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Course, academic year 2023/2024
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Methods of image analysis and sterology for biologists - MB130P01
Title: Metody analýzy obrazu a stereologie pro biology
Czech title: Metody analýzy obrazu a stereologie pro biology
Guaranteed by: Department of Experimental Plant Biology (31-130)
Faculty: Faculty of Science
Actual: from 2020 to 2023
Semester: winter
E-Credits: 3
Examination process: winter s.:
Hours per week, examination: winter s.:1/2, C+Ex [HT]
Capacity: unlimited
Min. number of students: 5
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Explanation: Vyučována turnusově na konci semestru
Additional information: http://kfrserver.natur.cuni.cz/stereo/
Note: enabled for web enrollment
Guarantor: prof. RNDr. Jana Albrechtová, Ph.D.
Teacher(s): prof. RNDr. Jana Albrechtová, Ph.D.
RNDr. Jiří Janáček, Ph.D.
Mgr. Zuzana Kubínová, Ph.D.
Mgr. Zuzana Lhotáková, Ph.D.
RNDr. Barbora Radochová, Ph.D.
Annotation -
Course deals with practical review of available methods for quantitative description of biological anatomical and morphological structures with demonstration of their application in biological research. Traditional morphometric and stereological methods, introduction to image analysis, experimental design, principles of statistical evaluation of data. Practical training includes hand-on examples of methods, way of data acquiring and processing, calculations. Image analysis is demonstrated on J-image and Ellipse software programs.
Last update: Albrechtová Jana, prof. RNDr., Ph.D. (22.09.2011)
Literature -

Kubínová L., Albrechtová J. 1999. Stereology in Plant Anatomy. Textbook to the adjoining course to the international conference S4G. http://kfrserver.natur.cuni.cz/lide/albrecht/pdf/1999_Kubinova,Albrechtova-stereology.pdfHoward CV, Reed MG. 1998. Unbiased Stereology. BIOS Scientific Publishers - Oxford.
Weibel ER. 1979. Stereological methods, Vol 1. Practical methods for biological morphometry. Academic Press.
Svoboda T., Kybic J., Hlavac V.: Image Processing, Analysis, and Machine Vision, A MATLAB Companion, Thomson Learning, Toronto, ISBN 0495295957, Sep 2007, 265 p.

Web page: http://kfrserver.natur.cuni.cz/stereo/

Sonka M., Hlavac V. , Boyle R.: Image Processing, Analysis, and Machine Vision, 3rd edition, Thomson Learning, Toronto, April 2007, 821 p, ISBN 049508252X (2nd edition Brooks/Cole, Pacific Grove, CA, 1999, 1st edition Chapman & Hall, London 1993, ).

Last update: Konrádová Hana, RNDr., Ph.D. (29.10.2019)
Requirements to the exam - Czech

Zkouška probíhá ústní formou. U zkoušky je kladen důraz na znalost dostupných metod pro řešení kvantifikace struktur, analýzy obrazu, znalost jejich principu a použití, nikolivěk na matematické odvození.

Last update: Albrechtová Jana, prof. RNDr., Ph.D. (12.11.2011)
Syllabus -

1. Introduction to quantitative plant anatomy

definition of scientific field, historical milestones, tradition in the Department of Plant Physiology, trends in current development of the field, fractal geometry, theory of Chaos, stereology, image analysis, application of quantitative plant anatomy in research

2. Traditional morphometric methods I.

Length measurements in 2D, calibration of measurements, thickness measurements, area estimation (point-counting method and method of linear integration). Examples - leaf thickness, diameter of root metaxylem vessels, stomatal density, etc.

3. Traditional morphometric methods II.

Measurements of 2D curve (line-intercept method, modified Buffon method, difference between isotrpic and anisotropic structures), counting of particles in 2D. Systematic uniform random sampling. Examples - measurement of length of leaf venation, stamatal density, Salisbury's index.

4. Stereological methods I.

Introduction to stereological methods, geometrical selection, types of geometrical selection.

5. Stereological methods II.

Cavalieri´s estimator, estimation of object volume and volumetric proportions by point-counting method. Examples: organ volume, e.g. leaf volume, proportion of tissues in an organ)

6. Stereological methods III.

Particle counting in 3D, volume of irregularly shaped particles, (disector principle). Examples - estimation of the cell number and the mean cell volume of leaf mesophyll cells.

7. Stereological methods IV.

Estimation of surface area (method of vertical sections and orientator). Examples - generation of isotropic sections, organ surface, inner leaf surface.

8. Stereological methods VI.

Modern methods (nukleator, selector, fakir, etc.) and current trends of development.

9. Measurement of root length

Curve measurement in 3D (method of total vertical projections, comparison with image analysis). Examples -measurement of root length by image analysis, line-intercept method and method of total vertical projection.

10. Introduction to image analysis

Basic terms, human image perception, historical milestones in development of computer technology and image processing and analysis, basic processes of image analysis, basic terms of operations of methematical morphology.

Image J - basics for users. Ellipse - image processing software.

11. Confocal microscopy, 3D image analysis

Excursion to confocal microscopy in Physiological Institute of CAS, demonstration of applications using confocal microscopy, stereological methods and 3D image analysis - space reconstructions.

12. Design of experiment, technical aspects of usage of stereological methods

General requirements during plannig of biological experiment. Unbiasedness of estimators, systematical uniform random sampling, sources of material variability, statistical measures of variability, example during application of point-counting method - determination of density and distribution of test system, number of sampling fields, etc., generalization of directions applied when planning experimental design.

Orientation in literature, requirements for examination, final discussion

Last update: Albrechtová Jana, prof. RNDr., Ph.D. (22.09.2011)
 
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