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.

Date	Time	Location	By	Supervision	Type Of Presentation
Oct 14	15:00-17:00	IMETUM Seminar	-	-	First Meeting
Nov 18	15:00-17:30	IMETUM Seminar	all	all	Rehearsal
Dec 9	15:00-17:30	IMETUM Seminar	all	all	Final

List of Papers

The papers that we are going to discuss in the seminar belong to four different research areas:

Area	Description
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.
Spatial Maps and Structures	Spatial atlases and parametric maps that encode the variation of anatomy throughout the population in a probabilistic fashion.
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.

Student	Tutor	Area	Author	Papers
Khakzar	Kowarschik	Spatial Maps and Structures	Lugauer et al.	PDF Precise Lumen Segmentation in Coronary Computed Tomography Angiography. MICCAI MCV 2014
	Kowarschik	Spatial Maps and Structures	Rempfler et al.	PDF Reconstructing cerebrovascular networks under local physiological constraints by integer programming. Medical Image Analysis 2015
	Sperl / Menze	Time series & signal models	Alexander et al.	PDF Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. MICCAI 2014
	Kelm	Time series & signal models	Kelm et al.	PDF Using spatial prior knowledge in the spectral fitting of MRS images. NMR in Biomedicine 2011
Keribin	Kelm	Time series & signal models	Kelm et al.	PDF Estimating kinetic parameter maps from dynamic contrast-enhanced MRI using spatial prior knowledge. IEEE Transactions on Medical Imaging 2006
	Valentinitsch	Spatial Maps and Structures	Danciu et al.	PDF 3D DCT Supervised Segmentation Applied on Liver Volumes. IEEE Transactions on Medical Imaging 2012
	Valentinitsch	Spatial Maps and Structures	Banerjee et al.	PDF 3D LBP-based Rotationally Invariant Region Description. Proc ACCV 2012 Workshops
Meryem	Shi	Spatio-temporal processes & signals	Hatt et al.	PDF 18F-FDG PET uptake characterization through texture analysis. Journal of Nuclear Medicine 2015
Tran	Shi	Spatio-temporal processes & signals	Waclaw et al.	PDF A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity. Nature 2015
Franzen	Menze	Spatio-temporal processes & signals	Unkelbach et al.	PDF Radiotherapy planning for glioblastoma based on a tumor growth model. Physics in Medicine and Biology 2013
	Menze	Spatio-temporal processes & signals	Konukoglu et al.	PDF Extrapolating glioma invasion margin in brain magnetic resonance images: Suggesting new irradiation margins. Medical Image Analyis 2010.

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:

• Microsoft Academic Search
• Google Scholar
• CiteSeer
• CiteULike
• Collection of Computer Science Bibliographies

Some publishers:

• ScienceDirect (Elsevier Journals)
• IEEE Journals
• ACM Digital Library

Libraries (online and offline):

• http://rzblx1.uni-regensburg.de/ezeit/ (Elektronische Zeitschriften Bibliothek)
• Verbundkatalog des Bibliotheksverbundes Bayern (BVB)
• Computer ORG
• http://www.ub.tum.de/ (TUM Library)
  • To get access onto the electronic library, see http://www.ub.tum.de/medien/ejournals/readme.html
  • "proxy.biblio.tu-muenchen.de" mit Port 8080 (nur fuer http). Damit klappen zumindest portal.acm.org und computer.org meistens
• Various proceedings of conferences in our AR-Lab, 03.13.036 (These proceedings are not for lending!)

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.