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

Hauptseminar/Master Seminar:
Image-based Biomedical Modeling

Bjoern Menze (TUM), Kuangyu Shi (TUM Klinikum Rechts der Isar), Jonathan Sperl (GE), Michael Kelm (Siemens), Markus Kowarschik (Siemens), Alexander Valentinitsch (TUM Klinikum Rechts der Isar), Michael Wels (Siemens)

Type: Master Seminar Module IN2107
SWS: 2+0
ECTS: 5 Credits
Location: IMETUM Seminar Room (to be confirmed)
Time: Wednesday 1500-1700 (to be confirmed)
Course Language: English


Many clinical imaging sequences include image modalities that provide unique insights into the human body: describing blood flow pattern or water diffusion, visualizing micro-structural tissue properties, or quantifying metabolic processes that have been found to be relevant for specific diseases. To access and explore the rich biological information of such multimodal CT, PET, and MR image data sets, different approaches from biophysical modeling and computational physiology are used.

The topic of this seminar is to survey such computational models by reading, discussing and understanding key publications in this field, for example, on:

  • spatial atlases that encode the variation of anatomy throughout the population in a probabilistic fashion,
  • dynamical models that describe blood flow patterns in MR and CT, or the the dynamics of metabolic pathways as measured via PET,
  • spatio-temporal models that describe cardiac electro-physiological excitations, or the growth patterns of tumors,
  • global probabilistic models that relate image features with clinical information or genetic variables.

Emphasis is put on improving presentation style. All presenters will present their talk twice during the course of the semester, and after the first time the group discussion will focus on presentation style.


  • [14.06.2016] Papers will be announced in September. The will also be a pre-meeting taking place in September.
  • [14.06.2016] In order to be updated on open topics and the pre-meeting, please indicate your interest in participating in the seminar by sending an email to bjoern.menze@tum.de with the subject "[IBBM seminar]".


In this Master Seminar (formerly Hauptseminar), each student is asked to select one paper from a list. In order to successfully complete the seminar, participants have to fulfill these requirements:

  • Presentation: The selected paper is presented to the other participants (20 minutes presentation 10 minutes questions). Use the CAMP templates for PowerPoint CAMPmaster.pot, or Latex: CAMP-latex-template.zip. All papers will be presented at two occasions. After the first presentation we will discuss presentation and presentation style, after the second presentation we will discuss the research topic of the paper.
  • Written Handout: A document of 4-8 pages is written and handed in two days before the presentation (i.e., on the Monday morning before the final presentation). Please download and use the llncs2e.zip Latex template. It can be edited and updated following comments in the final presentation.
  • Attendance: Participants have to participate actively in all seminar sessions.

Each presentation is followed by a discussion and everyone is encouraged to actively participate. The handout must include all references used and should be your own review of the paper (don't copy & paste). Both handout and presentation will have to be in English. It can follow the structure of the presentation: Intro (incl. statement of the problem, prior work, contribution of the present work), Methods (previously existing and improvements), Experiments (data and results), Conclusion / Summary.


The seminar consists of an introductory meeting and seminar sessions. Each of the sessions will consist of several student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.

List of Papers

The papers that we are going to discuss in the seminar belong to four different research areas:
Area Description down Presenter Tutor
  Alexander et al. Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. Miccai 2014    
  Batmanghelich et al. Generative Method to Discover Genetically Driven Image Biomarkers. Ipmi 2015    
  Bogo et al. Automated detection of new or evolving melanocytic lesions using a 3D body model. Miccai 2014 Martin Wels
Signals / Physiology Burgos et al. Subject-specific Models for the Analysis of Pathological FDG PET Data. Miccai 2015    
  Chen et al. Real time dynamic MRI with dynamic total variation. Miccai 2014 Luque Sperl
Anatomy / Disease Ebner et al. Towards Automatic Bone Age Estimation from MRI: Localization of 3D Anatomical Landmarks. Miccai 2014    
  Golkov et al. q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans. Miccai 2015 Rahman Sperl
  Khanal et al. A biophysical model of shape changes due to atrophy in the brain with Alzheimer’s disease. Miccai 2014 Papathanasis Valentinitsch
  Kwon et al. Combining Generative Models for Multifocal Glioma Segmentation and Registration. Miccai 2014 Jimenez Shi
Growth / Tumor Le et al. Bayesian Personalization of Brain Tumor Growth Model. Miccai 2015 Kewlani Shi
  Medrano-Gracia et al. Construction of a Coronary Atlas from CT Angiography. Miccai 2014 Spier Wels
  Nedjati-Gilani et al. Maching Learning Based Compartment Models with Permeability for White Matter Microstructure Imaging. Miccai 2014    
  Orlando et al. Learning fully-connected CRFs for blood vessel segmentation in retinal images. Miccai 2014    
  Rempfler et al. Extracting Vascular Networks under Physiological Constraints via Integer Programming. Miccai 2014    
Flow / Vascular Robben et al. Perfusion Paths: Inference of Voxelwise Blood Flow Trajectories in CT Perfusion. Miccai 2015 Waldmannstetter Kowarschik
  Sankaran et al. Real-time Sensitivity Analysis of Blood Flow Simulations to Lumen Segmentation Uncertainty. Miccai 2014 Barschkis Kowarschik
  Schlegl et al. Predicting Semantic Descriptions from Medical Images with Convolutional Neural Networks. Ipmi 2015    
  Towws et al. Feature-based Approach to Big Data Analysis of Medical Images. Ipmi 2015 Stelzl Kelm
  Wachinger et al. Brain Print: Identifying Subjects by their Brain. Miccai 2014 Estrada Valentinitsch
  Young et al. Multiple orderings of events in disease progression. Ipmi 2015    

Papers will be announced in September. Topics will be similar to those discussed in the previous seminars of SS 14 and of WS 15.


The seminar consists of an introductory meeting and seminar sessions. Each of the sessions will consist of several student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.

Date Time By Tutor Type Of Presentation
Oct 26 15:00-17:00 Intro -- First Meeting
Nov 2 15:00-17:00 Stelzl -- Rehearsal
Nov 9 15:00-17:00 Luque -- Rehearsal
Nov 16 15:00-17:00 Papathanasis, Estrada -- Rehearsal
Nov 23 15:00-17:00 --    
Nov 30 15:00-17:00 Jiminez, Spier -- Rehearsal
Dec 7 15:00-17:00 [Dies academicus] --  
Dec 14 15:00-17:00 Martin, Waldmanstetter,Kewlani [Kowarschik] Rehearsal
Dec 21 15:00-17:00 --    
Jan 11 15:00-17:00 Papathanasis, Estrada Valeninitsch Final
Jan 18 15:00-*19:00* Kewlani, Jiminez, Luque Shi, Sperl Final
Jan 25 15:00-*19:00* Spier, Martin, Waldmannstetter, Stelzl Wels, Kowarschik, Kelm Final
Feb 1 15:00-17:00 --   Final
Feb 8 15:00-17:00 --    

Literature and Helpful Links

A lot of scientific publications can be found online.

The following list may help you to find some further information on your particular topic:

Some publishers:

Libraries (online and offline):

Some further hints for working with references:

  • JabRef is a Java program for comfortable working with Bibtex literature databases. Handy feature: if you know the PubMed ID for an article, JabRef can import data from there (via "Web Search/Medline").
  • Mendeley is a cross-platform program for organising your references.

If you find useful resources that are not already listed here, please tell us, so we can add them for others. Thanks.

Title: Image-based biomedical modeling seminar
Professor: Prof. Bjoern Menze
Type: Hauptseminar
Information: Hauptseminar, SWS: 2, ECTS: 5
Term: 2016WiSe

Edit | Attach | Refresh | Diffs | More | Revision r1.18 - 03 Jan 2017 - 11:25 - BjoernMenze

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