TeachingSs08CAMP2Lecture

Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Computer Aided Medical Procedures II (CAMP II) - IN2022

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2+2 SWS, 5 ECTS, Praktische Informatik, Vertiefungsfach

Lecture by Prof. Dr. Nassir Navab.

 

Further Information:

Time & Location:

  • Tuesdays, 13:00-14:30 and Thursdays, 14:30-16:00
  • Classes (labeled "C" in the schedule below) are held in our seminar room MI 03.13.010, excercises (labeled "X") in the computer lab MI 03.13.008.

Abstract

This lecture teaches students to transfer their knowledge from the field of medical imaging and computer assisted interventions to practical algorithms. During the classes, the students get exposed to particular problems from segmentation, registration, navigation, tracking, and medical augmented reality and are then guided when implementing those algorithms themselves using MATLAB during the excercises.

The excercises take place in a lab room with MATLAB workstations.

For a more detailed overview, see last year's lecture.

Prerequisites

  • Basic knowledge in image computing (not necessarily acquired through the CAMP I lecture)
  • Interest in algorithmic/implementation aspects
  • Ability to work in small teams

  • Specific knowledge in MATLAB is not required but beneficial. However, you should be somehow skilled in programming.

Benefits

  • Deep insight into medical image computing
  • Ability to implement solutions for computer aided medical procedures

Course Schedule

Date Type Topic Conducted by Material/Literature Assignment/Solution
Tue, Apr 15, 2008 C Introduction and Overview Prof. Nassir Navab  CAMP Teaser
 Organizational Issues
 MATLAB Workshop,
 MATLAB Primer,
 Another external tutorial,  MATLAB Book
Thu, Apr 17, 2008 X Introduction to MATLAB Stefanie Demirci, Christian Wachinger    0Introduction.zip

 0IntroductionSolution.zip


 Face2_uncompressed.zip
    Image Processing: Filtering      
Tue, Apr 22, 2008 C Basic and Advanced Filtering (Linear Filters, Median Filtering, Anisotropic Diffusion, Edge Detection, Frangi Filter) Andreas Keil, Christian Wachinger  01Filtering.pdf  
Thu, Apr 24, 2008 I X Cardiovascular Informatics: How to Stop a Heart Attack Before it Happens Linear Filters, Anisotropic Diffusion Prof. Ioannis A. Kakadiaris, Andreas Keil  perona1990AnisotropicDiffusion.pdf,
 frangi1998VesselEnhancement.pdf
 1Filtering.zip
 1FilteringSolution.zip
    Segmentation      
Tue, Apr 29, 2008   no class due to CAMPing      
Thu, May 1, 2008   no class due to May Day      
Tue, May 6, 2008 C Basic Segmentation Approaches: Thresholding, Region Growing / Advanced Segmentation Techniques: Level Sets Andreas Keil  02BasicSeg.pdf
 02SnakesLevelSets.pdf
 
Thu, May 8, 2008 X Basic Segmentation Andreas Keil, Christian Wachinger    2Segmentation.zip
 2SegmentationSolution.zip
Tue, May 13, 2008   no class due to Pentecost        
Thu, May 15, 2008 C Advanced Segmentation Techniques: Graph Cuts, Active Shape Models, Active Appearance Models Stefanie Demirci, Christian Wachinger  03ShapeModelsAndHybrid.pdf
 03GraphCuts.pdf
 03GraphCutsHandout.pdf
   
Tue, May 20, 2008 X Segmentation Evaluation Stefanie Demirci, Christian Wachinger  03SegEval.pdf  3EvaluateSegmentation.zip
 3EvaluateSegmentationSolution.zip
 
    Transformations, Calibration and Point-Based Registration        
Thu, May 22, 2008   no class due to Feast of Corpus Christi        
Tue, May 27, 2008 C 2D/3D Transformations, Tracking, and Tool Calibration Joerg Traub  04CoordinateTransformations.pdf    
Thu, May 29, 2008 X 2D/3D Transformations and Tool Calibration Tassilo Klein, Lejing Wang    4CoordinateTransformations.zip  
Tue, Jun 3, 2008 C Camera Calibration and Optical Tracking Nassir Navab, Joerg Traub  05CameraCalibration.pdf    
Thu, Jun 5, 2008 X Camera Calibration and Optical Tracking Joerg Traub, Lejing Wang    05CameraCalibration.zip  
Tue, Jun 10, 2008 C Point-Based & Feature-Based Registration Martin Groher  06PCAandICP.pdf    
Thu, Jun 12, 2008 X Point-Based & Feature-Based Registration Christian Wachinger, Stefanie Demirci    06PCAandICP.zip
 06PCAandICPSolution.zip
 
    Advanced Registration        
Tue, Jun 17, 2008 C Invited Talk: Scale-Sensitive Shape Metrics Intensity-based Registration Carlos Tomasi Christian Wachinger  Scale-Sensitive Shape Metrics.pdf  
Thu, Jun 19, 2008 C X Intensity-based Registration Intensity-based Registration Christian Wachinger, Stefanie Demirci  07IntensityBasedRegistration.pdf  7IntensityBasedRegistration.zip
 7IntensityBasedRegistrationSolution.zip
 
Tue, Jun 24, 2008 C Deformable Registration Loren Schwarz  08GridBasedRegistration.pdf
 08VariationalRegistration.pdf
   
Thu, Jun 26, 2008 X Deformable Registration Loren Schwarz    08DeformableRegistration.zip  
    Visualization and Navigation        
Tue, Jul 1, 2008 C Advanced Visualization of 3D Data Oliver Kutter  09Advanced Visualization of 3D Data_2008_Videos.pdf
 09Advanced Visualization of 3D Data_2008_NoVideos.pdf
 Advanced Visualization of 3D Data_2008.ppt with working animations
   
Thu, Jul 3, 2008 X Hands on Volume Rendering Oliver Kutter    09VolumeRendering.zip  
Tue, Jul 8, 2008 C Live Demo of a Medical AR System at NarvisLab Oliver Kutter      
Thu, Jul 10, 2008 C Presentation of CAMP research projects        
Tue, Jul 15, 2008 C Invited Talk: Interactive Segmentation Refinement
_Conclusion, Questions and Answers_
Dr. Alexander Bornik
Stefanie Demirci, Christian Wachinger
     
Thu, Jul 17, 2008   Exam in room MI 03.13.010 at 3.30pm    Results.pdf  

Literature

Primary Literature

  • Image Processing / (Filtering, Morpholgical Operations, and Basic Segmentation Methods):
  • Segmentation:
  • Advanced Segmentation:
    • Leo Grady, Yiyong Sun, James Williams. Three interactive graph-based segmentation methods applied to cardiovascular imaging. In Nikos Paragios, Yunmei Chen, Olivier Faugeras, editors. Handbook of mathematical models in computer vision. Springer, 2006.
    • Yuri Boykov and Marie-Pierre Jolly. Interactive organ segmentation using graph cuts. In Scott L. Delp, Anthony M. DiGioia, and Branislav Jaramaz, editors, MICCAI, volume 1935 of Lecture Notes in Computer Science, pages 276--286. Springer, 2000.
    • Y. Boykov and O. Veksler. Graph cuts in vision and graphis: theories and applications. In Nikos Paragios, Yunmei Chen, Olivier Faugeras, editors. Handbook of mathematical models in computer vision. Springer, 2006.
    • Yuri Boykov, Gareth Funka-Lea. Graph Cuts and Efficient N-D Image Segmentation. In International Journal of Computer Vision (IJCV), vol. 70, no. 2, pp. 109-131, 2006.
    • Leo Grady and Gareth Funka-Lea. Multi-label image segmentation for medical applications based on graph-theoretic electrical potentials. In Milan Sonka, Ioannis A. Kakadiaris, and Jan Kybic, editors, Computer Vision and Mathematical Methods in Medical and Biomedical Image Analysis, ECCV 2004 Workshops CVAMIA and MMBIA, number LNCS3117 in Lecture Notes in Computer Science, pages 230--245, Prague, Czech Republic, May 2004. Springer.
    • Leo Grady and Eric Schwartz. Anisotropic interpolation on graphs: The combinatorial Dirichlet problem. Technical Report CAS/CNS-TR-03-014, Department of Cognitive and Neural Systems, Boston University, Boston, MA, July 2003.
    • Web Page of Leo Grady a.k.a. everything you gotta know about random walker...
  • Registration:
    • [Hajnal2001] J. V. Hajnal, D. L. G. Hill, and D. J. Hawkes: Medical Image Registration. CRC Press, Biomedical Engineering Series, 2001
  • Deformable Registration:
    • [Modersitzki2004] Jan Modersitzki. Numerical methods for image registration. Oxford University Press, 2004.
  • Visualization:
    • Christof Rezk-Salama, Klaus Engel, Markus Hadwiger, Joe M. Kniss and Daniel Weiskopf: Real Time Volume Graphics, Transatlantic Publishers, 2006

Secondary Literature


TeachingForm
Title: Computer Aided Medical Procedures II
Professor: Prof. Dr. Nassir Navab
Tutors: Stefanie Demirci, Christian Wachinger, Ben Glocker, Andreas Keil, Oliver Kutter, Joerg Traub, Martin Groher, Darko Zikic
Type: Lecture
Information: 2+2 SWS, 5 ECTS, Praktische Informatik, Vertiefungsfach
Term: 2008SoSe
Abstract: Computer science is playing an important, increasing role in medical practices. Medical imaging companies are no more asked by physicians to only produce images of anatomy. Instead, they are asked to design software and hardware systems to provide complex computer-aided solutions for diagnosis, intervention and therapy. There are more and more opportunities for computer science graduates to contribute to the development and deployment of medical solutions. Within the operating rooms, there is an increasing need for the integration and visualization of heterogeneous data acquired by numerous sensors. This course on computer aided medical procedures exposes the students to the challenges of building the operating rooms of the future. The main focus of the course is in imaging technologies especially intra-operative imaging as well as the visualization of this data. Techniques like segmentation and registration are explained in various classes.


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