16 – 17 March 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 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 omics. 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 Brillouin microscopy or basics of omics approaches. In addition to that the participants will process and analyse the data using traditional approaches, stereology or AI tools 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 – 5 November 2026
Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
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, 12-15 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.
Refreshments and meals are provided throughout the course.
26 – 27 May 2026
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 Basics of Light Microscopy Imaging in Plant Research organised by the Imaging Facility IEB in Prague.
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TBA
13 – 14 October 2026
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 Advanced Multimodal Light Microscopy Imaging in Plant Research’ organised by the Imaging Facility IEB in Prague.
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TBA
19 – 20 May 2026
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.
13 – 17 April 2026
Light Microscopy Core Facility, Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
The course will delve into 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 a new series of practical sessions utilizing Napari, a Python-based environment for image processing. Independent practical tasks involving Fiji and Huygens will also constitute a significant component of the course.
12 – 16 October 2026
Institute of Molecular Genetics, Vídeňská 1083, 142 20, Prague
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 and also by product specialists from leading microscopy companies. The five-day theoretical course with practical demonstrations and exercises, is intensively devoted to modern methodologies of light and electron microscopy. Compared to previous years, the program of the course has been updated to copy new trends in microscopy such as super-resolution light microscopy (SIM / PALM, STED, STORM) or Atomic Force Microscopy (AFM).
During the course, participants will see practical demonstration of confocal, 2-photon and also cutting-edge superresolution microscopy – STED and SIM. The course also deals with the processing of the image data, however, priority is to acquire practical skills in microscopy techniques (image analysis is the main topic of the course Processing and analysis of microscopic images in biomedicine ). After completing the course, the participant will be able to determine what is appropriate microscopic technique used to answer the research questions, including the preparation and data processing for publication.
Detailed methodological guidance and technical training are part of the more specialized courses. 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 students’ study obligations. The course will be taught in English.
The course is jointly organized with the IPHYS BIF core facility.
17-18 September 2026
CEITEC Brno University of Technology, B0.04, Purkyňova 123, Brno
Digital holographic, interference, fluorescence and confocal microscopy and its use in modern medicine, deployment of live cells, operating the Q-Phase microscope
TBA
Dear Czech-BioImaging Users and Friends,
with the beginning of the new year, we are pleased to announce the launch of the new visual identity of Czech-BioImaging. This update reflects the steady development and growth of our research infrastructure, as well as our effort to keep pace with recent trends in imaging and scientific communication. It also mirrors the expanding user community we serve and our ongoing commitment to quality, scientific excellence, reliability, and continuity.
Our new logo builds on the foundations of the previous one. It retains our signature blue colour to preserve continuity, while its simplified and modernised form improves clarity and readability across formats. The refreshed visual identity introduces a unified system that strengthens our communication across all facilities and enhances how we present Czech-BioImaging to the wider public.
Why we refreshed our identity
As Czech-BioImaging continues to grow, so does our responsibility to communicate clearly and consistently with our users, collaborators, and partners in the Czech Republic and abroad. A strong and coherent visual identity helps us represent who we are today and how our infrastructure has evolved over the years.
The refreshed identity enables us to:
The new identity is the outcome of a thoughtful design process carried out in collaboration with graphic designer Martin Vosátka. It is grounded in our long-term mission, shaped by feedback from our community, and guided by the principles set during the development of our brand.
A logo inspired by imaging
The new Czech-BioImaging logo is grounded in the visual language of imaging.
Its concentric, rotational elements reference lens adjustment and focus, symbolising precision, clarity, and the interconnected network of our facilities.
The accompanying logotype ensures readability and a modern, clean presentation suitable for both digital and print environments.
Together, the symbol and wordmark create a clear and flexible logo system that represents our scientific focus and the collaborative nature of Czech-BioImaging.
A colour palette built for clarity and impact
Our updated colour palette is designed to support clear communication while remaining visually distinctive. It is based on four primary tones:
A complementary secondary palette expands the system for posters, outreach materials, and digital communication, allowing flexibility without losing consistency.
Typography that supports readability
The primary typeface, Open Sauce One, was chosen for its balance of modern design and excellent readability. A clear typographic structure helps us communicate scientific content in a way that is accessible, precise, and visually coherent. Where required, Roboto serves as a reliable replacement.
Patterns derived from our core symbol
The new brand identity incorporates a modular pattern system derived directly from the logo symbol. These patterns can be used in both subtle and expressive applications — from digital backgrounds to printed materials — helping create a unified visual environment across Czech-BioImaging.
Where will the new identity appear?
The updated identity will gradually be introduced across:
Our goal is to make the transition smooth and ensure that all materials reflect the same high standard of clarity, professionalism, and visual cohesion.
A brand that represents our community
This new visual identity underscores our long-standing commitment to open access, expert support, and high-quality imaging services. It also reflects the collaborative nature of our infrastructure — shaped by the work of our facilities, the contributions of our staff, and the creativity and needs of our users.
We look forward to presenting Czech-BioImaging with an identity that supports our mission and strengthens the visibility of the imaging community in the Czech Republic and beyond.
In November 2025, Czech-BioImaging welcomed members of its International Advisory Board (IAB) for a series of on-site visits to Core Facilities across the national network. The IAB visits marked an important milestone in the Performance Assessment process, which provides an independent, international evaluation of the scientific quality, user services, and strategic development of the facilities.
Over three days, IAB panels specializing in Medical Imaging, Light Microscopy, and Electron Microscopy visited facilities in Olomouc, Brno, České Budějovice, Vestec and Prague, meeting Core Facility leaders, users, and local staff. The visits offered an opportunity to discuss scientific achievements, operational challenges, and visions for future development, as well as to benchmark the facilities against leading European infrastructures.
MUNI MAFIL CEITEC visit by Prof. Uwe Himmelreich, Prof. Karel Pacák, Prof. Petr Hluštík and Prof. Daniel Jirák.
MUNI CELLIM CEITEC visit by Dr. Dušan Chorvát, Dr. Timo Zimmermann, Dr. Paula Sampaio, Dr. Marek Cebecauer and Dr. Paolo Bianchini.
BC LEM visit by Prof. Klaus Qvortrup, Dr. Julia Fernandez-Rodriguez, and Dr. Eija Jokitalo.
The on-site program concluded with a joint discussion meeting in Prague and a network dinner, where IAB members and the Czech-BioImaging Steering Committee exchanged insights and preliminary reflections.
The goal of the IAB evaluation is to ensure that Czech-BioImaging maintains excellence, transparency, and continuous improvement in its research infrastructure. Through direct engagement and dialogue, the IAB provides feedback that supports both strategic planning and performance-based funding decisions within the national network.
BUT BCF CEITEC visit
IEM MSC visit
CUNI CAPI visit
Following the visits, Core Facility leaders will submit updated documentation for the evaluation period January 2023 – December 2025. The IAB panels will complete their assessments by May 2026, assigning ratings (A–D) that will impact facility’s total budget. The final results and recommendations will be discussed jointly with the Steering Committee in 2026, forming the basis for the next phase of strategic development across Czech-BioImaging.
3 December 2025
Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, Czech Republic
One day workshop filled with news from experts on brain imaging including EEG, MRI, microscopy, optics, miniscope and preclinical studies. Many different facilities with expertise in brain imaging will present their know-how.
The workshop is organized by the ISI MR core facility.
2 – 4 December 2025
Institute of Scientific Instruments of the Czech Academy of Sciences, Královopolská 147, Brno, Czech Republic
Learn principles of Electron microscopy and Raman spectroscopy in three days and try operating microscopes and preparing biological specimens. The course is aimed at university students and young scientists in the life sciences and soft materials who are planning to use advanced imaging and analytical methods in their research.
The course is organized by the ISI EM core facility and supported by the BC LEM and CUNI VMCF core facilities.
