Description:

This subject describes algorithms for digital image processing of 2D and 3D images, with emphasis on biomedical applications. We shall therefore concentrate on the most often used techniques in medical image processing: segmentation, registration, and classification. The methods will be illustrated by a range of examples on medical data. The students will implement some of the algorithms during the practice sessions.

Because of the very large overlap between courses A6M33ZMO and A4M33ZMO, the courses will be taught together this year.

Contents:

1. Segmentation - active contours, level sets
2. Segmentation - shape models,
3. Segmentation - superpixels, random walker, GraphCuts, graph search, normalized cuts
4. Segmentation - texture, texture descriptors, textons
5. Segmentation - CNN, U-net
6. Detection of cells and nuclei
7. Detection of vessels and fibers
8. Detection of nodules and mammographic lesions
9. Localization of organs and structures
10. Registration - ICP, coherent point drift, B-splines, rigid registration, multiresolution
11. Registration - rigid, elastic, daemons
12. Registration by CNN

Seminar contents:

Individual works will consist of independent practical work in a computer laboratory involving the use of algorithms covered by the course for analysis of specific medical data. Some algorithms will be implemented from scratch and some using existing freely available libraries and toolkits. Apart from a general overview, the students will gain a deeper understanding of some of the methods and will learn to apply them to practical problems.

Recommended literature:

[1] Sonka M., Fitzpatrick J. M.: Handbook of Medical Imaging, vol.2. SPIE Press, 2000.
[2] Bankman, I. Handbook of Medical Imaging, Processing and Analysis, vol.1. Academic Press, 2000.

Keywords:

image processing, medical imaging, registration, segmentation, classification, interpolation, detection, reconstruction, noise suppression, active contours.

Abbreviations used:

Semester:

• W ... winter semester (usually October - February)
• S ... spring semester (usually March - June)
• W,S ... both semesters

Mode of completion of the course:

• A ... Assessment (no grade is given to this course but credits are awarded. You will receive only P (Passed) of F (Failed) and number of credits)
• GA ... Graded Assessment (a grade is awarded for this course)
• EX ... Examination (a grade is awarded for this course)
• A, EX ... Examination (the award of Assessment is a precondition for taking the Examination in the given subject, a grade is awarded for this course)

Weekly load (hours per week):

• P ... lecture
• C ... seminar
• L ... laboratory
• R ... proseminar
• S ... seminar