Bjoern Menze

Short CV

Before joining the Department of Informatics at TUM as the first Rudolf Mößbauer Tenure Track Professor in 2013, Bjoern Menze was senior researcher and lecturer in the Computer Vision Lab at ETH Zurich (Gabor Szekely), Switzerland, and a lab member of the Asclepios Project at INRIA Sophia Antipolis, France (Nicholas Ayache). Before that, he worked as a postdoc in Boston, USA, in the Medical Vision group of the CSAIL at MIT (Polina Golland) and in the BWH Surgical Planning Lab of Harvard Medical School (Ron Kikinis), after having been with the Department of Anthropology of Harvard University (Jason Ur). Bjoern Menze received his Ph.D. in Computer Science in 2007, while working at the Interdisciplinary Center for Scientific Computing in Heidelberg (Fred Hamprecht), Germany, and obtained degrees in Physics from Heidelberg and from Uppsala University, Sweden. In 2019 he was visiting professor at Maastricht University. At TUM he heads the "Image-based Biomedical Modeling Group" at the Munich School of Bioengineering and the Center for Translational Cancer Research.

Selected Awards

2014 MICCAI Young Scientist Award Finalist & Selection for the MICCAI

2014 Best Paper Issue of Medical Image Analysis. M Rempfer et al., B Menze. ‚Extracting vascular networks under physiological constraints via integer programming’. MICCAI Conference 2014, Boston, USA

2014 Best Poster Award. J Lipkova, B Menze, P Koumoutsakos. 'Patient-specific modeling of glioma' Platform for Advanced Scientific Computing (PASC) Conference 2014, Zurich, Switzerland

2009 Leopoldina Research Fellow of the German National Academy of Sciences Leopoldina 2008 DFG Research Fellowship 2007 Fritz Thyssen Research Fellowship 1998 Fellow of the German National Academic Foundation / Studienstiftung des deutschen Volkes 

Research Interests

My research is in medical image computing, exploring topics at the interface of medical computer vision, image-based modeling and computational physiology. In this, I focus on applications in clinical neuroimaging and the modeling of tumor growth. My 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. I am also interested in how to apply such models to big data bases in order to learn about correlations between model features and disease patterns at a population scale.

Selected Publications

  • Menze, B. H.; Ur, J. A.: Mapping patterns of long-term settlement in Northern Mesopotamia at a large scale. Proceedings of the National Academy of Sciences 109 (14), 2012, E778-E787.
  • Kelm, B. Michael; Kaster, Frederik O.; Henning, Anke; Weber, Marc-André; Bachert, Peter; Boesiger, Peter; Hamprecht, Fred A.; Menze, Bjoern H.: Using spatial prior knowledge in the spectral fitting of MRS images. NMR in Biomedicine 25 (1), 2011, 1-13.
  • Menze, Bjoern H.; Van Leemput, Koen; Honkela, Antti; Konukoglu, Ender; Weber, Marc-André; Ayache, Nicholas; Golland, Polina: A Generative Approach for Image-Based Modeling of Tumor Growth. In: Lecture Notes in Computer Science. Springer Science + Business Media, 2011.
  • Menze, Bjoern H.; Kelm, B. Michael; Splitthoff, Daniel N.; Koethe, Ullrich; Hamprecht, Fred A.: On Oblique Random Forests. In: Machine Learning and Knowledge Discovery in Databases. Springer Science + Business Media, 2011.
  • Menze, Bjoern H.; van Leemput, Koen; Lashkari, Danial; Weber, Marc-André; Ayache, Nicholas; Golland, Polina: A Generative Model for Brain Tumor Segmentation in Multi-Modal Images. In: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2010. Springer Science + Business Media, 2010.

Publications as TUM-IAS-Fellow

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )

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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )
  • 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… BibTeX Full text ( DOI )