Course detail

Biomedical Data Visualization

FEKT-FVIZAcad. year: 2012/2013

The course is oriented to knowledge on computer graphics applied to biomedical data. The main focus is visualization of 3D image data acquired using magnetic resonance imaging, CT tomography, PET and SPECT. Furthermore, methods for visualization of higher-dimension data are included.

Language of instruction

Czech

Number of ECTS credits

6

Mode of study

Not applicable.

Guarantor

doc. Ing. Radovan Jiřík, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Learning outcomes of the course unit

Practical knowledge of methods used for visualization of three- and higher-dimensional biomedical data based mainly on mathematical description of elementary geometrical objects and on modeling of optical phenomena. Practical knowledge of programing in OpenGL

Prerequisites

The subject knowledge of programing and algorithms on the Bachelor´s degree level is requested.

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Teaching methods depend on the type of course unit as specified in the article 7 of BUT Rules for Studies and Examinations.

Assesment methods and criteria linked to learning outcomes

Requirements for completion of a course are specified by a regulation issued by the lecturer responsible for the course and updated for every year.

Course curriculum

Classification of visualization techniques. Representation of elementary 2D objects. Surface and volume representation of 3D objects. Illumination models, surface and volume rendering. Virtual reality. Higher-dimmension data visualization. Hardware means for visualization.

Work placements

Not applicable.

Aims

Knowledge of representation of simple geometrical objects and their use for description of real objects in medical imaging. Knowledge of methods used in visualization of biomedical data.

Specification of controlled education, way of implementation and compensation for absences

Limitations of controlled teaching and its procedures are specified by a regulation issued by the lecturer responsible for the course and updated for every year.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

UDUPA, J. K., HERMAN, G. T.: 3D imaging in medicine (2nd edition). CRC Press, 1991, ISBN:0-8493-4294-5 (EN)
ŽÁRA, J., BENEŠ, B., SOCHOR, J., FELKEL, P: Moderní počítačová grafika (2. vydání). Computer Press, 2005, ISBN 80-251-0454-0. (CS)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme BTBIO-F Master's

    branch F-BTB , 2 year of study, winter semester, compulsory

Type of course unit

 

Lecture

26 hod., optionally

Teacher / Lecturer

Ing. Vratislav Čmiel, Ph.D.
Ing. Vratislav Harabiš, Ph.D.

Syllabus

1. Introduction to visualization of biomedical data. Classification of visualization methods. Examples of use in medical applications.
2. Representation of elementary 2D objects: piecewise linear, circular and elliptical objects, interpolation and approximation of curves, region objects.
3. 3D object surface representation I: polygon representation, parametric surface representation (Bezier surfaces, B-spline surfaces).
4. 3D object surface representation II: set of outlines in parallel planes, implicit surfaces.
5. Representation of 3D objects: border representation, sweeping, octrees, constructive solid geometry.
6. Transformation of 3D image data to surface representation: methods of marching cubes, marching tetrahedra, dividing cubes.
7. Basics of visualization of 3D data: parallel and perspective projection, viewing transformations, theory of light.
8. Illumination models for surface rendering: diffuse scattering and reflection components of light, physical and empirical models.
9. Illumination models for volume rendering: methods of ray casting, formulation of light absorption, scattering and reflection on various levels of complexity.
10. Models of light sources and shading: point, surface, parallel, reflector, skye light sources; constant, Gouraud and Phong shading.
11. Virtual reality: stereoscopic view generation, DESCRIPTION of VRML language for modeling of virtual reality.
12. Methods for visualization of higher-dimension data for classification based on feature description.
13. Hardware means for visualization: hardware means for acceleration of graphical computing, technology of displays and 3D visualization systems.

Exercise in computer lab

26 hod., compulsory

Teacher / Lecturer

Ing. Vratislav Čmiel, Ph.D.
Ing. Vratislav Harabiš, Ph.D.

Syllabus

1. Introduction to laboratory lessons. Formats of image data.
2. Representation of elementary 2D objects - implementation of interpolation and approximation curves (Matlab).
3. Polygon representation of surface of a simple 3D object (Matlab).
4. Parametric representation of surface of a simple 3D object (Matlab).
5. Transformation of 3D image data to surface representation using marching cubes method, application to real data (Matlab, VTK).
6. Practical test 1.
7. Implementation of a simple illumination model for surface rendering (Matlab).
8. Comparison of illumination models for surface rendering (VTK Designer)
9. Implementation of a simple illumination model for volume rendering (Matlab).
10. Comparison of illumination models for volume rendering (VTK Designer)
11. Experimental acquisition of stereoscopic scenes, visualization using anaglyphs and active 3D glasses.
12. Calibration and quality measurement of LCD displays used in radiology.
13. Practical test 2.