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. Kuangyu Shi, Dr. Markus Kowarschik, Dr. Marie Piraud

Tutors: Giles Tetteh, Anjany Sekuboyina

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
  • Exams: will be in office 1.102 in the IMETUM/GSB building.


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 27.04.17 9:00-11:00 Intro and Overview Bjoern Menze Slides    
Thu 04.05.17 9:00-11:00 Tissue structure (makro) Bjoern Menze Slides    
Thu 11.05.17 9:00-11:00 Tissue structure (mikro) Bjoern Menze Slides    
Thu 18.05.17 9:00-11:00 Brain function (neurokinetics) Bjoern Menze Slides    
Thu 25.05.17   No Lecture [Himmelfahrt]        
Thu 01.06.17 9:00-11:00 Metabolism (MRI) Bjoern Menze Slides Brain structure and image segmentation Resources
Thu 08.06.17 9:00-11:00 Metabolism (PET, disease) Kuangyu Shi Slides Diffusion tensor imaging of the brain Resources/Sample Code
Thu 15.06.17   No Lecture [Fronleichnam]        
Thu 22.06.17 9:00-11:00 Metabolism (PET, general) Kuangyu Shi Slides    
Thu 29.06.17 9:00-11:00 NA     Blood flow (Perfusion) Resources
Thu 06.07.17 9:00-11:00 Blood flow (perfusion) Markus Kowarschik Slides/Resources    
Thu 13.07.17 9:00-11:00 Blood flow (perfusion / angiography) Markus Kowarschik Slides Brain Tumor Growth Resources
Thu 20.07.17 9:00-11:00 Disease progression (tumor growth, population) Bjoern Menze Slides    
Thu 3.08.17 9:00-11:00 Presentations of case studies, exams during the same week        


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

Case studies

Topic and tutor:


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

Title: Computational Physiology for Medical Image Computing
Professor: Prof. Bjoern Menze
Tutors: Markus Kowarschik, Kuangyu Shi, Marie Piraud
Type: Lecture
Information: 2 + 2 SWS, 6 ECTS Credits (IN2319)
Term: 2017SoSe

Edit | Attach | Refresh | Diffs | More | Revision r1.27 - 01 Aug 2017 - 15:11 - BjoernMenze

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