TeachingSs12CAMP2Lecture

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

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Computer Aided Medical Procedures II (CAMP II) - IN2022

Lecture by Prof. Dr. Nassir Navab
Type: Lecture Module IN2022
Programs: Informatics (Bachelor, Master), Informatics (Diploma: Praktische Informatik, Vertiefungsfach), Information Systems (Bachelor), Computational Science and Engineering (Master), TUM-BWL (Technikfach)
SWS: 2+2
ECTS: 5 Credits
Course Language: English

  

Further Information:

Announcements:

  • Repeat exam date has been announced! Please register for the exam via TUMOnline.
  • The final written exam is closed book. It consists of short and long answer questions.
  • The lecture "Medical Image Processing by Visual Programming" will not be questioned in the final written exam.
  • Results for the second attestation are out! See the course schedule below.
  • Results for the first attestation are out! See the course schedule below.
  • Due to the limited space in our computer labs, we recommend students to bring their MATLAB installed laptops to the exercise sessions. This page provides the necessary links for installing MATLAB on your laptops.
  • Note that exercise sessions will be taking place regularly. The exercises will be made available on the webpage before the session. You DON'T need to submit anything but you should bring your code to the attestation. Also note that it is obligatory to attend the attestation.

Dates

  • Wednesdays 12:30 - 14:00 MI 00.08.038 from 18.04.2012 to 18.07.2012 weekly
  • Thursdays 14:30 - 16:00 MI 03.13.008 from 19.04.2012 to 19.07.2012 weekly Exercise

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

Exam

  • Attestation days: Each student has to present and explain the exercises he has implemented. For each attestation you can earn 20 points. Note that all programs have to work in order to get all points. You are not required to hand-in the exercise every week. However, you are required to have all the exercises implemented, as indicated on the exercise sheets, for the attestation day to get the bonus points.
  • In the exam itself you can earn up to 80 points.
  • In total you can earn up to 120 points. In order to pass the exam (mask >= 4.0) you will need at least 50 points. For mark 1.0 you need at least 95 points.

Course Schedule

Date Type Topic Conducted by Material/Literature Assignment
Wed, April 18, 2012 L Introduction and Overview Prof. Nassir Navab   Become familiar with MATLAB:
 MATLAB Workshop,
 a friendly introduction (Jörn Behrens and Armin Iske),
 Numerical Computing with MATLAB, Introduction to MATLAB (Cleve Moler)
Thu, April 19, 2012 E Introduction to MATLAB Mehmet Yigitsoy, Athanasios Karamalis, Dr. Abouzar Eslami    Exercise 1
Wed, April 25, 2012 L Basic and Advanced Filtering Dr. Amin Katouzian Basic and Advanced Filtering  
Thu, April 26, 2012 E Basic and Advanced Filtering Dr. Amin Katouzian    Exercise 2
Wed, May 2, 2012 L Basic Segmentation Methods Dr. Abouzar Eslami Basic Segmentation Methods  
Thu, May 3, 2012 E Basic Segmentation Methods Dr. Abouzar Eslami    Exercise 3
Wed, May 9, 2012 L Advanced Segmentation Methods Athanasios Karamalis Advanced Segmentation Methods Supplementary material from Basic Math Tools course
Thu, May 10, 2012 E Advanced Segmentation Methods Athanasios Karamalis    Exercise 4
Wed, May 16, 2012 - No class due to CAMPING      
Thu, May 17, 2012 - No class due to Ascencion Day      
Wed, May 23, 2012 L Intensity Based Registration Mehmet Yigitsoy Intensity-Based Registration Supplementary material from Basic Math Tools course
Thu, May 24, 2012 E Intensity Based Registration Mehmet Yigitsoy    Exercise 5
Wed, May 30, 2012 L Deformable Registration Mehmet Yigitsoy Deformable Registration  
Thu, May 31, 2012 E Deformable Registration Mehmet Yigitsoy    Exercise 6
Wed, Jun 6, 2012 T Attestation Dr. Abouzar Eslami, Mehmet Yigitsoy, Dr. Amin Katouzian, Athanasios Karamalis Attestation Results  
Thu, Jun 7, 2012 - No class due to Corpus Christi      
Wed, Jun 13, 2012 L Transformation, Coordinate Systems and Point Based Registration Dr. Pascal Fallavollita Transform_Coordinates_Ptreg  
Thu, Jun 14, 2012 E Transformation, Coordinate Systems and Point Based Registration Dr. Pascal Fallavollita    Exercise 7
Wed, Jun 20, 2012 L Reconstruction Methods Dr. Tobias Lasser Reconstruction Methods  
Thu, Jun 21, 2012 E Reconstruction Methods Dr. Tobias Lasser    Exercise 8
Wed, Jun 27, 2012 L Machine Learning Methods I Dr. Diana Mateus, Olivier Pauly Machine Learning Methods I  Exercise 9
Thu, Jun 28, 2012 E Machine Learning Methods I Dr. Diana Mateus, Olivier Pauly    
Wed, July 4, 2012 L Machine Learning Methods II Olivier Pauly, Dr. Diana Mateus Machine Learning Methods II  
Thu, July 5, 2012 E Machine Learning Methods II Olivier Pauly, Dr. Diana Mateus    
Wed, July 11, 2012 L Medical Image Processing by Visual Programming Dr. Abouzar Eslami Medical Image Processing by Visual ProgrammingI  
Thu, July 12, 2012 E Medical Image Processing by Visual Programming Dr. Abouzar Eslami    Exercise 10
Wed, July 18, 2012 L Medical Augmented Reality Tobias Blum Medical Augmented Reality  
Thu, July 19, 2012 T Attestation Dr. Pascal Fallavollita, Dr. Tobias Lasser, Olivier Pauly, Dr. Abouzar Eslami Attestation Results  
Wed, Aug 1, 2012 T Final Exam
Room: MW 1050, MW 2050
Time: 13:00-14:30 		Dr. Abouzar Eslami, Dr. Amin Katouzian, Athanasios Karamalis, Mehmet Yigitsoy    
Fri, Oct 19, 2012 T Repeat Exam
Room: MI HS 2
Time: 16:30-18:00 		Dr. Abouzar Eslami, Dr. Amin Katouzian, Athanasios Karamalis, Mehmet Yigitsoy    

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: Abouzar Eslami,Amin Katouzian,Athanasios Karamalis, Mehmet Yigitsoy
Type: Lecture
Information: 2+2 SWS, 5 ECTS, Praktische Informatik, Vertiefungsfach
Term: 2012SoSe
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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