Hauptseminar/Master Seminar:
Image-based Biomedical Modeling
Bjoern Menze (TUM),
Dana Cobzas (U Alberta),
Kuangyu Shi (TUM Klinikum Rechts der Isar),
Vladimir Golkov (GE),
Michael Kelm (Siemens)
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Type: Master Seminar
Module IN2107
SWS: 2+0
ECTS: 4 Credits
Location: 03.13.010 (NB: will be 01.16.020 on April 9th and May 7th)
Time: 10.00-12.00
Course Language: English
Content
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.
Optional: Some of the topics will allow the presenter to use related software tools and available image data to reproduce (some of) the experiments of these publications. Interested participants can make this demonstration a part of their presentation.
Announcements
- [07.04.2014] The first meeting in on April 9th in 01.16.020.
- [29.01.2014] If you missed the intro meeting and are still interested in participating, please see the intro slides and drop me a note via email.
- [23.01.2014] There will be a short preliminary meeting on Wednesday January 29th, 2014 at 14h in 03.13.010. The list of papers will be made available after the introduction meeting in April.
Regulations
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.
- Written Handout: A document of 4-8 pages is written and sent two days before the presentation to Fausto Milletari (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.
Schedule
The seminar consists of a preliminary meeting, 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 |
|---|
| Spatial Maps and Structures | Spatial atlases and parametric maps that encode the variation of anatomy throughout the population in a probabilistic fashion. |
| Time series & signal models | Dynamical models that describe blood flow patterns in MR and CT, or the dynamics of metabolic pathways as measured via PET, or the signals of short term water diffusion. |
| Spatio-temporal processes & signals | Spatio-temporal models that describe spatially coupled time signal models, tumor growth, model personalisation. |
| Global processes | Global probabilistic models that relate image features with global clinical information or global genetic variables. |
In order to express your preferences about the topic you would like to discuss in your presentation and essay, please send an email to
img.based.biomedical.modeling@gmail.com indicating the
two papers your are most interested in. We will discuss the assignments in the meeting on April 9th.
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.
