CANCELLED FOR 2025
Microscopy Service Unit of the IEM CAS / Bioimaging Facility of the IPHYS CAS / Core Facility – Magnetic Resonance of the ISI CAS
The course aims to teach multimodal preclinical imaging techniques, including in vivo two-photon microscopy, in vivo multi-photon-based label-free techniques (SHG, THG, CARS), and magnetic resonance imaging (MRI) of small rodents. Participants will acquire theoretical knowledge and practical skills in various neuroimaging techniques, with a focus on intravital multi-photon microscopy and MRI principles. Emphasizing the importance of animal models in physiological research, the course guides participants through the entire process of conducting preclinical bioimaging experiments. It includes a detailed pipeline for analyzing brain tumour structures and functional parameters, covering cranial window surgery, two-photon microscopy usage, perfusion MRI and subsequent image analysis. Additionally, the workshop addresses the challenges in using animal models for research and provides access to field experts.
Course fee: 11500 CZK incl. VAT (approx. 450 EUR)
Registration deadline: 30. 6. 2025
Registration is handled on a first-come, first-served basis, and places are limited to 10 participants. To secure a spot, payment must be completed upon receiving the invoice.
As part of the registration process, applicants are asked to describe their expectations for the course, the challenges they would like to address, and how the knowledge gained will benefit their research. The response should be 200-300 words long.
If the number of applicants exceeds the available spots before all registrations are confirmed, priority will be given based on the relevance of each applicant’s description of their expectations and how they plan to apply the knowledge gained.
Once registered, applicants will receive an invoice, and their place will be confirmed once payment is received.
The fee covers all course materials and teaching, meals throughout the course, refreshments during the opening and closing social events, transportation between Prague and Brno, and accommodation in Brno for the night from Thursday to Friday. It does not include travel costs to and from the course location (except for the provided transportation between Prague and Brno) or accommodation from Monday to Thursday.
12 – 14 November 2025
Institute of Experimental Medicine, Vídeňská 1083, 142 20, Prague
The course is tailored to users already familiar with the basics of image processing. It will be focused on automatization, high throughput and basic scripting. Course participants will learn how to create and edit macros in ImageJ and how to write more sophisticated scripts for batch processing. Furthermore, they will learn the basics of image processing in Matlab and Cellpose.
22 – 23 May 2025
Institute of Experimental Medicine, Vídeňská 1083, 142 20, Prague
This course is designed to introduce participants to the fundamentals of volumetric and time-lapse data processing. It covers various tools for processing, visualization, and quantitative analysis of 3D/4D microscopy data. The first part of the course will provide an introduction to Imaris software, while the second part will explore several other software options.
The course includes hands-on sessions, giving participants the opportunity to personally explore and use the tools. No prior knowledge of the software is required.
27 – 28 May 2025
Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6
TBD
13 – 14 October 2025
+ 20 – 21 October 2025
Imaging Methods Core Facility, BIOCEV, Průmyslová 595, 252 50, Vestec
This course is structured in two parts and applicants may register for either part or both:
Introductory Session (October 13-14): Tailored for absolute beginners in Python programming, with a particular emphasis on image analysis and processing. While the skills learned will have broad applications, the focus will center on essential techniques for working with digital images. Prior knowledge of digital imaging is helpful but not required, as all methods will be clearly demonstrated and explained to build a strong foundation in the basics.
Advanced Session (October 20-21): A continuation of the introductory session, focusing on more complex methods, alternative approaches, and hands-on practice with tools like Napari for advanced visualization and AI tools like Cellpose for segmentation. This session builds on skills from the first part, making it ideal for participants who have completed the beginner session and wish to deepen their expertise.
Applicants may register for either part or both.
Covered topics:
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.
