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:
27-31 January 2025
Viničná Microscopy Core Facility, Viničná 1594/7, 128 00 Prague
Join the comprehensive course organized by the Viničná Microscopy Core Facility at the Charles University, Prague to master image analysis using cutting-edge tools like ImageJ, Huygens, Arivis Vision4D, and Python. You’ll learn key techniques including deconvolution, segmentation, colocalization, and deep learning models, alongside practical applications in biological imaging.
Course Highlights:
Perfect for researchers and scientists looking to elevate their image analysis skills!
Course website:
To sign up contact the course organizer Mgr. Zuzana Burdíková, Ph.D. at burdika@natur.cuni.cz
2-5 December 2025
MUNI CELLIM CEITEC
This comprehensive course is designed specifically for biologists to master cutting-edge image analysis software. It covers both the theory of image processing and its practical applications, focusing on precise and efficient image quantification, segmentation, and visualization techniques. Participants will gain hands-on experience with industry-leading commercial and open-source tools and elevate their data analysis skills to the next level.
The course also introduces the FAIR principles for scientific data and demonstrates effective strategies for data management using the OMERO database.
The course is organized by the Cellular Imaging Core Facility (CELLIM) and the Data Management Core Facility of CEITEC MU, in collaboration with the CBIA Core Facility of the Faculty of Informatics, Masaryk University.
The practical course “Image Data Presentation” is designed to explore the processing of scientific images, especially microscopic data, for presentation, mainly in scientific journals.
What Will We Learn?
• Understanding Image Quality: What are the standards for high-quality scientific images? How do we define this quality?
• Differences in Image Data: What distinguishes images meant for analysis from those intended for presentation?
• Tools and Software: How we can use the Adobe suite or viable freeware alternatives?
• Image Formats and Compression: Which formats are best for scientific presentation? Can we compress these images without losing quality?
Course Structure: This course will combine lectures and practical sessions. We will use real examples using different softwares (Adobe Photoshop, Adobe Illustrator, GIMP, Inkscape).
Additionally, we will briefly discuss quick finalization and data export formats for presentation using Fiji ImageJ. We’ll also compare text input in MS Word and LaTeX.
The course is focused on theoretical explanation and practical demonstration of advanced methods of HR SEM, such as FIB-SEM, SBF SEM, micro-array tomography, low-voltage STEM and cryo application in biology. The program will also include specimen preparation, basics of 3D reconstruction, and data interpretation.
The selective practical course “Live cell imaging” is an intensive educational block focused on the investigation of living cells and whole organisms using light and fluorescence microscopy. During the course, participants will learn about a wide range of instruments using a variety of methods suitable for imaging live specimens. They will learn what methods can be chosen for a given type of specimen, what their advantages are, as well as what their limitations and shortcomings are. They will also learn about the possibilities of studying the kinetics of processes in living cells and the procedures for preparing samples containing living cells, tissues and organisms.
The morning of each of the three days is filled with lectures on microscopy systems and methods, including several short scientific papers aimed at demonstrating the data that can be obtained by these approaches. The emphasis is then primarily on the afternoon practical part of the course, where participants will try their hand at working with a selection of microscopes on real live specimens. During the hands-on sessions, participants will be motivated to actively participate in the set-up of each instrument, data acquisition and subsequent data evaluation. Day one will focus primarily on widefield systems, day two will focus on confocal methods, and day three will cover advanced methods including superresolution and kinetic measurements.
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.The course will cover the most widespread FLIM realization – acquisition in time domain based on raster scanning combined with pulsed lasers and time-correlated single photon counting (TCSPC). Participants will hands-on three different systems, covering pulsed diode lasers, white-light laser source as well as two-photon excitation, SPAD, HyD and GaAsP NDD detectors and three different TCSPC systems and software.The demonstrated applications will include FLIM-FRET, environmental sensing and label free imaging (autofluorescence, SHG, THG, CARS).
The course is designed to provide an orientation to basic and special techniques in biomedical electron microscopy in an application-oriented manner. The course will include both theoretical and practical sessions. Sample preparation under room temperature and cryo conditions will be covered, including special workflows such as immunolabeling, freeze-fracture replica, or cryo-CLEM workflow on FIB-milled lamella. Practical aspects will be explained in the lectures and prepared as a set of practical tasks for the participants. Besides basic imaging, special techniques such as (cryo)FIB-SEM, STEM tomography and EDS analysis will be demonstrated. Special emphasis will be placed on discussing how to choose the appropriate methodology for a specific scientific project.
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