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
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
- [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]".
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 | Presenter | Tutor |
|---|
| Flow / Vascular | Robben et al. Perfusion Paths: Inference of Voxelwise Blood Flow Trajectories in CT Perfusion. Miccai 2015 | Waldmannstetter | Kowarschik |
| | Rempfler et al. Extracting Vascular Networks under Physiological Constraints via Integer Programming. Miccai 2014 | | |
| | Sankaran et al. Real-time Sensitivity Analysis of Blood Flow Simulations to Lumen Segmentation Uncertainty. Miccai 2014 | Barschkis | Kowarschik |
| | Orlando et al. Learning fully-connected CRFs for blood vessel segmentation in retinal images. Miccai 2014 | | |
| | Medrano-Gracia et al. Construction of a Coronary Atlas from CT Angiography. Miccai 2014 | Spier | Wels |
| Growth / Tumor | Le et al. Bayesian Personalization of Brain Tumor Growth Model. Miccai 2015 | Kewlani | Shi |
| | Bogo et al. Automated detection of new or evolving melanocytic lesions using a 3D body model. Miccai 2014 | Martin | Wels |
| | Kwon et al. Combining Generative Models for Multifocal Glioma Segmentation and Registration. Miccai 2014 | Jimenez | Shi |
| | Khanal et al. A biophysical model of shape changes due to atrophy in the brain with Alzheimer’s disease. Miccai 2014 | Papathanasis | Valentinitsch |
| Signals / Physiology | Burgos et al. Subject-specific Models for the Analysis of Pathological FDG PET Data. Miccai 2015 | | |
| | Golkov et al. q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans. Miccai 2015 | Rahman | Sperl |
| | Chen et al. Real time dynamic MRI with dynamic total variation. Miccai 2014 | Luque | Sperl |
| | Alexander et al. Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. Miccai 2014 | | |
| | Nedjati-Gilani et al. Maching Learning Based Compartment Models with Permeability for White Matter Microstructure Imaging. Miccai 2014 | | |
| Anatomy / Disease | Ebner et al. Towards Automatic Bone Age Estimation from MRI: Localization of 3D Anatomical Landmarks. Miccai 2014 | | |
| | Young et al. Multiple orderings of events in disease progression. Ipmi 2015 | | |
| | Batmanghelich et al. Generative Method to Discover Genetically Driven Image Biomarkers. Ipmi 2015 | | |
| | Wachinger et al. Brain Print: Identifying Subjects by their Brain. Miccai 2014 | Estrada | Valentinitsch |
| | 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 |
Papers will be announced in September. Topics will be similar to those discussed in the previous seminars of SS 14 and of WS 15.
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.
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.
