2 – 4 December 2026
Institute of Experimental Medicine, Vídeňská 1083, 142 20, Prague
This course is aimed at participants familiar with the basics of image processing, who want to automate their analysis using scripting. We will work with ImageJ macro language and use it to create a workflow for segmentation, batch processing and analysis of fluorescence microscopy images. In the second part of the course, we will introduce Cellpose, a machine learning algorithm for cell segmentation, demonstrate its use through command line and ImageJ plugin, and incorporate its output into the ImageJ workflow.
No previous programming knowledge is expected, and the course will therefore also briefly introduce basic programming concepts, such as variables, for loops and conditionals (if-else statements). Most of the sessions will be hands-on, and the last day will be dedicated to individual consultations of user projects and questions.
The course is primarily aimed at participants with some experience with ImageJ and basic understanding of bioimage analysis. We expect no or minimal knowledge of programming.
Participants are required to bring their own laptop for hands-on exercises. If you do not have access to a laptop, please inform us in advance, and we will provide you with one. Prior to the event, you will receive a list of the required software programs to install for the course.
Please make sure that all required software is installed and works prior to the workshop, especially if your laptop runs macOS or Linux (we work mostly with Windows and are therefore not as familiar with the other operating systems, therefore troubleshooting during the course is difficult).
28 – 29 May 2026
Institute of Experimental Medicine, Vídeňská 1083, 142 20, Prague
This course introduces participants to the fundamentals of volumetric and time-lapse microscopy data processing, with a focus on visualization, segmentation, and quantitative analysis. The first day offers a hands-on introduction to Imaris, covering its core modules (Spots, Surfaces, and Filaments). The second day builds on this and includes a broader discussion on big data challenges, alternative 3D processing tools in ImageJ/Fiji, and options for data storage, sharing, and reuse (FAIR data).
The course is organized in hybrid form and it is possible to join either in-person or online.
Imaris is the main software used, and the course is designed to provide a comprehensive overview of its capabilities. As such, it is primarily aimed at participants with no or limited experience. However, advanced features and exercises will also be included to benefit those already familiar with the software.
24 – 25 November 2026
Building Da I. IPHYS BIF, Krc Campus, Videnska 1083, Prague
Course fee is 40 Euros
The two-day course consists of lectures and hands-on sessions which will demonstrate basic mechanical testing methods such as atomic force microscopy, Brillouin 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 or confocal reflectance microscopy.
1 – 4 December 2026
Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, Czech Republic
The three/four-day (TBD) course organized by the ISI EM team at the Institute of Scientific Instruments of the Czech Academy of Sciences will offer students and young researchers in the fields of life sciences and soft materials both theoretical and practical training in electron microscopy and Raman spectroscopy. Participants will gain hands-on experience with SEM and FIB-SEM microscopes, biological sample preparation, EDX analysis, and cryo-SEM workflow. The program will combine introductory lectures with intensive hands-on sessions in small groups and will be complemented by a social evening and discussion sessions at the end of each day.
Link coming soon
20 – 24 April 2026
First Medical Faculty, Charles University, CAPI, Salmovská 3, 120 00 Prague
Language: Czech
Course for acquiring qualification and professional competence (designing experiments and experimental projects) in the field of experimental animal use according of Act No. 246/1992 On the Protection of Animals Against Cruelty.
Link coming soon
9 – 13 March 2026
First Medical Faculty, Charles University, CAPI, Salmovská 3, 120 00 Prague
Language: English
Course for acquiring qualification and professional competence (designing experiments and experimental projects) in the field of experimental animal use according of Act No. 246/1992 On the Protection of Animals Against Cruelty.
Link coming soon
6-12 September 2026
Centre for Biomedical Image Analysis Faculty of Informatics, Masaryk University, Botanická 68a Brno, 602 00
The summer school is focused on the advanced methods of biomedical image analysis with emphasis on bio- (microscopy) image analysis. The main goal is to make the students familiar with the advanced state-of-the-art techniques of mathematical morphology, image segmentation, object detection and tracking, synthetic image generation, benchmarking, etc. The focus will be on the methodology suitable for multiple applications. Special attention will be paid to the combination of machine learning and classical approaches.
Target groups are Master and Ph.D. students of computer science, mathematics or engineering backgrounds specialized in signal and image processing. Students are supposed to know the basics of signal and image processing, machine learning and have some programming experience in this field. The main activities of the course will be theoretical lectures supplemented by practical examples run on students’ computers.
29 June – 3 July 2026
Viničná Microscopy Core Facility, Viničná 1594/7, 128 00 Prague
This workshop will provide a hybrid experience, including presentations and hands-on sessions in-person only. Our program will cover topics ranging from introduction to super-resolution microscopy to image processing and data visualization. We have a lineup of expert speakers and instructors, who will share their knowledge and guide you through the hands-on sessions.
Day 1 will feature an introduction to super-resolution microscopy, image processing, and image analysis in FIJI, ImageJ. There will also be an optional facility tour and installation session for ImageJ and Thunderstorm.
Day 2 will include a session on ThunderSTORM, a comprehensive ImageJ plug-in for SMLM data analysis and super-resolution imaging, as well as a scientific lecture on the functional organization of the cell nucleus revealed by quantitative super-resolution microscopy. The day will culminate with hands-on sessions in ThunderSTORM, where participants will be divided into groups based on their experience level.
Day 3 will focus on customizing Fiji/ImageJ with ImageJ Macro and the interactive design of GPU-accelerated image data flow graphs in Fiji.
Day 4 will focus on UC2 technology with a hands-on part
Day 5 will be dedicated to the Airyscan microscopy with a hands-on part
In addition to the technical sessions, there will be an informal discussion in the Academic Club on the second evening, providing an opportunity to network and exchange ideas with your peers.
12-13 + 16-17 February 2026
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
While the skills learned during the course will have broad applications (data analysis, plotting, scripting…), the focus of exercises will be on image analysis and processing topics. Prior knowledge of digital imaging is helpful but not required.
This course is structured in two parts:
Introductory Session: Tailored for absolute beginners in Python programming. Participants will start with Python installation and basic syntax, progressing to practical exercises focused on working with digital images and relevant libraries for I/O, measurements, ploting and more. Batch processing of multiple images and an intro to Napari (a Python-based interactive image visualization tool) will also be covered.
Advanced Session: This session offers extended hands-on practice, more complex image analysis cases, alternative approaches, and the use of AI tools such as Cellpose for segmentation. This session builds on python skills from the first session. It is ideal for those who completed the introductory session, but also open to participants with basic Python experience. The ability to set up and run a working Python environment is a prerequisite.
Applicants may register for either part or both.
10 – 13 November 2026
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
Hands-on training on selected time-resolved experimental techniques and data analysis, commonly called Fluorescence Lifetime Imaging Microscopy.
The course focuses on explaining the principles of nano-second time-resolved fluorescence detection, on demonstration of different hardware realizations, on trying various applications of FLIM in biological imaging and on testing of several ways of FLIM data analysis.The aim is to uncover the richness of information hidden in multiparametric fluorescence imaging and to inspire the participants to use the easily obtainable extra contrast in their imaging applications. An important part is to make the FLIM data analysis understandable.
Testing of your own samples is available anytime after (or even before) the FNOB course upon agreement with IMCF staff (may be a subject to instrument fees).
8 – 10 June 2026
Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
The practical hands-on oriented course is strongly focused on super-resolution methods in light fluorescence microscopy field. The major objective of the course is to introduce newly available methods and cutting-edge machines to potential users: PhD students, postdocs and researchers in the biology.
The course is operating on the scale behind the resolution barrier for standard fluorescence microscope; from lateral resolution 180 nm down to the 25 nm. To solve this, the course theoretically and practically covers methods from high-resolution confocal microscope through computational super-resolution, structured illumination and stimulated depletion microscopy up to the single molecule localization microscopy.
The course covers theoretical background of all presented super-resolution techniques. Each practical session is designed like a demo and continuous to a hands-on.
13 – 16 April 2026
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
This course provides participants with an insight into the complexity and principles of biological sample preparation necessary for routine ultrastructural analysis by Transmission or Scanning electron microscopy. An emphasis is given to definition of critical steps in sample preparation workflows and their optimization to suit specific type of samples (from nanoparticles to cells, tissues and bio-composites) and to specific aims of the analysis. The practical part of the course will cover sample harvesting, chemical fixation, contrasting, resin embedding, ultra-thin sectioning, negative staining, critical point drying, plunge freezing and more. The EM-SPS course is organized by the Imaging Methods Core Facility at BIOCEV as an annual course supported by the National Infrastructure for Biological and Medical Imaging (Czech-BioImaging, Ministry of Education, Youth and Sports – Large Research Infrastructure, LM2023050).
