Characteristics

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.

You can also expect lessons with Imaris software package (http://www.bitplane.com/imaris/imaris). The lessons will be given by a professional specialist and will include practical exercises using company computers.

The course will be taught in English.




Venue

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)




Coordinators

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




Content

 
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 ♦

 

Faculty




Michaela Efenberkova
Martin Čapek
Vlada Philimonenko
Jindřiška Fišerová



     




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 – LM2015062)“ and from the National Programme for Sustainability I of Ministry of Education, Youth and Sports ("Biomodels for health" - LO1419).