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

Computational Physiology for Medical Image Computing - IN2319


Lecture: Prof. Bjoern Menze, Dr. Marie Piraud, TBA

Tutors: TBA

Time & Location

  • Lecture: Thursdays, 9:00am - 11:00pm in the IMETUM lecture hall
  • Work on Case Studies (Exercises): Thursdays, 11:00am - 12:00am in the same room, and group work


Upon completion of the course, participants will be able to use computational models for extracting diagnostic information from different types of clinical image data sets. These data sets may provide information, for example, about blood perfusion or micro-structural tissue properties, about metabolic processes, or patterns of disease progression. The participants will understand the physiological concepts underlying the computational algorithms employed, and will know of advantages and shortcomings of different modeling strategies. This will allow them to analyze clinical imaging protocols with respect to the underlying physiological information, and to propose diagnostic algorithms that combine anatomical and physiological information of different imaging. A focus will be on applications from neuroimaging.

During the first part of the course, participants will implement and evaluate small case studies in team of up to three people. The use of public Python libraries, such as NiPy and NiPype, is encouraged. Towards the end of the course, teams will demonstrate their work to other course participants in a short oral presentation and in a short summary paper.


  • Basic knowledge in image computing (e.g., CAMP I lecture or related courses).
  • Interest in algorithmic/implementation aspects of signal processing and image computing tasks.
  • Specific knowledge in Python is not required. However, you should be willing to acquire skills during the course.


  • Module Specification: IN2319
  • SWS: 2+2
  • ECTS: 6 Credits
  • Course Language: English
  • Exam: presentation of course project, and oral or written exam

Course Schedule

NB: ZIP files of the lecture slides can be unzipped using 'CpMic'.

Date Time Topic Lecturer Material Exercise Execise Resources
Thu 12.04.17   No Lecture [150 years of TUM]        
Thu 19.04.17 9:00-11:00 Intro & Tissue structure (makro) Bjoern Menze slides    
Thu 26.04.17 9:00-11:00 Overview case studies Giles Tetteh   Brain structure and image segmentation + Diffusion tensor imaging of the brain Resources 1 / Resources 2 / Source Code
Thu 03.05.17 9:00-11:00 Tissue structure (mikro) Bjoern Menze slides No use cases (TUM 150)  
Thu 10.05.17   No Lecture [Himmelfahrt]        
Thu 17.05.17 9:00-11:00 Blood flow (perfusion) Cagdas Ulas slides Blood perfusion Resources Questions
Thu 24.05.17 9:00-11:00 Blood flow (fluid dynamics) Augusto Sanches slides / Questions Computational Hemodynamics Resources
Thu 31.05.17   No Lecture [Fronleichnam]        
Thu 07.06.17 9:00-11:00 Brain function (neurokinetics) Bjoern Menze slides PET & metabolism  
Thu 14.06.17 9:00-11:00 Metabolism (MRI) Franz Schilling slides Brain tumor growth resources / Additional Materials
Thu 21.06.17 9:00-11:00 Metabolism (PET) Bjoern Menze slides    
Thu 28.06.17 9:00-11:00 Disease progression (tumor growth, population) Bjoern Menze slides    
Thu 05.07.17 9:00-11:00 Recap & Presentations of case studies Bjoern Menze      
Thu 12.07.17 9:00-11:00 Presentations of case studies (contd.) & Oral exams the same week Bjoern Menze      


Pointers to freely available literature are given at the end of the lecture slides.

Case studies

Topic and tutor:

NB: There scripts for the case studies will work with a little effort on Ubuntu and Mac. For windows users I will recommend you run an ubuntu virtual machine for convenience. You can check on this link for step by step tutorial on installing the Ubuntu virtual machine. Please install Ubuntu 16.04 LTS desktop version


Send an email to Bjoern Menze with your two favorite topics, mention 'CPMIC lecture' on the subject.

Title: Computational Physiology for Medical Image Computing
Professor: Prof. Bjoern Menze
Tutors: Marie Piraud; TBA
Type: Lecture
Information: 2 + 2 SWS, 6 ECTS Credits (IN2319)
Term: 2018SoSe

Edit | Attach | Refresh | Diffs | More | Revision r1.21 - 02 Jul 2018 - 12:55 - GilesTetteh

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