Bjoern Menze - Publications

Selected publications, for a complete list refer to my Google Scholar profile.

Image-Based Modeling

We seek for new techniques in multimodal data analysis that combine physiological, bio-physical, and probabilistic models of imaging process and image information. The focus is on tumor imaging and applications in clinical neuroscience.

Gómez P, Molina-Romero M, Buonincontri G, Menzel M, Menze BH. Designing contrasts for rapid, simultaneous parameter quantification and flow visualization with quantitative transient-state imaging. arXiv preprint arXiv:1901.07800 2019
(preprint)
⇒ "This paper introduces an approach for designig specifc biomarkers of interest using MR fingerprinting and blood flow as an example."

Lipkova J, Angelikopoulos P, Wu S, Alberts E, Wiestler B, Diehl C, Preibisch C, Pyka T, Combs S, Hadjidoukas P, Van Leemput K, Koumoutsakos P, Lowengrub J, Menze BH. Personalized radiotherapy design for glioblastoma: integrating mathematical tumor models, multimodal scans and Bayesian inference. IEEE Transactions on Medical Imaging 2019. In press
(preprint)
⇒ "This paper introduces a Bayesian approach for calibrating the Fisher-Kolmogorov tumor growth model against FET PET and multi-parametric MR images."

Molina‐Romero M, Gómez P, Sperl J, Czisch M, Sämann P, Jones DK, Menze MI, Menze BH. A diffusion model‐free framework with echo time dependence for free‐water elimination and brain tissue microstructure characterization. Magnetic Resonance in Medicine 2018. 80 (5), 2155-2172
(PubMed) (preprint)

Ulas C, Tetteh G, Kaczmarz S, Preibisch C, Menze BH. DeepASL: kinetic model incorporated loss for denoising arterial spin labeled MRI via deep residual learning. Proc MICCAI 2018. Springer LNCS. 8p
(publisher) (preprint)

Ulas C, Tetteh G, Thrippleton MJ, Armitage PA Makin SD, Wardlaw JM, Davies M, Menze BH. Direct estimation of pharmacokinetic parameters from DCE-MRI using deep CNN with forward physical model loss. Proc MICCAI 2018. 8p
(publisher) (preprint)

Molina-Romero M, Wiestler B, Gómez P, Menzel M, Menze BH. Deep learning with synthetic diffusion MRI data for free-water elimination in glioblastoma cases. Proc MICCAI 2018. Springer LNCS. 8p
(publisher) (preprint)
⇒ "This paper illustrates who to eliminate water effects from DTI data (even in a retrospective fashion) using a DL model trained on synthetic data."

Ulas C, Das D, Thrippleton MJ, Hernández MCV, Armitage PA, Makin SD, Wardlaw JM, Menze BH. Convolutional neural networks for direct inference of pharmacokinetic parameters: application to stroke dynamic contrast-enhanced MRI. Frontiers in Neurology 2018. 9
(PubMed) (publisher, open access)

Das D, Coello E, Schulte R, Menze BH. Quantification of metabolites in magnetic resonance spectroscopic imaging using machine learning. Proc MICCAI 2017. Springer LNCS. 8p
(publisher) (preprint)
⇒ "This paper is the first attempt to infer resonance line model parameters directly from magnetic resonance spectra using a machine learning approach."

Gomez PA, Molina-Romero M, Ulas C, Bounincontri G, Sperl J, Jones DK, Menzel MI, Menze BH. Simultaneous parameter mapping, modality synthesis, and anatomical labeling of the brain with MR fingerprinting. Proc MICCAI 2016.
(preprint)
⇒ "This is the first paper at MICCAI dealing with the processing and analysis of magnetic resonance fingerprinting signals."

Das D, Coello E, Schulte RF, Menze BH. Spatially adaptive spectral denoising for MR spectroscopic imaging using frequency-phase non-local means. Proc MICCAI 2016.
(preprint)

Ulas C, Gomez PA, Krahmer F, Sperl JI, Menzel MI, Menze BH. Robust reconstruction of accelerated perfusion MRI using local and nonlocal constraints Proc MICCAI-RAMBO 2016.
(preprint)

Menze BH, Van Leemput K, Lashkari D, Riklin-Raviv T, Geremia E, Alberts E, Gruber P, Wegener S, Weber MA, Szekely G, Ayache N, Golland P. A generative probabilistic model and discriminative extensions for brain lesion segmentation - with application to tumor and stroke. IEEE Transactions on Medical Imaging 2016.et35:933-946.
(PubMed) (publisher, open access) (preprint)

Rempfler M, Schneider M, Ielacqua GD, Xiao X, Stock SR, Klohs J, Szekely G, Andres B, Menze BH. Reconstructing cerebrovascular networks under local physiological constraints by integer programming. Medical Image Analysis 2015. 25:86-94. MICCAI Medical Image Analysis Award 2015
(PubMed) (publisher) (preprint)

Schneider M, Hirsch S, Weber B, Szekely G, Menze BH. TGIF: Topological gap in-fill for vascular networks - a generative physiological modeling approach. Proc MICCAI 2014.
(PubMed) (publisher) (preprint)

Rempfler M, Schneider M, Ielacqua GD, Xiao X, Stock SR, Klohs J, Szekely G, Andres B, Menze BH. Extracting vascular networks under physiological constraints via integer programming. Proc MICCAI 2014. Young Scientist Award, Runner-up
(PubMed) (publisher) (preprint)

Unkelbach J, Menze BH, Konukoglu E, Dittmann F, Ayache N, Shi H. Radiotherapy planning for glioblastoma based on a tumor growth model: implications for spatial dose redistribution. Physics in Medicine and Biology 2014. 59:771-89
(PubMed) (publisher) (preprint)

Unkelbach J, Menze BH, Konukoglu E, Dittmann F, Le M, Ayache N, Shi H. Radiotherapy planning for glioblastoma based on a tumor growth model: improving target volume delineation. Physics in Medicine and Biology 2014. 59:747-70
(PubMed) (publisher) (preprint)

Lorenzi M, Menze BH, Niethammer M, Ayache N, Pennec X. Sparse scale-space decomposition of volume changes in deformations fields. Proc MICCAI 2013. LNCS 8150, 328-335.
(publisher) (preprint)

Menze BH, Strettin E, Konukoglu E and Ayache N. Image-based modeling of tumor growth in patients with glioma. In: CS Garbe, R Rannacher, U Platt, T Wagner (eds.), Optimal control in image processing. Springer, Heidelberg. In press.
(preprint)

Menze BH, Geremia E, Ayache N, Szekely G. Segmenting glioma in multi-modal images using a generative-discriminative model for brain lesion segmentation. Proc MICCAI BRATS (Brain Tumor Segmentation Challenge). 2012
(publisher) (preprint)

Menze BH, Van Leemput K, Lashkari D, Weber MA, Ayache N, Golland P. Segmenting glioma in multi-modal images using a generative model for brain lesion segmentation. Proc MICCAI BRATS (Brain Tumor Segmentation Challenge). 2012
(publisher) (preprint)

Riklin-Raviv T, Van Leemput K, Menze BH. Multi-modal brain tumor segmentation via latent atlases. Proc MICCAI BRATS (Brain Tumor Segmentation Challenge). 2012
(publisher) (preprint)

Geremia E, Menze BH, Prastawa M, Criminisi A, Ayache N. Brain tumor cell density estimation from multi-modal MR images based on a synthetic tumor growth model. Proc MICCAI MCV 2012 (Workshop on Medical Computer Vision). LNCS 7766, 273-282.
(publisher) (preprint)

Menze BH, Van Leemput K, Honkela A, Konukoglu E, Weber MA, Ayache N and Golland P. A generative approach for image-based modeling of tumor growth. Proc IPMI 2011. LNCS 6801, 735-47.
(PubMed) (publisher) (preprint)

⇒ "This paper introduces a joint generative model of tumor growth and image observation. Model personalization relies on a forward model of the patho-physiological process combined with different image likelihood functions, and an efficient Bayesian inference approach."

Kelm BM, Kaster FO, Henning A, Weber MA, Bachert P, Boesiger P, Hamprecht FA and Menze BH. Using spatial prior knowledge in the spectral fitting of magnetic resonance spectroscopic images. NMR in Biomedicine 2011. 28: 1534-47.
(PubMed) (publisher) (preprint)

⇒ "This paper introduces a Bayesian smoothness prior in the spectral fitting of the metabolic model functions which can be used in addition to commonly employed prior knowledge in the quantification of MRS images."

Konukoglu E, Clatz O, Menze BH, Stieltjes B, Weber MA, Mandonnet E, Delinegette H and Ayache N. Image guided personalization of reaction-diffusion type tumor growth models using modified anisotropic Eikonal equations. IEEE Transactions on Medical Imaging 2010. 29:77-95
(PubMed) (publisher) (preprint)

Riklin-Raviv T, Van Leemput K, Menze BH, Wells WM and Golland P. Segmentation of image ensembles via latent atlases. Medical Image Analysis 2010. 14:654-65.
(PubMed) (publisher) (preprint)

Menze BH, Van Leemput K, Lashkari D, Weber MA, Ayache N and Golland P. A generative model for brain tumor segmentation in multi-modal images. Proc MICCAI 2010. LNCS 6362, 151-59 MICCAI Young Scientist Publication Impact Award 2015
(PubMed) (publisher) (preprint)

⇒ "This paper introduces a generative probabilistic model for segmenting brain lesions in multi-dimensional images with different lesion boundaries in each channel, reflecting difference in tumor appearance across modalities. The model augments an atlas of healthy tissue priors with a latent atlas of the lesion."

Kelm BM, Menze BH, Nix O, Zechmann C and Hamprecht FA. Estimating kinetic parameter maps from dynamic contrast-enhanced MRI using spatial prior knowledge. IEEE Transaction on Medical Imaging 2009. 28:1534-47.
(PubMed) (publisher) (preprint)

Riklin Raviv T, Menze BH, Van Leemput K, Stieltjes B, Weber MA, Ayache N, Wells WM and Golland P. Joint segmentation via patient-specific latent anatomy model. Proc MICCAI-PMMIA 2009. 244-55
(publisher) (preprint)

Menze BH, Konukoglu E, Clatz O, Stieltjes B, Nix O, Weber MA, Kikinis R and Ayache N. Estimating the growth process of gliomas using physiological models. Proc ISMRM Workshop on Frontiers of Magnetic Resonance: From Tumor Cell to Cancer Patient. Nice, France. 2008
(publisher)

Kelm BM, Müller N, Menze BH and Hamprecht FA. Bayesian estimation of smooth parameter maps for dynamic contrast-enhanced magnetic resonance images with block-ICM. Proc CVPR-MMBIA 2006. 96-103
(publisher) (preprint)

Medical Computer Vision and Machine Learning

We seek for new machine learning approaches for detection, localization, segmentation, and classification tasks in medical image analysis. Key applications are in structural anatomy, tumor quantification, and biomedical testing for radiomic decision support. The validation of such algorithms is the objectice of several benchmark and open data efforts.

Tetteh G, Efremov V, Forkert ND, Schneider M, Kirschke J, Weber B, Zimmer C, Piraud M, Menze BH. DeepVesselNet: vessel segmentation, centerline prediction, and bifurcation detection in 3-D angiographic volumes. arXiv preprint arXiv:1803.09340
(preprint)

Simpson A, Antonell Mi, Bakas S, Bilello M, Farahani K, van Ginneken B, ... (incl. Menze BH). A large annotated medical image dataset for the development and evaluation of segmentation algorithms. arXiv preprint arXiv:1902.09063 2019
(preprint)

Bilic P, Christ P, Vorontsov E, …, Menze BH. The liver tumor segmentation benchmark (LITS). arXiv preprint arXiv:1901.04056 2019
(preprint)
⇒ "This is a draft of the refernece paper for the LITS challenge."

Pan C, Schoppe O, Parra-Damas A, Cai R, Todorov M, Gondi G, ... (incl. Menze BH). Deep learning reveals cancer metastasis and therapeutic antibody targeting in whole body. bioRxiv, 541862 2019
(preprint)

Bakas S, Reyes M, Jakab A, ..., Menze BH. Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. arXiv preprint arXiv:1811.02629 2018
(preprint)
⇒ "This is a draft of the summary paper of seven years of BRATS challenges, with more than 200 coauthors."

Zhao Y, Li H, Wan S, Sekuboyina A, Hu X, Tetteh G, Piraud M, Menze BH Knowledge-aided convolutional neural network for small organ segmentation. IEEE Journal of Biomedical and Health Informatics 2019. In press
(PubMed)

Cai R, Pan C, Ghasemigharagoz A, Todorov MI, Förstera B, Zhao S, Bhatia HS, Parra-Damas A, Mrowka L Theodorou D, Rempfler M, Xavier ALR, Kress BT, Benakis C, Steinke H, Liebscher S, Bechmann I, Liesz A, Menze BH, Kerschensteiner M, Nedergaard M, Ertürk A. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections. Nature Neuroscience, 2019. 22(2):317-327
(PubMed) (preprint)

Rempfler M, Stierle V, Ditzel K, Kumar S, Paulitschke P, Andres B, Menze BH. Tracing cell lineages in videos of lens-free microscopy. Medical Image Analysis 2018. 48, 147-161 MICCAI-Medical Image Analysis Best Paper Award 2018, Runner-up
(PubMed) (publisher)

Maier-Hein L, Eisenmann M, Reinke A, Onogur S, Stankovic M, Scholz P, Arbel T, Bogunovic H, Bradley AP, Carass A, Feldmann C, Frangi AF, Full PM, van Ginneken B, Hanbury A, Honauer K, Kozubek M, Landman BA, März K, Maier O, Maier-Hein K, Menze BH, Müller H, Neher PF, Niessen W, Rajpoot N, Sharp GC, Sirinukunwattana K, Speidel S, Stock C, Stoyanov D, Taha AA, van der Sommen F, Wang CW, Weber MA, Zheng G, Jannin P, Kopp-Schneider A. Why rankings of biomedical image analysis competitions should be interpreted with care. Nature Communications 2018. 9 (1), 5217
(PubMed) (preprint)

Li H, Jiang G, …, Menze BH. Fully convolutional network ensembles for white matter hyper-intensities segmentation in MR images. Neuroimage 2018. 183: 650-665 Winner of the WMH Segmentation Challenge at MICCAI 2017
(publisher) (preprint)

Sekuboyina A, Rempfler M, Kukačka J, Tetteh G, Valentinitsch A, ..., Menze BH. Btrfly Net: Vertebrae labelling with energy-based adversarial learning of local spine prior. Proc MICCAI 2018. Springer LNCS. 8p
(PubMed) (preprint)

Reinke A, Eisenmann M, Onogur S, ... (incl. Menze BH). How to exploit weaknesses in biomedical challenge design and organization. Proc MICCAI 2018. Springer LNCS. 8p
(Publisher) (preprint)

Han X, Kwitt R, Aylward S, Bakas S, Menze BH, Asturias A, Vespa PM, Van Horn J, Niethammer M. Brain extraction from normal and pathological images: A joint PCA/image-reconstruction approach. Neuroimage 2018. 176: 431-445
(PubMed) (preprint)

Bieth M, Peter L, Nekolla S, Eiber M, Langs G, Schwaiger M, Menze BH. Segmentation of skeleton and organs in whole-body CT images via iterative trilateration. IEEE Transactions on Medical Imaging 2017. 36 (11): 2276-2286
(PubMed) (preprint)

Rempfler M, Kumar S, Stierle V, Paulitschke P, Andres B, Menze BH. Cell lineage tracing in lens-free microscopy videos. Proc MICCAI 2017. Springer LNCS. 8p Selected for the MICCAI 2017 best paper special issue of Medical Image Analyis
(Publisher) (preprint)

Christ P, Elshaer M, Ettlinger F, Tatavarty S, Bickel M, Bilic P, Rempfler M, Armbruster M, Hofmann M, D'Anastasi M, Sommer W, Ahmadi A, Menze BH. Automatic liver and lesion segmentation in CT using cascaded fully convolutional neural networks and 3D conditional random fields. Proc MICCAI 2016. Springer LNCS. 8p
(code) (preprint)
⇒ "This paper is among the three most cited paper of MICCAI 2016."

Rempfler M, Andres B, Menze BH. The minimum cost connected subgraph problem in medical image analysis Proc MICCAI 2016. Springer LNCS. 8p
(publisher) (preprint)

Maier O*, Menze BH*, von der Gablentz J, Ḧani L, Heinrich MP, Liebrand M, Winzeck S, Basit A, Bentley P, Chen L, Christiaens D, Dutil F, Egger K, Feng C, Glocker B, Götz M, Haeck T, Halme HL, Havaei M, Iftekharuddin KM, Jodoin PM, Kamnitsas K, Kellner E, Korvenoja A, Larochelle H, Ledig C, Lee JH, Maes F, Mahmood Q, Maier-Hein KH, McKinley R, Muschelli J, Pal C, Pei L, Rangarajan JR, Reza SMS, Robben D, Rueckert D, Salli E, Suetens P, Wang CW, Wilms M, Kirschke JS, Kr Amer UM, Münte TF, Schramm P, Wiest R, Handels H, Reyes M. ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical Image Analysis 2016. 35: 250-269 (*shared authorship)
(PubMed) (publisher) (preprint)

Jimenez-Del-Toro O, Muller H, Krenn M, Gruenberg K, Taha AA, Winterstein M, Eggel I, Foncubierta-Rodriguez A, Goksel O, Jakab A, Kontokotsios G, Langs G, Menze BH, Salas Fernandez T, Schaer R, Walleyo A, Weber MA, Dicente Cid Y, Gass T, Heinrich M, Jia F, Kahl F, Kechichian R, Mai D, Spanier A, Vincent G, Wang C, Wyeth D, Hanbury A. Cloud-based evaluation of anatomical structure segmentation and landmark detection algorithms: VISCERAL anatomy benchmarks. IEEE Transaction on Medical Imaging 2016. 35: 2459-2475.
(PubMed) (publisher) (preprint)
⇒ "This is the reference paper to the VISCERAL challenge and data set that we co-organized in 2012-14."

Shen J, Baum T, Cordes C, Ott B, Skurk T, Kooijman H, Rummeny EJ, Hauner H, Menze BH*, Karampinos DC*. Automatic segmentation of abdominal organs and adipose tissue compartments in water-fat MRI: Application to weight-loss in obesity. (* shared authorship) European Journal of Radiology 2016. 85: 1613-21
(PubMed) (publisher)

Gomez PA, Ulas C, Sperl JI, Sprenger T, Molina-Romero M, Menzel MI, Menze BH. Learning a spatiotemporal dictionary for magnetic resonance fingerprinting with compressed sensing Proc MICCAI-PMI 2015. 8p.
(preprint)

Zografos Z,Valentinitsch A, Rempfler M, Tombari B, Menze BH. Hierarchical multi-organ segmentation without registration in 3D abdominal CT images Proc MICCAI-MCV 2015. 8p.
(preprint)

Dvorak P, Menze BH. Local structure prediction with convolutional neural networks for multimodal brain tumor segmentation. Proc MICCAI-MCV 2015. 8p.
(preprint)

Bieth M, Donner R, Langs G, Schwaiger M, Menze BH. Anatomical triangulation: from sparse landmarks to dense annotation of the skeleton in CT images. Proc BMVC 2015. 8p.
(preprint)

Tarabalka Y, Charpiat G, Brucker L, Menze BH. Spatio-temporal video segmentation with shape growth or shrinkage constraint. IEEE Transactions on Image Processing 2014. 23:3829-3840 .
(PubMed) (publisher) (preprint)

Menze BH, ... [60+ co-authors] ... , Van Leemput K. The multimodal brain tumor image segmentation challenge (BRATS). IEEE Transactions on Medical Imaging 2015. 34:1993-2024.
(PubMed) (publisher, open access) (preprint)

⇒ "In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation (BRATS) benchmark organized in conjunction with the MICCAI 2012 and 2013 conferences.

Schneider M, Hirsch S, Szekely G, Menze BH. Joint 3-D vessel segmentation and centerline extraction using oblique Hough forests with steerable filters. Medical Image Analysis 2015. 19:220-49
(PubMed) (publisher) (preprint)

Tarabalka Y, Charpiat G, Brucker L, Menze BH. Enforcing monotonous shape growth or shrinkage in video segmentation. Proc BMVC 2013. 8p.
(preprint)

Menze BH, Langs G, Tu Z, Criminisi A. Whole-body anatomy localization via classification and regression forests. (Editorial) Medical Image Analysis 2013, 17:1282.
(PubMed) (publisher)

Donner R, Menze BH, Bischof H, Langs G. Global localization of 3D anatomical structures by pre-filtered Hough forests and discrete optimization. Medical Image Analysis 2013, 17:1304-14.
(PubMed) (publisher, open access)

Hanbury A, Muller H, Langs G, Menze BH. Cloud–based evaluation framework for big data. Proc Future Internet Assembly 2013. LNCS 7858, 104-114.
(publisher, open access)

Geremia E, Menze BH, Ayache N. Spatially adaptive random forests. Proc IEEE ISBI 2013 (International Symposium on Biomedical Imaging: From Nano to Macro). 2013
(preprint)

Geremia E, Zikic D, Clatz O, Menze BH, Glocker B, Konukoglu E, Shotton J, Thomas O, Price S, Das T, Jena R, Ayache N, Criminisi A. Classification forests for semantic segmentation of brain lesions in multi-channel MRI. In: Criminisi A, Shotton J (eds.). Decision Forests for Computer Vision and Medical Image Analysis. Springer Publishing 2013, 245-260.
(publisher)

Menze BH, Langs G, Lu L, Montillo A, Tu Z and Criminisi A (eds.). Medical Computer Vision: Recognition techniques and applications in medical imaging. Proceedings of the MICCAI 2012 Workshop on Medical Computer Vision (MCV 2012). Lecture Notes in Computer Science 7766. Springer Publishing, Heidelberg. 294 pages, 2013.
(publisher) (workshop)

Schneider M, Hirsch S, Weber B, Szekely G, Menze BH. Oblique random forests for 3-D vessel detection using steerable filters and orthogonal subspace filtering. Proc MICCAI MCV 2012 (Workshop on Medical Computer Vision). LNCS 7766, 142-154.
(publisher) (preprint) (supplementary material)

Donner R, Langs G, Menze BH, Bischof H. Fast anatomical structure localization using top-down image patch regression. Proc MICCAI MCV 2012 (Workshop on Medical Computer Vision). LNCS 7766, 133-141. Best Paper Award
(publisher) (preprint)

Geremia E, Menze BH, Ayache N. Spatial decision forests for glioma segmentation in multi-channel MR images. Proc MICCAI BRATS (Brain Tumor Segmentation Challenge). 2012
(publisher) (preprint)

Langs G, Müller H, Menze BH, Hanbury A. VISCERAL: towards large data in medical imaging - challenges and directions. Proc MICCAI MCBR-CDS 2012 (Workshop on Medical Content-based Retrieval for Clinical Decision Support). LNCS 7723, 92-98.
(publisher) (preprint)

Ziegler A, Stock RS, Menze BH, Smith AB. Large structural diversity among sea urchin teeth revealed by micro-computed tomography. SPIE Optics Meeting. 2012
(publisher)

Hanbury A, Muller H, Langs G, Weber MA, Menze BH, Salas Fernandez T. Bringing the algorithms to the data: cloud-based benchmarking for medical image analysis. Proc CLEF 2012. LNCS 7488, 24-29
(publisher) (preprint)

Ziegler A, Menze BH. Accelerated analysis of animal anatomy. In: J Zander (ed.). Computation technology to advance society, CRC Press. New York. 2012

Zechmann CM *, Menze BH *, Kelm BM, Zamecnik P, Ikinger U, Waldherr R, Delorme S, Hamprecht FA, Bachert P. Automated vs. manual pattern recognition of 3D 1H MRSI data of patients with prostate cancer. Academic Radiology 2012. 19: 675-84. (* contributed equally)
(PubMed) (publisher)

Geremia E, Clatz O, Menze BH, Konukoglu E, Criminisi A and Ayache N. Spatial decision forests for MS lesion segmentation in multi-channel magnetic resonance images. Neuroimage 2011. 15: 378-90.
(PubMed) (publisher) (preprint)

Langs G, Menze BH, Lashkari D and Golland P. Detecting stable distributed patterns of brain activation in fMRI using Gini contrast. Neuroimage 2011. 15: 497-507.
(PubMed) (publisher) (preprint)

Menze BH, Kelm BM, Splitthoff DN, Koethe U, Hamprecht F. On oblique random forests. Proc ECML 2011. LNCS 6912, 453-469.
(publisher) (preprint) (R Package) (Videolecture)

⇒ "This paper proposes to employ 'oblique' split directions at internal nodes of the trees using linear discriminative models, rather than using random coefficients or univariate splits as in the original random forest. It is among the three most cited papers of ECML 2011."

Menze BH, Langs G, Tu Z and Criminisi A (eds.). Medical Computer Vision: Recognition techniques and applications in medical imaging. Proceedings of the MICCAI 2010 Workshop on Medical Computer Vision (MCV 2010). Lecture Notes in Computer Science 6533. Springer Publishing, Heidelberg. 226 pages, 2011.
(publisher) (workshop)

Geremia E, Menze BH, Clatz O, Konukoglu E, Criminisi A and Ayache N. Spatial decision forests for MS lesion segmentation in multi-channel magnetic resonance images. Proc MICCAI 2010. LNCS 6362, 664-772 Young Scientist Award, Runner-up
(PubMed) (preprint)

Kaster FO, Menze BH, Weber MA and Hamprecht FA. Comparative validation of graphical models for learning tumor segmentations from noisy manual annotations. Proc MICCAI-MCV 2010. LNCS 6533, 84-94
(publisher) (preprint)

Menze BH, Kelm BM, Masuch R, Himmelreich U, Bachert P, Petrich W and Hamprecht FA. A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data. BMC Bioinformatics 2009. 10: 213.
(PubMed) (publisher, open access)

Koenig T, Menze BH, Kirchner M, Monigatti F, Parker KC, Patterson T, Jebanathirajah Steen JA, Hamprecht FA and Steen H. Robust Prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics. Journal of Proteome Research 2008. 7: 3708-17.
(PubMed) (publisher) (preprint)

Menze BH, Kelm BM, Weber MA, Bachert P and Hamprecht FA. Mimicking the human expert: pattern recognition for an automated assessment of data quality in magnetic resonance spectroscopic images. Magnetic Resonance in Medicine 2008. 59: 1457-66.
(PubMed) (publisher) (preprint)

Gorlitz L*, Menze BH*, Weber MA, Kelm BM and Hamprecht FA. Semi-supervised tumor detection in magnetic resonance spectroscopic images using discriminative random fields. (* contributed equally) Proc DAGM 2007. LNCS 4713, 224-33
(publisher) (preprint)

Menze BH, Petrich W and Hamprecht FA. Multivariate feature selection and hierarchical classification for infrared spectroscopy: serum-based detection of bovine spongiform encephalopathy. Analytical and Bioanalytical Chemistry 2007. 387: 801-1807 ABC Best Poster Award at SPEC 2006
(PubMed) (publisher) (preprint)

Kelm BM, Menze BH, Zechmann CM, Baudendistel KT and Hamprecht FA. Automated estimation of tumor probability in prostate magnetic resonance spectroscopic imaging: pattern recognition vs. quantification. Magnetic Resonance in Medicine 2007. 57: 150-159
(PubMed) (publisher) (preprint)

Menze BH, Lichy MP, Bachert P, Kelm BM, Schlemmer HP and Hamprecht FA. Optimal classification of long echo time in vivo magnetic resonance spectra in the detection of recurrent brain tumors. NMR in Biomedicine 2006. 19: 599-60
(PubMed) (publisher) (preprint)

Archaeological Remote Sensing

This work aims at developing quantitative methods for archaeological prospection in the Near East using remote sensing techniques at a large scale.

Menze BH and Ur JA. Multitemporal fusion for the detection of static spatial patterns in multispectral satellite images - with application to archaeological survey. IEEE JSTARS (Journal of Selected Topics in Applied Earth Observations and Remote Sensing) 2014. In press
(preprint)

Menze BH and Ur JA. Multi-temporal classification of multi-spectral images for settlement survey in Northeastern Syria In: DC Comer, MJ Harrower (eds.), Mapping archaeological landscapes from space. Springer Briefs in Archaeology. 2013, 219-228.
(publisher)

Menze BH and Ur JA. Mapping patterns of long-term settlement in Northern Mesopotamia at a large scale. Proceedings of the National Academy of Science of the United States 2012. 109: E778-87
(PubMed) (publisher) (preprint) (data repository)

⇒ "This paper establishes a comprehensive record of ancient settlement sites in the Khabur Basin, north-eastern Syria, representing the largest systematic satellite-imagery-based survey in archaeology."

Press coverage: Nature, BBC, CNN, ABC, Huffington Post, Dailymail, The Atlantic, Archaeology Magazine, Discovery, Discover Magazine, Smithsonian, io9, Mashable (Video), NPR (Radio), Harvard Gazette Der Standard, GEO Magazin, Focus, Spiegel Online,

Menze BH and Ur JA. Detection of early settlements in the central Tigris region by classifying multi-spectral satellite imagery. In: P Miglus (ed.), Between the Cultures: The Central Tigris Region in Mesopotamia from the 3rd to the 1st Millennium BC, Heidelberger Studien zum Alten Orient 12. Heidelberger Orientverlag, Heidelberg, Germany. 2011.

Menze BH and Ur JA. Classification of multispectral ASTER imagery in the archaeological survey for settlement sites of the Near East. In: ME Schaepman et al. (eds.), Proc 10th Intern Symp on Physical Measurements and Signature in Remote Sensing (ISPMSRS 07), Davos, Switzerland. Intern Arch of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Vol. 36. 2007 244-249
(publisher) (preprint)

Menze BH, Mühl S, Sherratt AG. Virtual survey on north Mesopotamian tell sites by means of satellite remote sensing. In: B Ooghe, G Verhoeven (eds.), Broadening horizons: Multidisciplinary Approaches to Landscape Study. Cambridge Scholars Publishing, Newcastle upon Tyne, UK. 2007 5-29
(publisher) (preprint)

Menze BH, Kelm BM and Hamprecht FA. From Eigenspots to Fisherspots: Latent spaces in the nonlinear detection of spot patterns in a highly variable background. In: HJ Lenz, R Decker (eds.), Advances in Data Analysis., vol. 33 of Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Heidelberg and Berlin. 2007 255-262
(publisher) (preprint)

Menze BH, Ur JA and Sherratt AG. Detection of ancient settlement mounds: Archaeological survey based on the SRTM terrain model. Photogrammetric Engineering and Remote Sensing 2006. 72: 321-327
(publisher, open access)

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