TeachingSs14CAMP2Lecture

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:

  • Please check the announcements section at least once per week!
  • The classes and exams are in English.
  • This lecture is the second part of "Computer Aided Medical Procedures" (which is recommended but not obligatory).
  • General questions, please contact Peter Maday.

  • For an overview of which subjects are likely to be covered by the lecture please refer to last year's lecture
  •  Exam results Pass: 40 points, 5 point increments for grades after
  • Exam inspection this Friday 01.08.2014 from 10:00 - 12:00

Overview

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 exercises. They thus gain deep insight into medical image computing and will be, by the end, able to implement solutions for computer aided medical procedures.

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.

Registration

  • Last day for registration is 30th of April, 2014. Last day for deregistration is 19th of June, 2014.
  • Registration for this lecture is via TUM Online. We have to limit the number of students due to space constraints in the lecture halls. If more people register than space is available, preference will be given to BMC students who registered before 14th of March, 2014, at 17h. There will be a waiting list.
  • There will be exceptions for exchange students who want to take this class. Please send an e-mail with your details and motivation to Peter Maday.

Regulations

The student's performance in the exercises will be assessed during an attestation. Each student will randomly be assigned two exercise topics that he will have to present to the respective tutor. If both presentations are positive, a bonus of 0.3 points on the final mark is obtained. There will be a written, closed-book exam at the end of the semester.

Announcements

  • [10.10.2014] The CAMP 2 repeat exam will take place on Friday, 10th of October 2014, from 14h30 to 16h00 in the MI HS 2.
  • [23.06.2014] CAMP 2 attestation reschedules to 17th of July, 8:30 - 12:30
  • [12.05.2014] The final exam takes place on 21st of July, 2014, from 8:30 to 10:00, in Interimshörsaal (5620.01.102).
  • [25.04.2014] Introduced registration and deregistration deadlines.
  • [07.03.2014] Introduction of quotas for the lecture. We hope to get a bigger auditorium to be able to accept students on the waiting list.

Dates

These are preliminary slots. Both the location and the time are subject to changes!

  • Lectures: Wednesdays 12:30 - 14:00, MI 03.13.010, from 09.04.2014 to 09.07.2014 (weekly)
  • Excercises: Thursdays 14:30 - 16:00, MI 03.13.010, from 10.04.2014 to 10.07.2014 (weekly)

Course Schedule

Date Type Topic Conducted by Material/Literature Assignment
Wed, 09.04.2014 L CAMP2 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, 10.04.2014 E Introduction to Matlab Peter Maday  Important preparations
 MATLAB installation instructions 		 Exercise 1.
Wed, 16.04.2014 L Filtering Tingying Peng  SpatialFiltering  
Wed, 23.04.2014 L Wavelets Tingying Peng  Fourier&WaveletFiltering  
Thu, 24.04.2014 E Filtering+Wavelets Tingying Peng, Peter Maday    Exercise_filteringandwavelet.
Wed, 30.04.2014 L Intensity-based Registration Mehmet Yigitsoy  Intensity-based Registration  
Wed, 07.05.2014 L Deformable Registration Mehmet Yigitsoy  Deformable Registration  
Thu, 08.05.2014 E Registration Mehmet Yigitsoy    RegistrationExercise
Wed, 14.05.2014 L Segmentation Stefanie Demirci  Segmentation
 Segmentation Videos 		 
Thu, 15.05.2014 E Segmentation Stefanie Demirci    Segmentation Exercise
Wed, 21.05.2014 L Histology Martin Groher  Histology  
Thu, 22.05.2014 E Histology Andreas Keil    Histology Exercise
Wed, 28.05.2014 L Physics of Imaging Benjamin Frisch    
Wed, 04.06.2014 L Medical Visualization Christian Schulte Zu Berge  Medical Visualization  
Thu, 05.06.2014 E Medical Visualization Christian Schulte Zu Berge    Exercise on Medical Visualization
Wed, 11.06.2014 L Augmented Reality Pascal Fallavollita  Medical Augmented Reality  
Thu, 12.06.2014 L Transformations & Point-based Registration Pascal Fallavollita  Transformations  
Wed, 18.06.2014 L Medical Simulation Environments Patrick Wucherer  Medical Simulation Environments  
Wed, 25.06.2014 L Machine Learning Stefanie Demirci, Lichao Wang  MachineLearning  
Thu, 26.06.2014 E Machine Learning Stefanie Demirci, Lichao Wang    MachineLearning Excercise
Wed, 02.07.2014 L Physics of Imaging 2 Benjamin Frisch    
Thu, 03.07.2014 L Variational Methods Maximilian Baust  Variational Denoising  
Wed, 09.07.2014 E Variational Methods Maximilian Baust    08VariationalDenoising.zip
Thu, 17.07.2014 E Attestation Tutors    
Mon, 21.07.2014   Final Exam Everybody 8:30 - 10:00, Interimshörsaal 2
90 minutes closed book exam 		 
Fri, 10.10.2014   Repeat Exam   14:30-16:00, MI HS2,
90 minutes closed book exam 		 

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: Dr. Benjamin Frisch; Peter Maday
Type: Lecture
Information: 2+2 SWS, 5 ECTS Credits (Module IN2022)
Term: 2014SoSe
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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