course is particularly suitable for beginners in cryoEM with little or no experience in the field.
31 March – 4 April 2025
Light Microscopy Core Facility, Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
The course will address fundamental aspects of image data acquisition, processing, and analysis, encompassing techniques in stereology. Alongside theoretical principles, the course will prioritize hands-on practical learning. Participants will gain proficiency in utilizing the freely available software package Fiji for both basic and advanced analyses. They will learn to assess co-localizations, analyze data from FRAP and electron microscopy, track particles, segment objects in images, and explore methods of employing artificial intelligence for image segmentation.
Additionally, participants will master techniques to enhance data quality through deconvolution using Huygens software. An interactive session featuring Imaris software will be complemented by practical exercises. Furthermore, this year introduces new demos for analyses using the NIS Elements package and a lecture about the proper way of publishing images in scientific journals. Independent practical tasks involving Fiji and Huygens will also constitute a significant component of the course.
While the course aligns with the Microscopy Methods in Biomedicine, prior attendance is not a prerequisite for participation.
3-7 March 2025
Electron Microscopy Core Facility, Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
The course is designed for users of electron microscopes in biomedical field, both from scientific laboratories and from core facilities. The aim of the course is to provide an orientation to basic and special techniques in biomedical electron microscopy in an application-oriented manner. In the theroretical and practical sessions, sample preparation under room temperature and cryo conditions will be covered, including special workflows such as cryo-sectioning, freeze-fracture replica, or cryo-CLEM workflow on FIB-milled lamella. Besides basic imaging, special techniques such as (cryo)FIB-SEM, STEM tomography and EDS analysis will be demonstrated, with introduction to data processing and interpretation. Special emphasis will be placed on discussing how to choose the appropriate methodology for a specific scientific project.
28-30 May 2025
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
The fastest and most gentle 3D live-cell imaging on the Carl Zeiss Lattice Lightsheet 7, used for tracking the trafficking of fluorescently labeled proteins in living cells, will be complemented by FRAP on the Nikon iLas 2 ring-TIRF/FRAP and Nikon CSU-W1, as well as by FCS on the Leica TCS SP8 WLL SMD-FLIM for measuring protein diffusion in the plasma membrane of living cells. Finally, model systems of molecular motors walking along microtubules, visualized using the Nikon Ti-E H-TIRF, will demonstrate the benefits of single-molecule approaches for studying molecular motion.
This course includes theoretical and hands-on training in four complementary microscopy approaches for visualizing and measuring the lateral movement of molecules in living cells or model systems.
The microscopy techniques covered in the course:
11-12 February 2025
Building Da I. IPHYS BIF, Krc Campus, Videnska 1083, Prague
The two-day course consists of lectures and hands-on sessions which will demonstrate basics in design of experiments, for instance hypothesizing, sampling, data dependency, statistical power or hypothesis testing in biology. The examples will be provided in the field of light microscopy and proteomics. The participants will learn the ways to correctly acquire data using high-end microscopes using a wide pallet of methods such as FLIM, SHG or CARS or proteomic approaches. In addition to that the participants will process and analyse the data using traditional approaches, stereology or AI tools or VR in Fiji or Python. Finally, the participants will be taught the data interpretation and presentation.
Although the course is biology science oriented, the skills you will acquire are valid and necessary in any area of research, development or industry.
3-7 February 2025
Room B311, Viničná Microscopy Core Facility, Viničná 1594/7, 128 00 Prague
This 5-day workshop is intended to give a thorough introduction to Bioimage analysis for individuals with little to no prior experience but who want to develop some basic skills in image processing and analysis workflows using both open-source and proprietary software. Participants will get hands-on experience with image restoration, segmentation techniques, feature extraction and tracking using classical and advanced machine and deep learning tools. Most importantly, students will gain insight in data visualization and analysis for reproducible research. By the end of the workshop, attendees will have the opportunity to work on a final project, in which they will be able to apply the newly learned skills on a real-world bioimage analysis challenge.
By the end of this workshop, participants will be able to:
