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 FIJI (ImageJ) for basic or more advanced analyses and make their own macros, how to analyse co-localizations, data from FRAP, particle tracking or how to segment or deconvolve your images, see program). The course follows the course 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. Lucie Kubínová, CSc (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. Convolution. Point operations with the image. Look-up table, histogram, contras and brightness, gamma correction ♦ Basic segmentation methods and deconvolution ♦

II. Biological applications of the image analyses

Evaluation of co-localization of microscopic images ♦ Volume reconstruction from the confocal data ♦ Particle Tracking ♦ FRAP Data analyses ♦ 3D electron microscopy introduction: Tomography 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
Jindřiška Fišerová


The course is organized by the Microscopy Centre - Core Facility for Light Microscopy & 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 – LM2015062)“ and from the National Programme for Sustainability I of Ministry of Education, Youth and Sports ("Biomodels for health" - LO1419).