Computer Aided Medical Procedures II (CAMP II) - IN2022

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

Lecture by Prof. Dr. Nassir Navab.

Abstract Prerequisites Benefits Course Schedule Literature Primary Literature Secondary Literature

Further Information: The classes and exam are in English. This lecture is the successor of "Computer Aided Medical Procedures" (which is recommended but not obligatory). In case of organizational questions, please contact Ben Glocker. 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. Exam: Type: written, closed book (no material), approx. 90min Topics Covered: Basically everything from this lecture with focus on comprehension and algorithms. Grading: You may earn points for every of the excercise classes. The final exam is worth approx. 80-100 points. The sum of all points yields your grade. Points will be given for the excercises starting from Exercise 1 (Filtering) on. The deadline for handing in solutions is always Mondays, 18:00.

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 17, 2007	C	Introduction and Overview	Prof. Dr. N. Navab	CAMP 2 Teaser
Thu, Apr 19, 2007	X	Introduction to MATLAB	B. Glocker and A. Keil	MATLAB Workshop,  MATLAB Primer,  Another external tutorial	0Introduction.zip  Solution.zip
		Image Processing: Filtering
Tue, Apr 24, 2007	C	Basic and Advanced Filtering (Linear Filters, Median Filtering, Anisotropic Diffusion, Edge Detection, Frangi Filter)	B. Glocker and Prof. Dr. N. Navab	01Filtering.pdf
Thu, Apr 26, 2007	X	Linear Filters, Anisotropic Diffusion	B. Glocker and A. Keil	perona1990AnisotropicDiffusion.pdf	1Filtering.zip  Solution.zip
Tue, May 1, 2007		no class due to May Day
		Segmentation
Thu, May 3, 2007	C	Basic Segmentation Approaches: Thresholding, Region Growing / Advanced Segmentation Techniques: Graph Cuts	B. Glocker and Prof. Dr. N. Navab	02BasicSegmentation.pdf  03GraphCutsSegmentation.pdf  GraphCutsHandout.pdf
Tue, May 8, 2007	X	Basic Segmentation	B. Glocker and A. Keil		2Segmentation.zip  Solution.zip
Thu, May 10, 2007	C	Advanced Segmentation Techniques: Atlas-based Segmentation	B. Glocker and Prof. Dr. N. Navab	04AtlasSegmentation.pdf
Tue, May 15, 2007	X	Segmentation Evaluation	B. Glocker		3EvalSeg.zip  Solution.zip
Thu, May 17, 2007		no class due to Ascension Day
		Transformations, Calibration and Point-Based Registration
Tue, May 22, 2007	C	2D/3D Transformations, Tracking, and Tool Calibration	J. Traub	05TransformationTracking.pdf
Thu, May 24, 2007	X	2D/3D Transformations and Tool Calibration	J. Traub		4TransTrack.zip  Solution.zip
Tue, May 29, 2007		no class due to Pentecost
Thu, May 31, 2007	C	Point-Based & Feature-Based Registration	M. Groher	06PCAandICP.pdf
Tue, Jun 5, 2007	X	Point-Based & Feature-Based Registration	B. Glocker		5PCAandICP.zip  Solution.zip
Thu, Jun 7, 2007		no class due to Feast of Corpus Christi
Tue, Jun 12, 2007	C	Camera & Hand-eye Calibration	M. Feuerstein	07CameraCalibration.pdf  08HandEyeCalibration.pdf
Thu, Jun 14, 2007	X	Camera & Hand-eye Calibration	M. Feuerstein		6CameraCalib.zip  7HandEyeCalib.zip  Solution.zip
		Advanced Registration
Tue, Jun 19, 2007	C	Intensity-based Registration	T. Lasser and Prof. Dr. N. Navab	09IntensityBasedRegistration.pdf
Thu, Jun 21, 2007	X	Intensity-based Registration	T. Lasser		8IntBasedReg.zip  Solution.zip
Tue, Jun 26, 2007	C	Deformable Registration	D. Zikic and Prof. Dr. N. Navab	10DeformableRegistration.pdf  DefRegHandout.pdf
Thu, Jun 28, 2007	X	Deformable Registration	D. Zikic and B. Glocker		9DefRegistration.zip  Solution.zip
		Visualization and Navigation
Tue, Jul 3, 2007	C	The devil is in the detail: Advanced visualization systems (Synchronization, Visual Perception and Information Representation of 3D Data)	T. Sielhorst	11TheDevilIsInTheDetails.pdf
Thu, Jul 5, 2007	C	Advanced Visualization of 3D Data	Oliver Kutter	12_Advanced_3D_Visualization.pdf
Tue, Jul 10, 2007	X	Hands on Volume Rendering	Oliver Kutter		RaycastTemplate.zip
Thu, Jul 12, 2007	C	Live Demo of a Medical AR System
Tue, Jul 17, 2007		Conclusion, Questions and Answers	B. Glocker
Thu, Jul 19, 2007		Exam in room MI 03.13.010

Literature

Primary Literature

• Image Processing / (Filtering, Morpholgical Operations, and Basic Segmentation Methods):
  • [GonzalezImageProcessing] R. C. Gonzalez and R.E. Woods: Digital Image Processing. Prentice Hall (see also the companion web site for downloads)
  • [GonzalezImageProcessingMatlab] R. C. Gonzalez, R.E. Woods, and S.L. Eddins: Digital Image Processing Using MATLAB. Prentice Hall (see also the companion web site for downloads)
  • [JähneImageProcessing] B. Jähne: Digital Image Processing. Springer
  • [PeronaAnisotropicDiffusion] P. Perona and J. Malik. Scale-space and edge detection using anisotropic diffusion. IEEE Trans. Pattern Anal. Machine Intell., 12(7):629-639, 1990. doi:10.1109/34.56205
  • [FrangiVesselFilter] A. F. Frangi, W. J. Niessen, K. L. Vincken, M. A. Viergever. Multiscale vessel enhancement filtering. MICCAI 1998, LNCS 1496. Springerlink
• Segmentation:
  • [Pham2000] Dzung L. Pham, Chenyang Xu, and Jerry L. Prince. Current methods in medical image segmentation. Annual Review of Biomedical Engineering, 2:315-337, 2000. doi:10.1146/annurev.bioeng.2.1.315
  • [SethianLevelSetFastMarching] 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
• 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.
  • 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

• Overview:
  • [Peters2000] Terry M. Peters: Image-guided surgery: From X-rays to Virtual Reality. Comput Methods Biomech Biomed Engin, 4(1):27-57, 2000
  • [MICCAI] Various Proceedings of MICCAI (International Society and Conference Series on Medical Image Computing and Computer-Assisted Intervention)
  • [TMI] Various IEEE Transactions on Medical Imaging
• Modalities:
  • [Natterer1986] F. Natterer: The Mathematics of Computerized Tomography. John Wiley and Sons Ltd., 1986
  • [Kak2001] Avinash C. Kak and Malcolm Slaney: Principles of Computerized Tomographic Imaging. SIAM Society for Industrial & Applied Mathematics, 2001 (online version)
  • [Mueller1998] K. Mueller: Fast and accurate three-dimensional reconstruction from cone-beam projection data using algebraic methods. PhD dissertation, The Ohio State University, June, 1998
• Computer Aided Surgery:
  • [CAS] Various Volumes of Computer Aided Surgery
  • [CARS] Various Proceedings of CARS (Computer Assisted Radiology and Surgery - International Congress and Exhibition)
  • [Grimson1999] W. Eric L. Grimson, Ron Kikinis, Ferenc A. Jolesz, and Peter McL. Black: Image-Guided Surgery. Scientific American, 280(6) pp. 62-69, 1999
• Computer Vision:
  • [Navab3DCV] N . Navab: Lecture on 3D Computer Vision
  • [HartleyCV] Richard Hartley and Andrew Zisserman: Multiple View Geometry in Computer Vision. Cambridge University Press, 2nd edition, 2004