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)
Type: Master Seminar
Module IN2107
SWS: 2+0
ECTS: 4 Credits
Location: IMETUM Seminar Room (1st Floor)
Time: Wednesday 1500-1700
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.
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.
Announcements
- [1.10.2015] The list of paper is available. We still have open seats for additional students.
- [13.07.2015] The list of papers will be made available by the end of September.
- [13.07.2015] Registration: please register by sending an email to Bjoern Menze after the list of papers will have been made available and indicate two papers you are interested in.
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. 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.
Schedule
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 |
|---|
| 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 Bjoern Menze 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.
