Design Experiment with Examples from Microscopy and Omics

Course description:

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. 

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Live Cell Imaging

Course description:

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.

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Basics of Light Microscopy Imaging in Plant Research

Course description:

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

Advanced Multi-modal Light Microscopy Imaging in Plant Research

Course description:

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

AI-based Segmentation and Tracking

Course description:

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.

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Processing and Analysis of Microscopic Images in Biomedicine

Course description:

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.

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Microscopy Methods in Biomedicine

Course description:

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.

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Experimental Biophotonics

Course contents:

Digital holographic, interference, fluorescence and confocal microscopy and its use in modern medicine, deployment of live cells, operating the Q-Phase microscope

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TBA

Multimodal workshop: Inside the living brain

Workshop description:

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.

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Advanced Microscopic and Spectroscopic Techniques 2025

Course description:

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.

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Experimental Biophotonics

Course description:

This course is the introduction to light microscopy and to the Biophotonics Core Facility. It is particularly suitable for potential users of the facility. The course can also be registered for a PhD study program as the TEB-A subject available at the Faculty of Mechanical Engineering.

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NeuroImaging: Mapping the Function and Structure of Brain

Course description:

This course, organized by the MUNI MAFIL CEITEC Core Facility is designed for master’s and doctoral students specializing in human brain mapping, regardless of their primary academic background. While prior knowledge of brain mapping is beneficial, it is not mandatory. Participants will gain both theoretical and practical expertise in various neuroimaging techniques.

Registration and a course fee are required for participation.

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