TeachingSs16CpMic

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

Computational Physiology for Medical Image Computing - IN2319

Organization

Lecture: Prof. Bjoern Menze, Dr. Kuangyu Shi and Esther Alberts, Miguel Molina, Pedro Gomez, Cagdas Ulas, Markus Rempfler.

Time & Location

  • Lecture: Wednesdays, 2:30pm - 4:00pm in room MI 03.09.012
  • Work on Case Studies (Exercises): Wednesdays, 4:00pm - 5:30pm in room MI 03.09.012

Overview

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.

Prerequisites

  • 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.

Regulations

  • Module Specification: IN2319
  • SWS: 2+2
  • ECTS: 6 Credits
  • Course Language: English
  • Exam: presentation of course project, and oral exam (20 minutes)

Course Schedule

NB: ZIP files of the lecture slides can be unzipped using 'CpMic16'.

Date Time Room Type Topic Lecturer Material
Wed 13.04.16 2:30pm - 4:00pm MI 03.09.012   Intro and Overview Bjoern Menze Slides
Wed 20.04.16 2:30pm - 4:00pm MI 03.09.012   Tissue structure (makro) Bjoern Menze Slides
Wed 27.04.16 2:30pm - 4:00pm MI 03.09.012   Intro Python Markus Rempfler Slides and notebooks
Wed 04.05.16 2:30pm - 4:00pm MI 03.09.012   Tissue structure (mikro) Bjoern Menze Slides
Wed 11.05.16 2:30pm - 4:00pm MI 03.09.012   Blood flow (dynamics) Bjoern Menze Slides
Wed 18.05.16 2:30pm - 4:00pm MI 03.09.012   Blood flow (neurokinetics) Bjoern Menze Slides
Wed 25.05.16 2:30pm - 4:00pm MI 03.09.012   Metabolism (MRI) Bjoern Menze Slides
Wed 01.06.16 2:30pm - 4:00pm MI 03.09.012   Metabolism (PET) Kuangyu Shi Slides
Wed 08.06.16 2:30pm - 4:00pm MI 03.09.012   Disease progression (tumor growth) Bjoern Menze Slides
Wed 15.06.16 No Lecture          
Wed 22.06.16 2:30pm - 4:00pm MI 03.09.012   Disease progression (population) Bjoern Menze Slides
Wed 29.06.16 2:30pm - 4:00pm MI 03.09.012   Case studies Bjoern Menze  
Wed 07.07.16 Exams          
Wed 13.07.16 No Lecture          


Literature

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.

TeachingForm
Title: Computational Physiology for Medical Image Computing
Professor: Prof. Bjoern Menze
Tutors: Esther Alberts, Miguel Molina, Pedro Gomez, Cagdas Ulas, Markus Rempfler
Type: Lecture
Information: 2 + 2 SWS, 6 ECTS Credits (IN2319)
Term: 2016SoSe
Abstract:  


Edit | Attach | Refresh | Diffs | More | Revision r1.14 - 03 Jul 2016 - 20:11 - BjoernMenze

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