Hauptseminar: Methods and Tools in Medical Imaging
by
Joerg Traub,
Wolfgang Wein &
Prof. N. Navab
Introduction
The use of computers in medicine had a rapid development over the last decade. More and more computer based technology is integrated in the surgery room and in the surgical workflow. Nowadays, medical images are available in digital form. Computers are used very extensively to preprocess, segment or register different imaging modalities such as computed tomography (CT), ultrasound (US), or magnetic resonance imaging (MRI). Furthermore, the fusion of these different imaging modalities often provide very valuable information for physicians and surgeons and can enable the intra-operative navigation.
In this seminar we present the various methods that are applicable in medical imaging. We will focus on specific and interesting algorithmic and mathematical topics in this field. After two introductory courses every student will prepare a talk on the basis of the selected topics (see table below). A short problem statement of the topic as well as the basic references is provided. It is conducted in English and should be about 45 minutes long. In addition the upcoming discussion has to be moderated.
Registration
- Preliminary discussion on Thursday 2004-01-29 3:00PM (MI 02.12.51)
Time and Location
- Weekly Meeting - Tuesday 4:00PM-6:00PM, room 02.13.010
Schedule
| Date | Topic | by | Supervision |
|---|
| April 20, 2004 | Introduction: Application Domain, Motivation and Computer Vision Overview ( Slides) | Joerg Traub | |
| April 27, 2004 | Introduction: Modalities & Projective Geometry ( Slides) | Wolfgang Wein | |
| May 04, 2004 | 3D Rotations and Quaternions ( Slides, Handout ) | Darko Zikic | Wolfgang Wein |
| May 11, 2004 | SEP: Stereo Endoscope Calibration & 3D Visualization ( Slides) | Benjamin Stetter | Joerg Traub |
| May 18, 2004 | Edge Detection ( Slides, Handout ) | Michael Maurer | Wolfgang Wein |
| May 25, 2004 | Computed Tomography Reconstruction (Algebraic and Stochastic Approach) (Slides, Handout, Matlab Scripts ) | Darko Zikic | Joerg Traub |
| June 08, 2004 | Fourier Transformation for Computed Tomography Reconstruction ( Slides, Handout ) | Tobias Lasser | Joerg Traub |
| June 15, 2004 | Pose Estimation ( Slides, Handout) | Sefika Elvin Eren | Wolfgang Wein |
| June 22, 2004 | Feature Based Registration ( Slides, Handout ) | Stefan Wiesner | Wolfgang Wein |
| June 29, 2004 | Intensity Based Registration ( Slides, Handout ) | Oliver Kutter | Wolfgang Wein |
| July 06, 2004 | Volume Segmentation ( Slides, Handout ) | Benjamin Glocker | Marco Feuerstein |
| July 13, 2004 | 3D Tracking Techniques ( Slides, Handout ) | Benedikt Strecker | Joerg Traub |
| July 20, 2004 | Level-Set Methods ( Slides, Handout ) | Hedi Hadhri | Joerg Traub |
Schein Requirements
- active and motivated participation in all classes
- conduct one class (presentation about 45min and discussion at least 20min) in English
- structure of the presentation has to be discussed at least 2 weeks in advance with the supervisor
- slides have to be send to supervisor two days before the presentation
- short handout (up to 5 pages)
Literature Overview
This literature provides the general background in computer vision and medical imaging.
- Numerical Recipes in C; William H. Press, Saul A. Teukolsky, William T. Vetterling
- Procedures of the Int. Conference on Medical Image Computing and
Computer-Assisted Intervention (MICCAI)
- Medical Image Registration; Joseph Hajnal (Editor), D. J. Hawkes (Editor), Derek Hill (Editor),
J V Hajnal
- Three-Dimensional Computer Vision, by Olivier Faugeras
- Multiple View Geometry in Computer Vision, Richard Hartley,
Andrew Zisserman
Specific Literature
3D Rotations and Quaternions
- Leandra Vicci: Quaternions and Rotations in 3-Space: The Algebra and its Geometric Interpretation
- Gary Bishop, Greg Welch, and B. Danette Allen: Tracking: Beyond 15 Minutes of Thought
Camera Models and Camera Calibration
- Zhenghyou Zhang: A Flexible Technique for Camera Calibration, MSR Tech. Report MSR-TR-98-71
- R. TSAI, A Versatile Camera Calibration Technique for High-Accuracy 3D Machine Vision Metrology Using Off-the-Shelf TV Cameras, IEEE Journal of Robotics and Automation, RA-3(4), 1987, pp. 323–344.
- Olivier Faugeras: Three-Dimensional Computer Vision (1993) Chapter 3 (Modeling and Calibrating Cameras)
Edge Detection
- J. F. Canny, A Computational approach to edge detection, IEEE Transactions on Pattern Analysis and Machine Intelligence, 8(6) pp. 679-698, 1986
- Olivier Faugeras: Three-Dimensional Computer Vision, Chapter 4 (Edge Detection)
Computed Tomography Reconstruction (Algebraic and Stochastic Approach
- Albert Macovski: Medical Imaging Systems 1983
- G.T. Herman Image reconstruction from projections Academic Press 1980
Fourier Transformation for Computed Tomography Reconstruction
- Albert Macovski: Medical Imaging Systems 1983
- Henrik Turbell: Cone-Beam Reconstruction Using Filtered Backprojection ;Linköping University, Sweden, 2001
Pose Estimation
- K.S. Arun, T.S. Huang and S.D. Blostein: Least-Squares Fitting of Two 3-D Point Sets
- Shinji Umeyama: Least-Squares Estimation of Transformation Parameters Between Two Point Patterns
- Berthold K.P. Horn: Tsai's camera calibration method revisited
Feature Based Registration
- Zhengyou Zhang: Iterative Point Matching for Registration of Free-Form Curves, INRIA, March 1992
- Selected chapters of Joseph V. Hajnal, Derek L.G. Hill and David J. Hawkes: Medical Image Registration
- J.B.A. Maintz and M.A. Viergever: An Overview of Medical Image Registration Methods
Intensity Based Registration
- Selected chapters of Joseph V. Hajnal, Derek L.G. Hill and David J. Hawkes: Medical Image Registration
- Josien P. W. Pluim, J. B. Antoine Maintz and Max A. Viergever: Mutual information based registration of medical images: a survey
- P. Viola: Alignment by Maximization of Mutual Information, Int. Conference on Computer Vision 1995
- W. Wein: Intensity-Based Rigid 2D-3D Registration Algorithms for Radiation Therapy, Diplomarbeit, TU München
Volume Segmentation
- Dzung L. Pham, Chenyang Xu, Jerry L. Prince, "A survey of current methods in medical image segmentation" (http://www.rfai.li.univ-tours.fr/rousselle/docum/pdf/p124r.pdf)
- Gabriele Lohmann, "Volumetric image analysis", Chapter 8 - Region segmentation
- D. L. Pham and J. L. Prince, "An adaptive fuzzy c-means algorithm for image segmentation in the presence of intensity inhomogeneities," in Proc. SPIE Medical Imaging 1998: Image Processing, 1998, vol. 3338, pp. 555--563 (http://citeseer.nj.nec.com/cache/papers/cs/11590/http:zSzzSziacl.ece.jhu.eduzSzpubszSzp094c.pdf/pham98adaptive.pdf)
- David Forsyth, "Computer Vision - A Modern Approach", Chapter 16 - Segmentation by Clustering (http://www.cs.fsu.edu/~liux/courses/research/textbook/clustering.pdf)
3D Tracking Techniques
Level-Set Methods
- Selected chapters of J.A. Sethian; Level Set Methods and Fast Marching Methods Evolving Interfaces in Computational Geometry, Fluid Mechanics, Computer Vision, and Materials Science, Cambridge University Press, 1999
- Selected chapters of Stanley Osher, Nikos Paragios: Geometric Level Set Methods in Imaging, Vision, and Graphics
