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Technical University of Munich
Technical University of Munich

Image-Based Biomedical Modeling

In the Focus Group "Image-based Biomedical Modeling" Rudolf Mößbauer Tenure Track Professor Bjoern Menze and his group explore topics at the interface of medical computer vision, image-based modeling and computational physiology. In this, they primarily deal with applications in clinical neuroimaging and the modeling of tumor growth. Their work strives towards transforming the descriptive interpretation of biomedical images into a model-driven analysis that infers properties of the underlying physiological and patho-physiological processes by using models from biophysics and computational physiology. A related effort is the application of such models to big data bases in order to learn about correlations between model features and disease patterns at a population scale.

Current projects follow two main lines of research:

The first direction is the modeling of processes underlying images acquired in common diseases of the brain. The focus is on the analysis of images acquired in glioma and stroke patients, including the development of algorithms for the longitudinal analysis of brain lesions using parametric and non-parametric lesion evolution models, and the quantitative interpretation of blood flow patterns at population scale.  The main sources of information are multimodal and multi-parametric clinical image data sets featuring MR, PET and CT scans.

The second direction deals with the task of optimal oncological staging. It includes the anatomical annotation of large field of view images – such as abdominal scans or whole body images – the detection of lesion across modalities and in repeated scans, and the analysis of individual lesion using descriptive pathophysiological models.

Emphasis is put on the clinical applicability, and algorithms are supposed to scale well to large data sets enabling the development of population wide disease progression models.

TUM-IAS funded doctoral candidate:
Esther Alberts, Computer-Aided Medical Procedures & Augmented Reality / Neuroradiology
Jana Lipkova, Computer-Aided Medical Procedures & Augmented Reality
Markus Rempfler, Computer-Aided Medical Procedures & Augmented Reality

Postdoctoral Researcher:
Dr. Vasileios Zografos, Computer Aided Medical Procedures & Augmented Reality

Publications by the Focus Group

2019

  • Ezhov, Ivan; Lipkova, Jana; Shit, Suprosanna; Kofler, Florian; Collomb, Nore; Lemasson, Benjamin; Barbier, Emmanuel; Menze, Bjoern: Neural Parameters Estimation for Brain Tumor Growth Modeling. In: Lecture Notes in Computer Science. Springer International Publishing, 2019 more…
  • Gómez, Pedro A.; Molina-Romero, Miguel; Buonincontri, Guido; Menzel, Marion I.; Menze, Bjoern H.: Designing contrasts for rapid, simultaneous parameter quantification and flow visualization with quantitative transient-state imaging. Scientific Reports 9 (1), 2019 more…
  • Li, Hongwei; Paetzold, Johannes C.; Sekuboyina, Anjany; Kofler, Florian; Zhang, Jianguo; Kirschke, Jan S.; Wiestler, Benedikt; Menze, Bjoern: DiamondGAN: Unified Multi-modal Generative Adversarial Networks for MRI Sequences Synthesis. In: Lecture Notes in Computer Science. Springer International Publishing, 2019 more…
  • Li, Hongwei; Zhang, Jianguo; Muehlau, Mark; Kirschke, Jan; Menze, Bjoern: Multi-scale Convolutional-Stack Aggregation for Robust White Matter Hyperintensities Segmentation. In: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Springer International Publishing, 2019 more…
  • Lipkova, Jana; Angelikopoulos, Panagiotis; Wu, Stephen; Alberts, Esther; Wiestler, Benedikt; Diehl, Christian; Preibisch, Christine; Pyka, Thomas; Combs, Stephanie E.; Hadjidoukas, Panagiotis; Van Leemput, Koen; Koumoutsakos, Petros; Lowengrub, John; Menze, Bjoern: Personalized Radiotherapy Design for Glioblastoma: Integrating Mathematical Tumor Models, Multimodal Scans, and Bayesian Inference. IEEE Transactions on Medical Imaging 38 (8), 2019, 1875-1884 more…
  • Piraud, Marie; Sekuboyina, Anjany; Menze, Björn H.: Multi-level Activation for Segmentation of Hierarchically-Nested Classes. In: Lecture Notes in Computer Science. Springer International Publishing, 2019 more…
  • Piraud, Marie; Wennmann, Markus; Kintzelé, Laurent; Hillengass, Jens; Keller, Ulrich; Langs, Georg; Weber, Marc-André; Menze, Björn H.: Towards quantitative imaging biomarkers of tumor dissemination: A multi-scale parametric modeling of multiple myeloma. Medical Image Analysis 57, 2019, 214-225 more…
  • Sekuboyina, Anjany; Rempfler, Markus; Valentinitsch, Alexander; Loeffler, Maximilian; Kirschke, Jan S.; Menze, Bjoern H.: Probabilistic Point Cloud Reconstructions for Vertebral Shape Analysis. In: Lecture Notes in Computer Science. Springer International Publishing, 2019 more…
  • Zhao, Yu; Li, Hongwei; Wan, Shaohua; Sekuboyina, Anjany; Hu, Xiaobin; Tetteh, Giles; Piraud, Marie; Menze, Bjoern: Knowledge-Aided Convolutional Neural Network for Small Organ Segmentation. IEEE Journal of Biomedical and Health Informatics 23 (4), 2019, 1363-1373 more…

2018

  • Cai, Ruiyao; Pan, Chenchen; Ghasemigharagoz, Alireza; Todorov, Mihail I.; Förstera, Benjamin; Zhao, Shan; Bhatia, Harsharan S.; Mrowka, Leander; Theodorou, Delphine; Rempfler, Markus; Xavier, Anna; Kress, Benjamin T.; Benakis, Corinne; Liesz, Arthur; Menze, Bjoern; Kerschensteiner, Martin; Nedergaard, Maiken; Ertürk, Ali: Panoptic vDISCO imaging reveals neuronal connectivity, remote trauma effects and meningeal vessels in intact transparent mice. bioRxiv, 2018 more…
  • Cai, Ruiyao; Pan, Chenchen; Ghasemigharagoz, Alireza; Todorov, Mihail Ivilinov; Förstera, Benjamin; Zhao, Shan; Bhatia, Harsharan S.; Parra-Damas, Arnaldo; Mrowka, Leander; Theodorou, Delphine; Rempfler, Markus; Xavier, Anna L. R.; Kress, Benjamin T.; Benakis, Corinne; Steinke, Hanno; Liebscher, Sabine; Bechmann, Ingo; Liesz, Arthur; Menze, Bjoern; Kerschensteiner, Martin; Nedergaard, Maiken; Ertürk, Ali: Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections. Nature Neuroscience 22 (2), 2018, 317-327 more…
  • Coello, Eduardo; Noeske, Ralph; Burns, Brian L.; Gordon, Jeremy W.; Jakary, Angela; Menze, Bjoern; Haase, Axel; Larson, Peder E.Z.; Li, Yan; Schulte, Rolf F.: High-resolution echo-planar spectroscopic imaging at ultra-high field. NMR in Biomedicine 31 (11), 2018, e3950 more…
  • Fahmy, Ahmed S.; Rausch, Johannes; Neisius, Ulf; Chan, Raymond H.; Maron, Martin S.; Appelbaum, Evan; Menze, Bjoern; Nezafat, Reza: Automated Cardiac MR Scar Quantification in Hypertrophic Cardiomyopathy Using Deep Convolutional Neural Networks. JACC: Cardiovascular Imaging 11 (12), 2018, 1917-1918 more…
  • Han, Xu; Kwitt, Roland; Aylward, Stephen; Bakas, Spyridon; Menze, Bjoern; Asturias, Alexander; Vespa, Paul; Van Horn, John; Niethammer, Marc: Brain extraction from normal and pathological images: A joint PCA/Image-Reconstruction approach. NeuroImage 176, 2018, 431-445 more…
  • Jang, Jihye; Tschabrunn, Cory M.; Barkagan, Michael; Anter, Elad; Menze, Bjoern; Nezafat, Reza: Three-dimensional holographic visualization of high-resolution myocardial scar on HoloLens. PLOS ONE 13 (10), 2018, e0205188 more…
  • Li, Hongwei; Jiang, Gongfa; Zhang, Jianguo; Wang, Ruixuan; Wang, Zhaolei; Zheng, Wei-Shi; Menze, Bjoern: Fully convolutional network ensembles for white matter hyperintensities segmentation in MR images. NeuroImage 183, 2018, 650-665 more…
  • Licandro, Roxane; Hofmanninger, Johannes; Weber, Marc-André; Menze, Bjoern; Langs, Georg: Predicting Future Bone Infiltration Patterns in Multiple Myeloma. In: Patch-Based Techniques in Medical Imaging. Springer International Publishing, 2018 more…
  • Lipková, Jana; Arampatzis, Georgios; Chatelain, Philippe; Menze, Bjoern; Koumoutsakos, Petros: S-Leaping: An Adaptive, Accelerated Stochastic Simulation Algorithm, Bridging $$\tau $$τ-Leaping and R-Leaping. Bulletin of Mathematical Biology, 2018 more…
  • Maier-Hein, Lena; Eisenmann, Matthias; Reinke, Annika; Onogur, Sinan; Stankovic, Marko; Scholz, Patrick; Arbel, Tal; Bogunovic, Hrvoje; Bradley, Andrew P.; Carass, Aaron; Feldmann, Carolin; Frangi, Alejandro F.; Full, Peter M.; van Ginneken, Bram; Hanbury, Allan; Honauer, Katrin; Kozubek, Michal; Landman, Bennett A.; März, Keno; Maier, Oskar; Maier-Hein, Klaus; Menze, Bjoern H.; Müller, Henning; Neher, Peter F.; Niessen, Wiro; Rajpoot, Nasir; Sharp, Gregory C.; Sirinukunwattana, Korsuk; Speidel, Stefanie; Stock, Christian; Stoyanov, Danail; Taha, Abdel Aziz; van der Sommen, Fons; Wang, Ching-Wei; Weber, Marc-André; Zheng, Guoyan; Jannin, Pierre; Kopp-Schneider, Annette: Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications 9 (1), 2018 more…
  • Molina-Romero, Miguel; Gómez, Pedro A.; Sperl, Jonathan I.; Czisch, Michael; Sämann, Philipp G.; Jones, Derek K.; Menzel, Marion I.; Menze, Bjoern H.: A diffusion model-free framework with echo time dependence for free-water elimination and brain tissue microstructure characterization. Magnetic Resonance in Medicine 80 (5), 2018, 2155-2172 more…
  • Molina-Romero, Miguel; Wiestler, Benedikt; Gómez, Pedro A.; Menzel, Marion I.; Menze, Bjoern H.: Deep Learning with Synthetic Diffusion MRI Data for Free-Water Elimination in Glioblastoma Cases. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018 more…
  • Perkonigg, Matthias; Hofmanninger, Johannes; Menze, Björn; Weber, Marc-André; Langs, Georg: Detecting Bone Lesions in Multiple Myeloma Patients Using Transfer Learning. In: Data Driven Treatment Response Assessment and Preterm, Perinatal, and Paediatric Image Analysis. Springer International Publishing, 2018 more…
  • Reinke, Annika; Eisenmann, Matthias; Onogur, Sinan; Stankovic, Marko; Scholz, Patrick; Full, Peter M.; Bogunovic, Hrvoje; Landman, Bennett A.; Maier, Oskar; Menze, Bjoern; Sharp, Gregory C.; Sirinukunwattana, Korsuk; Speidel, Stefanie; van der Sommen, Fons; Zheng, Guoyan; Müller, Henning; Kozubek, Michal; Arbel, Tal; Bradley, Andrew P.; Jannin, Pierre; Kopp-Schneider, Annette; Maier-Hein, Lena: How to Exploit Weaknesses in Biomedical Challenge Design and Organization. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018 more…
  • Rempfler, Markus; Stierle, Valentin; Ditzel, Konstantin; Kumar, Sanjeev; Paulitschke, Philipp; Andres, Bjoern; Menze, Bjoern H.: Tracing cell lineages in videos of lens-free microscopy. Medical Image Analysis 48, 2018, 147-161 more…
  • Sekuboyina, Anjany; Rempfler, Markus; Kukačka, Jan; Tetteh, Giles; Valentinitsch, Alexander; Kirschke, Jan S.; Menze, Bjoern H.: Btrfly Net: Vertebrae Labelling with Energy-Based Adversarial Learning of Local Spine Prior. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018 more…
  • Ulas, Cagdas; Tetteh, Giles; Kaczmarz, Stephan; Preibisch, Christine; Menze, Bjoern H.: DeepASL: Kinetic Model Incorporated Loss for Denoising Arterial Spin Labeled MRI via Deep Residual Learning. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018 more…
  • Ulas, Cagdas; Tetteh, Giles; Thrippleton, Michael J.; Armitage, Paul A.; Makin, Stephen D.; Wardlaw, Joanna M.; Davies, Mike E.; Menze, Bjoern H.: Direct Estimation of Pharmacokinetic Parameters from DCE-MRI Using Deep CNN with Forward Physical Model Loss. In: Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. Springer International Publishing, 2018 more…
  • Wennmann, Markus; Kintzelé, Laurent; Piraud, Marie; Menze, Bjoern H.; Hielscher, Thomas; Hofmanninger, Johannes; Wagner, Barbara; Kauczor, Hans-Ulrich; Merz, Maximilian; Hillengass, Jens; Langs, Georg; Weber, Marc-André: Volumetry based biomarker speed of growth: Quantifying the change of total tumor volume in whole-body magnetic resonance imaging over time improves risk stratification of smoldering multiple myeloma patients. Oncotarget 9 (38), 2018 more…
  • Xu, Lina; Tetteh, Giles; Lipkova, Jana; Zhao, Yu; Li, Hongwei; Christ, Patrick; Piraud, Marie; Buck, Andreas; Shi, Kuangyu; Menze, Bjoern H.: Automated Whole-Body Bone Lesion Detection for Multiple Myeloma on 68Ga-Pentixafor PET/CT Imaging Using Deep Learning Methods. Contrast Media & Molecular Imaging 2018, 2018, 1-11 more…
  • Xu, Lina; Vaupel, Peter; Menze, Bjoern H.; Shi, Kuangyu: Impact of Temporal Heterogeneity of Acute Hypoxia on the Radiation Response of Experimental Tumors. In: Advances in Experimental Medicine and Biology. Springer International Publishing, 2018 more…
  • Zimmermann, Judith; Demedts, Daniel; Mirzaee, Hanieh; Ewert, Peter; Stern, Heiko; Meierhofer, Christian; Menze, Bjoern; Hennemuth, Anja: Wall shear stress estimation in the aorta: Impact of wall motion, spatiotemporal resolution, and phase noise. Journal of Magnetic Resonance Imaging 48 (3), 2018, 718-728 more…

2017

  • Alberts, Esther; Tetteh, Giles; Trebeschi, Stefano; Bieth, Marie; Valentinitsch, Alexander; Wiestler, Benedikt; Zimmer, Claus; Menze, Bjoern H.: Multi-modal Image Classification Using Low-Dimensional Texture Features for Genomic Brain Tumor Recognition. In: Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics. Springer International Publishing, 2017 more…
  • Bieth, Marie; Alberts, Esther; Schwaiger, Markus; Menze, Bjoern: From Large to Small Organ Segmentation in CT Using Regional Context. In: Machine Learning in Medical Imaging. Springer International Publishing, 2017 more…
  • Bieth, Marie; Krönke, Markus; Tauber, Robert; Dahlbender, Marielena; Retz, Margitta; Nekolla, Stephan G.; Menze, Bjoern; Maurer, Tobias; Eiber, Matthias; Schwaiger, Markus: Exploring New Multimodal Quantitative Imaging Indices for the Assessment of Osseous Tumor Burden in Prostate Cancer Using68Ga-PSMA PET/CT. Journal of Nuclear Medicine 58 (10), 2017, 1632-1637 more…
  • Bieth, Marie; Peter, Loic; Nekolla, Stephan G.; Eiber, Matthias; Langs, Georg; Schwaiger, Markus; Menze, Bjoern: Segmentation of Skeleton and Organs in Whole-Body CT Images via Iterative Trilateration. IEEE Transactions on Medical Imaging 36 (11), 2017, 2276-2286 more…
  • Bothmann, Ludwig; Menzel, Annette; Menze, Bjoern H.; Schunk, Christian; Kauermann, Göran: Automated processing of webcam images for phenological classification. PLOS ONE 12 (2), 2017, e0171918 more…
  • Das, Dhritiman; Coello, Eduardo; Schulte, Rolf F.; Menze, Bjoern H.: Quantification of Metabolites in Magnetic Resonance Spectroscopic Imaging Using Machine Learning. In: Springer Proceedings in Physics. Springer Singapore, 2017 more…
  • Eichinger, Paul; Alberts, Esther; Delbridge, Claire; Trebeschi, Stefano; Valentinitsch, Alexander; Bette, Stefanie; Huber, Thomas; Gempt, Jens; Meyer, Bernhard; Schlegel, Juergen; Zimmer, Claus; Kirschke, Jan S.; Menze, Bjoern H.; Wiestler, Benedikt: Diffusion tensor image features predict IDH genotype in newly diagnosed WHO grade II/III gliomas. Scientific Reports 7 (1), 2017 more…
  • Hofmanninger, Johannes; Menze, Bjoern; Weber, Marc-André; Langs, Georg: Mapping Multi-Modal Routine Imaging Data to a Single Reference via Multiple Templates. In: Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support. Springer International Publishing, 2017 more…
  • Maier, Oskar; Menze, Bjoern H.; von der Gablentz, Janina; Häni, Levin; Heinrich, Mattias P.; Liebrand, Matthias; Winzeck, Stefan; Basit, Abdul; Bentley, Paul; Chen, Liang; Christiaens, Daan; Dutil, Francis; Egger, Karl; Feng, Chaolu; Glocker, Ben; Götz, Michael; Haeck, Tom; Halme, Hanna-Leena; Havaei, Mohammad; Iftekharuddin, Khan M.; Jodoin, Pierre-Marc; Kamnitsas, Konstantinos; Kellner, Elias; Korvenoja, Antti; Larochelle, Hugo; Ledig, Christian; Lee, Jia-Hong; Maes, Frederik; Mahmood, Qaiser; Maier-Hein, Klaus H.; McKinley, Richard; Muschelli, John; Pal, Chris; Pei, Linmin; Rangarajan, Janaki Raman; Reza, Syed M.S.; Robben, David; Rueckert, Daniel; Salli, Eero; Suetens, Paul; Wang, Ching-Wei; Wilms, Matthias; Kirschke, Jan S.; Krämer, Ulrike M.; Münte, Thomas F.; Schramm, Peter; Wiest, Roland; Handels, Heinz; Reyes, Mauricio: ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical Image Analysis 35, 2017, 250-269 more…
  • P. Christ, F. Ettlinger, G. Kaissis, S. Schlecht, F. Ahmaddy, F. Grün, A. Valentinitsch, S.-A. Ahmadi, R. Braren, and B. H. Menze: SurvivalNet: predicting patient survival from diffusion weighted magnetic resonance images using cascaded fully convolutional and 3D convolutional neural network,. 2017 more…
  • Rempfler, Markus; Andres, Bjoern; Menze, Bjoern H.: Uncertainty Estimation in Vascular Networks. In: Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics. Springer International Publishing, 2017 more…
  • Rempfler, Markus; Kumar, Sanjeev; Stierle, Valentin; Paulitschke, Philipp; Andres, Bjoern; Menze, Bjoern H.: Cell Lineage Tracing in Lens-Free Microscopy Videos. In: Lecture Notes in Computer Science. Springer International Publishing, 2017 more…
  • Rempfler, Markus; Lange, Jan-Hendrik; Jug, Florian; Blasse, Corinna; Myers, Eugene W.; Menze, Bjoern H.; Andres, Bjoern: Efficient Algorithms for Moral Lineage Tracing. 2017 IEEE International Conference on Computer Vision (ICCV), IEEE, 2017 more…
  • Tetteh, Giles; Rempfler, Markus; Zimmer, Claus; Menze, Bjoern H.: Deep-FExt: Deep Feature Extraction for Vessel Segmentation and Centerline Prediction. In: Machine Learning in Medical Imaging. Springer International Publishing, 2017 more…
  • Ulas, Cagdas; Gómez, Pedro A.; Krahmer, Felix; Sperl, Jonathan I.; Menzel, Marion I.; Menze, Bjoern H.: Robust Reconstruction of Accelerated Perfusion MRI Using Local and Nonlocal Constraints. In: Reconstruction, Segmentation, and Analysis of Medical Images. Springer International Publishing, 2017 more…
  • Xu, Lina; Tetteh, Giles; Mustafa, Mona; Lipkova, Jana; Zhao, Yu; Bieth, Marie; Christ, Patrick; Piraud, Marie; Menze, Bjoern; Shi, Kuangyu: W-Net for Whole-Body Bone Lesion Detection on ${68}$ Ga-Pentixafor PET/CT Imaging of Multiple Myeloma Patients. In: Lecture Notes in Computer Science. Springer International Publishing, 2017 more…

2016

  • Alberts, Esther; Charpiat, Guillaume; Tarabalka, Yuliya; Huber, Thomas; Weber, Marc-André; Bauer, Jan; Zimmer, Claus; Menze, Bjoern H.: A Nonparametric Growth Model for Brain Tumor Segmentation in Longitudinal MR Sequences. In: Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Springer International Publishing, 2016 more…
  • Alberts, Esther; Rempfler, Markus; Alber, Georgina; Huber, Thomas; Kirschke, Jan; Zimmer, Claus; Menze, Bjoern H.: Uncertainty quantification in brain tumor segmentation using CRFs and random perturbation models. 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), IEEE, 2016 more…
  • Andreasen, Daniel; Edmund, Jens M.; Zografos, Vasileios; Menze, Bjoern H.; Van Leemput, Koen: Computed tomography synthesis from magnetic resonance images in the pelvis using multiple random forests and auto-context features. Medical Imaging 2016: Image Processing, SPIE, 2016 more…
  • Christ, Patrick Ferdinand; Elshaer, Mohamed Ezzeldin A.; Ettlinger, Florian; Tatavarty, Sunil; Bickel, Marc; Bilic, Patrick; Rempfler, Markus; Armbruster, Marco; Hofmann, Felix; D’Anastasi, Melvin; Sommer, Wieland H.; Ahmadi, Seyed-Ahmad; Menze, Bjoern H.: Automatic Liver and Lesion Segmentation in CT Using Cascaded Fully Convolutional Neural Networks and 3D Conditional Random Fields. In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2016. Springer International Publishing, 2016 more…
  • Christ, Patrick Ferdinand; Lachner, Florian; Hösl, Axel; Menze, Bjoern; Diepold, Klaus; Butz, Andreas: Human-Drone-Interaction: A Case Study to Investigate the Relation Between Autonomy and User Experience. In: Lecture Notes in Computer Science. Springer International Publishing, 2016 more…
  • Das, Dhritiman; Coello, Eduardo; Schulte, Rolf F.; Menze, Bjoern H.: Spatially Adaptive Spectral Denoising for MR Spectroscopic Imaging using Frequency-Phase Non-local Means. In: Lecture Notes in Computer Science. Springer International Publishing, 2016 more…
  • Gómez, Pedro A.; Molina-Romero, Miguel; Ulas, Cagdas; Bounincontri, Guido; Sperl, Jonathan I.; Jones, Derek K.; Menzel, Marion I.; Menze, Bjoern H.: Simultaneous Parameter Mapping, Modality Synthesis, and Anatomical Labeling of the Brain with MR Fingerprinting. In: Lecture Notes in Computer Science. Springer International Publishing, 2016 more…
  • Hershkovich, Tsachi; Shalmon, Tamar; Shitrit, Ohad; Halay, Nir; Menze, Bjoern H.; Dolgopyat, Irit; Kahn, Itamar; Shelef, Ilan; Riklin Raviv, Tammy: Probabilistic model for 3D interactive segmentation. Computer Vision and Image Understanding 151, 2016, 47-60 more…
  • Jimenez-del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andras; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H.; Salas Fernandez, Tomas; Schaer, Roger; Walleyo, Anna; Weber, Marc-Andre; Dicente Cid, Yashin; Gass, Tobias; Heinrich, Mattias; Jia, Fucang; Kahl, Fredrik; Kechichian, Razmig; Mai, Dominic; Spanier, Assaf B.; Vincent, Graham; Wang, Chunliang; Wyeth, Daniel; Hanbury, Allan: Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks. IEEE Transactions on Medical Imaging 35 (11), 2016, 2459-2475 more…
  • Menze, Bjoern H.; Van Leemput, Koen; Lashkari, Danial; Riklin-Raviv, Tammy; Geremia, Ezequiel; Alberts, Esther; Gruber, Philipp; Wegener, Susanne; Weber, Marc-Andre; Szekely, Gabor; Ayache, Nicholas; Golland, Polina: A Generative Probabilistic Model and Discriminative Extensions for Brain Lesion Segmentation— With Application to Tumor and Stroke. IEEE Transactions on Medical Imaging 35 (4), 2016, 933-946 more…
  • Nagaraj, Yeshaswini; Menze, Bjoern; Friebe, Michael: US/MRI fusion with new optical tracking and marker approach for interventional procedures inside the MRI suite. Current Directions in Biomedical Engineering 2 (1), 2016 more…
  • Rempfler, Markus; Andres, Bjoern; Menze, Bjoern H.: The Minimum Cost Connected Subgraph Problem in Medical Image Analysis. In: Lecture Notes in Computer Science. Springer International Publishing, 2016 more…
  • Shen, Jun; Baum, Thomas; Cordes, Christian; Ott, Beate; Skurk, Thomas; Kooijman, Hendrik; Rummeny, Ernst J.; Hauner, Hans; Menze, Bjoern H.; Karampinos, Dimitrios C.: Automatic segmentation of abdominal organs and adipose tissue compartments in water-fat MRI: Application to weight-loss in obesity. European Journal of Radiology 85 (9), 2016, 1613-1621 more…
  • Sivalingam, Udhayaraj; Wels, Michael; Rempfler, Markus; Grosskopf, Stefan; Suehling, Michael; Menze, Bjoern H.: Inner and outer coronary vessel wall segmentation from CCTA using an active contour model with machine learning-based 3D voxel context-aware image force. Medical Imaging 2016: Computer-Aided Diagnosis, SPIE, 2016 more…
  • Ulas, Cagdas; Gomez, Pedro A.; Sperl, Jonathan I.; Preibisch, Christine; Menze, Bjoern H.: Spatio-temporal MRI reconstruction by enforcing local and global regularity via dynamic total variation and nuclear norm minimization. 2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI), IEEE, 2016 more…
  • Zografos, Vasileios; Valentinitsch, Alexander; Rempfler, Markus; Tombari, Federico; Menze, Bjoern: Hierarchical Multi-Organ Segmentation Without Registration in 3D Abdominal CT Images. In: Medical Computer Vision: Algorithms for Big Data. Springer International Publishing, 2016 more…

2015

  • Bieth, Marie; Donner, Rene; Langs, Georg; Schwaiger, Markus; Menze, Bjoern: Anatomical triangulation: from sparse landmarks to dense annotation of the skeleton in CT images. Procedings of the British Machine Vision Conference 2015, British Machine Vision Association, 2015 more…
  • Gómez, Pedro A.; Ulas, Cagdas; Sperl, Jonathan I.; Sprenger, Tim; Molina-Romero, Miguel; Menzel, Marion I.; Menze, Bjoern H.: Learning a Spatiotemporal Dictionary for Magnetic Resonance Fingerprinting with Compressed Sensing. In: Patch-Based Techniques in Medical Imaging. Springer International Publishing, 2015 more…
  • Menze, Bjoern H.; Jakab, Andras; Bauer, Stefan; Kalpathy-Cramer, Jayashree; Farahani, Keyvan; Kirby, Justin; Burren, Yuliya; Porz, Nicole; Slotboom, Johannes; Wiest, Roland; Lanczi, Levente; Gerstner, Elizabeth; Weber, Marc-Andre; Arbel, Tal; Avants, Brian B.; Ayache, Nicholas; Buendia, Patricia; Collins, D. Louis; Cordier, Nicolas; Corso, Jason J.; Criminisi, Antonio; Das, Tilak; Delingette, Herve; Demiralp, Cagatay; Durst, Christopher R.; Dojat, Michel; Doyle, Senan; Festa, Joana; Forbes, Florence; Geremia, Ezequiel; Glocker, Ben; Golland, Polina; Guo, Xiaotao; Hamamci, Andac; Iftekharuddin, Khan M.; Jena, Raj; John, Nigel M.; Konukoglu, Ender; Lashkari, Danial; Mariz, Jose Antonio; Meier, Raphael; Pereira, Sergio; Precup, Doina; Price, Stephen J.; Raviv, Tammy Riklin; Reza, Syed M. S.; Ryan, Michael; Sarikaya, Duygu; Schwartz, Lawrence; Shin, Hoo-Chang et al.: The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS). IEEE Transactions on Medical Imaging 34 (10), 2015, 1993-2024 more…
  • Rempfler, Markus; Schneider, Matthias; Ielacqua, Giovanna D.; Xiao, Xianghui; Stock, Stuart R.; Klohs, Jan; Székely, Gábor; Andres, Bjoern; Menze, Bjoern H.: Reconstructing cerebrovascular networks under local physiological constraints by integer programming. Medical Image Analysis 25 (1), 2015, 86-94 more…
  • Schneider, Matthias; Hirsch, Sven; Weber, Bruno; Székely, Gábor; Menze, Bjoern H.: Joint 3-D vessel segmentation and centerline extraction using oblique Hough forests with steerable filters. Medical Image Analysis 19 (1), 2015, 220-249 more…

2014

  • Menze, Bjoern H.; Ur, Jason A.: Multitemporal Fusion for the Detection of Static Spatial Patterns in Multispectral Satellite Images—With Application to Archaeological Survey. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 7 (8), 2014, 3513-3524 more…
  • Rempfler, Markus; Schneider, Matthias; Ielacqua, Giovanna D.; Xiao, Xianghui; Stock, Stuart R.; Klohs, Jan; Székely, Gábor; Andres, Bjoern; Menze, Bjoern H.: Extracting Vascular Networks under Physiological Constraints via Integer Programming. In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014. Springer International Publishing, 2014 more…
  • Schneider, Matthias; Hirsch, Sven; Weber, Bruno; Székely, Gábor; Menze, Bjoern H.: TGIF: Topological Gap In-Fill for Vascular Networks. In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2014. Springer International Publishing, 2014 more…
  • Tarabalka, Yuliya; Charpiat, Guillaume; Brucker, Ludovic; Menze, Bjoern H.: Spatio-Temporal Video Segmentation With Shape Growth or Shrinkage Constraint. IEEE Transactions on Image Processing 23 (9), 2014, 3829-3840 more…
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