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:
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.
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.
The papers that we are going to discuss in the seminar belong to four different research areas:
Area | Description ![]() | Presenter | Tutor |
---|---|---|---|
Young et al. Multiple orderings of events in disease progression. Ipmi 2015 | |||
Wachinger et al. Brain Print: Identifying Subjects by their Brain. Miccai 2014 | Estrada | Valentinitsch | |
Towws et al. Feature-based Approach to Big Data Analysis of Medical Images. Ipmi 2015 | Stelzl | Kelm | |
Schlegl et al. Predicting Semantic Descriptions from Medical Images with Convolutional Neural Networks. Ipmi 2015 | |||
Sankaran et al. Real-time Sensitivity Analysis of Blood Flow Simulations to Lumen Segmentation Uncertainty. Miccai 2014 | Barschkis | Kowarschik | |
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 | |||
Orlando et al. Learning fully-connected CRFs for blood vessel segmentation in retinal images. Miccai 2014 | |||
Nedjati-Gilani et al. Maching Learning Based Compartment Models with Permeability for White Matter Microstructure Imaging. 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 |
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 | |
Golkov et al. q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans. Miccai 2015 | Rahman | Sperl | |
Anatomy / Disease | Ebner et al. Towards Automatic Bone Age Estimation from MRI: Localization of 3D Anatomical Landmarks. Miccai 2014 | ||
Chen et al. Real time dynamic MRI with dynamic total variation. Miccai 2014 | Luque | Sperl | |
Signals / Physiology | Burgos et al. Subject-specific Models for the Analysis of Pathological FDG PET Data. Miccai 2015 | ||
Bogo et al. Automated detection of new or evolving melanocytic lesions using a 3D body model. Miccai 2014 | Martin | Wels | |
Batmanghelich et al. Generative Method to Discover Genetically Driven Image Biomarkers. Ipmi 2015 | |||
Alexander et al. Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. Miccai 2014 |
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.
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:
If you find useful resources that are not already listed here, please tell us, so we can add them for others. Thanks.
TeachingForm | |
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Title: | Image-based biomedical modeling seminar |
Professor: | Prof. Bjoern Menze |
Tutors: | |
Type: | Hauptseminar |
Information: | Hauptseminar, SWS: 2, ECTS: 5 |
Term: | 2016WiSe |
Abstract: |