Dear participants,

We would like to inform you that due to the current anti-pandemic rules the course "PROCESSING AND ANALYSIS OF MICROSCOPIC IMAGES IN BIOMEDICINE" will be organized in two parts.

The second part will be given again online via ZOOM, it will take place in May 17-20, four days.

The 5-day intense course intended for Ph.D. students and early-stage researchers will provide participants with knowledge on image data processing and analysis. No previous knowledge is expected, the course will lead you step by step through the basis of microscopy data processing (e.g. what is an image, how it is created and processed to get the most of it), modern methods of image reconstruction and stereology. Apart from theoretical background, the emphasis is put on practical experience, the participants will learn how to use free software package Fiji for basic or more advanced analyses, how to evaluate co-localizations, analyse data from FRAP and electron microscopy data, how to track particles in images or segment objects. They will learn how to improve data by deconvolution in Huygens software. We will also have a lesson with Imaris together with practical exercises.

The course follows the Microscopy methods in biomedicine, the previous attendance of this course, however, is not necessary.

The course will be taught in English.


Institute of Molecular Genetics of the CAS, Vídeňská; 1083, Prague 4, Czech Republic

Scientific supervisors

Prof. RNDr. Pavel Hozák, DrSc. (Institute of Molecular Genetics of the CAS, Prague)
RNDr. Jiří Janáček, Ph.D. (Institute of Physiology of the CAS, Prague)


RNDr. Michaela Blažíková, Ph.D. (Institute of Molecular Genetics of the CAS, Prague)
Ing. Martin Čapek, Ph.D. (Institute of Molecular Genetics of the CAS, Prague)


I. The image data collection and image pre-processing

Essentials (pixel, voxel, resolution, levels of grey, matrix) ; Luminescence, intensity and color ; Image as a data matrix. Human eye parameters in comparison to digital image parameters ; Formats of image files (binary, greyscale, RGB, HSV, Lab) ; Filtration and image pre-processing. Look-up table, histogram, contrast and brightness, gamma correction ; Basic segmentation methods and deconvolution ; Image deconvolution ; Macro development

II. Biological applications of the image analyses

Evaluation of co-localization of light microscopic images ; Particle Tracking ; FRAP Data analyses ; 3D electron microscopy introduction: Tomography, Colocalization and Single particle analysis

III. Stereology

Introduction to stereology; Sampling in stereology ; Cavalieri's principle for measuring volume ; Point-counting method ; Methods for measuring length and surface area from thin sections ; Methods based on focusing through thick sections: disector principle for counting three-dimensional particles (e.g., cells), methods for length measurement of spatial curves (e.g., capillaries) and surface area ;



Michaela Blažíková
Martin Čapek
Vlada Philimonenko
Helena Chmelová


logistics support

The course is organized by the Microscopy Centre and the Light Microscopy Core Facility & Core Facility for Electron Microscopy, which are supported from the program for large research infrastructures of the Ministry of Education, Youth and Sports within the project “National Infrastructure for Biological and Medical Imaging (Czech-BioImaging – LM2018129)“ and from the National Programme for Sustainability I of Ministry of Education, Youth and Sports ("Biomodels for health" - LO1419).