ARTORG Center for Biomedical Engineering Research

Group Members

Prof. Dr. Mauricio Reyes

Group Head

University of Bern, ARTORG Center for Biomedical Engineering Research, Medical Image Analysis Group

Phone
+41 31 684 14 26
E-Mail
mauricio.reyes@med.unibe.ch
Postal Address
University of Bern
ARTORG Center
Murtenstrasse 50
CH-3008 Bern

Curriculum Vitae

2005 Ph.D. in in Informatics, Institut National de Recherche en Informatique et en Automatique (INRIA), Epidaure Team. Sophia Antipolis, France
2000 Electrical Engineer, Universidad de Santiago de Chile. Santiago, Chile
1999 Bachelor in Engineering Sciences, Universidad de Santiago de Chile. Santiago, Chile

Teaching

2014 - today Lecturer of the MSc program in Biomedical Engineering Medical Image Analysis Laboratory University of Bern, Switzerland.
2007 - today Lecturer of the MSc program in Biomedical Engineering Medical Image Analysis ETHZ, Switzerland.
2007 - today Lecturer of the MSc program in Biomedical Engineering Medical Image Analysis University of Bern, Switzerland.
2004 Lecturer at the Summer School in Medical Imaging, Santiago, Chile Nuclear medicine, image reconstruction and the breathing problem Universidad de Santiago de Chile
1999 - 2000 Laboratory Instructor of Intelligent Control Electrical Engineering department, Universidad de Santiago de Chile
1999 - 2000 Laboratory Instructor of Digital Control Electrical Engineering department, Universidad de Santiago de Chile
1999 Participated in the preparation of the teaching project: “Construction and Application of Educational Video Programs for Electrical Engineering Laboratories” Universidad de Santiago de Chile, Santiago, Chile

Honors & Awards

2020 Award “Best PhD Thesis 2020 Graduate for School Cellular ” and Biomedical Sciences, University of Bern Supervision of PhD student, Fabian Balsiger
2017 Award “Best MSc Thesis Biomedical Engineering Master Program, Univ. Bern” Fast and Accurate Human Brain Morphometry Estimation with Deep Learning Co-supervision of MSc student Michael Rebsamen
2017 Award “Second Prize Survival Prediction Challenge. & BRATS 2017 ” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Alain Jungo
2017 Award “Ypsomed Innovation Award (20000CHF)” Human-Machine Learning for Brain Lesion Image Analysis Bern, Switzerland
2016 Award “Second Prize Longitudinal Brain Tumor Segmentation Challenge. & BRATS 2016 ” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Raphael Meier
2016 Award “First Prize Multiple Sclerosis Segmentation Challenge. & MSSEG 2016 ” Medical Image Computing and Computer Assisted Interventions In collaboration with Richard McKinley
2016 Award “Young Scientist Publication Impact Award” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Stefan Bauer
2016 Award “Second Prize Ischemic Stroke Lesion Segmentation Challenge. & ISLES 2016 ” Medical Image Computing and Computer Assisted Interventions In collaboration with Richard McKinley
2015 Award “Second Prize in Interactive Medical Image Computing” “Fast Correction Method for Abdominal Multi-Organ Segmentation Using 2D/3D Free Form Deformation and Posterior Shape Models”. Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Waldo Valenzuela.
2015 Award “First Prize Ischemic Stroke Lesion Segmentation Challenge. & ISLES 2015 ” Medical Image Computing and Computer Assisted Interventions In collaboration with Richard McKinley
2013 Award “Best paper Siemens award Workshop on Medical Computer Vision” “Integrated spatio-temporal segmentation of longitudinal brain tumor imaging studies”. Supervision of PhD student, Stefan Bauer
2013 Award “2nd Prize Brain Tumor Segmentation Challenge. & BRATS 2013 ” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Raphael Meier
2012 Award “2nd Prize Brain Tumor Segmentation Challenge. & BRATS 2012 ” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Stefan Bauer
2011 Award “Christof Seiler recipient of Miccai Young Scientist Award. & Miccai 2011 ” Medical Image Computing and Computer Assisted Interventions Supervision of PhD student, Christof Seiler
2009 Honor “Swiss National Science Foundation, NCCR Success Stories - 2009” Representing the NCCR Co-Me project and the selected topic 2009 “statistical shape modeling” - SNSF press release highlighting successful NCCR stories
2008 Award “Best Technical Paper Presentation & Poster - CAOS 2008 ” Supervision of PhD students, Nina Kozic and Matthias Peterhans
2007 Award “Swiss National Science Foundation, Picture of the Month - October 2007” SNSF Press release highlighting important research projects
2001 Award “Roberto Ovalle Aguirre” Given by the Chilean Institute of Engineers for the best 2001 2001 electrical engineering thesis of the Universidad de Santiago de Chile. Santiago, Chile.
2001 First prize in “First National Contest of Technologic Innovation - 2001” Title of work : Three-dimensional Reconstruction of a Human Embryo Hand Using Artificial Vision Techniques. Universidad de Santiago de Chile. Santiago, Chile.
1994 Award: Best Student 1994 class Don Orione Industrial School, Santiago, Chile

Supervised PhD Thesis

Nina Kozic (2009) “Statistical shape space analysis based on level sets for optimization of orthopaedic implant design”.

Hyungmin Kim (2011) “Computer-Assistance in Cranio-Maxillofacial Surgery: A Clinically-Driven Approach”.

Thiago Oliveira dos Santos (2011) “A Soft Tissue Image Guidance System for Percutaneous Needle Interventions Based on Multimodal Images”.

Serena Bonaretti (2012) “Statistical Finite Element Modeling: Application to Orthopaedic Implant Design”.

Christof Seiler (2012) “Trees on Geometrical Deformations to Model the Statistical Variability of Organs in Medical Images”.

Huanxiang Lu (2012) “Multi-modal Deformable Registration for Magnetic Resonance Image”.

Habib Bou-Sleiman (2012) “A Computational Anatomy Approach to Orthopaedic Research”.

Stefan Bauer (2013) “Medical Image Analysis and Image-based Modeling for Brain Tumor Studies”.

Elham Taghizadeh (2016) “Statistical Shape Model of the Leg to Improve the Treatment of Patella Pathology in Total Knee Arthroplasty”.

Waldo Valenzuela (2016) “Effective Human Machine Interfaces for Medical Image Analysis”.

Carlos Correa Schokiche (2016) “MicroCT based kidney morphometry: A machine learning approach”.

Vimal Chandran (2017) “Comprehensive and Effective Machine Learning based Computational Modelling of the Human Proximal Femur”.

Raphael Meier (2017) “Towards Automatic Segmentation of Longitudinal Brain Tumor Imaging Data”.

Ping Lu (2017) “Advanced Medical Image Analysis of the Human Facial Nerve based on Machine Learning Technologies”.

Alain Jungo (2020) “Applications and Insights of Uncertainty Estimates in Automated Brain Tumor Segmentation”.

Fabian Balsiger (2020) “Quantitative Magnetic Resonance Imaging to Monitor and Diagnose Neuromuscular Diseases”.

Yannick Suter (2021) “Advanced Machine Learning Technologies for Robust Longitudinal Radiomics and Response Assessment in Glioblastoma Multiforme”.

Publications

Robert Poel, Elias R ̈ufenacht, Ekin Ermis, Michael M ̈uller, Michael K Fix, Daniel M Aebersold, Peter Manser, and Mauricio Reyes. Impact of random outliers in auto-segmented targets on radiotherapy treatment plans for glioblastoma. Radiation Oncology, 17(1):1–18, 2022.
Dwarikanath Mahapatra, Alexander Poellinger, and Mauricio Reyes. Interpretability-guided inductive bias for deep learning based medical image. Medical image analysis, 81:102551, 2022
Dwarikanath Mahapatra, Alexander Poellinger, and Mauricio Reyes. Graph node based interpretability guided sample selection for active learning. IEEE Transactions on Medical Imaging, 2022.
Sook-Lei Liew, Bethany P Lo, Miranda R Donnelly, Artemis Zavaliangos-Petropulu, Jessica N Jeong, Giuseppe Barisano, Alexandre Hutton, Julia P Simon, Julia M Juliano, Anisha Suri, et al. A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms. Scientific data, 9(1):1–12, 2022.
Mahapatra D., Zongyuan G., and Reyes M. Self-supervised generalized zero shot learning for medical image classification using novel interpretable saliency maps. IEEE Transactions on Medical Imaging, pages 1–1, 2022.
Miao Kang, Xiaojun Hu, Weilin Huang, Matthew R. Scott, and Mauricio Reyes. Dual-stream pyramid registration network. Medical Image Analysis, 78:102379, 2022.
Michael Rebsamen, Richard McKinley, Piotr Radojewski, Maximilian Pistor, Christoph Friedli, Robert Hoepner, Anke Salmen, Andrew Chan, Mauricio Reyes, Franca Wagner, et al. Reliable brain morphometry from contrast-enhanced t1w-mri in patients with multiple sclerosis. Human brain mapping, 2022. 73:102161, 2021.
Rebsamen M., Radojewski P., McKinley R., Reyes M., Wiest R., and Rummel C. A quantitative imaging biomarker supporting radiological assessment of hippocampal sclerosis derived from deep learning-based segmentation of t1w-mri. Frontiers in Neurology, 13, 2022 73:102161, 2021.
Poel R., Rufenacht E., Herrmann E., Scheib S., Manser P., Aebersold D., and Reyes M. The predictive value of segmentation metrics on dosimetry in organs at risk of the brain. Medical Image Analysis, 73:102161, 2021.
Mahapatra D., Pollinger A., Shao L., and Reyes M. Interpretability-driven sample selection using self supervised learning for disease classification and segmentation. IEEE Trans Med Imaging, PP, Feb 2021.
Arsany Hakim, Søren Christensen, Stefan Winzeck, Maarten G Lansberg, Mark W Parsons, Christian Lucas, David Robben, Roland Wiest, Mauricio Reyes, and Greg Zaharchuk. Predicting infarct core from computed tomography perfusion in acute ischemia with machine learning: Lessons from the isles challenge. Stroke, pages STROKEAHA–120, 2021.
Pinto A., Pereira S., Meier R., Wiest R., Alves V., Reyes M., and Silva C. Combining unsupervised and supervised learning for predicting the final stroke lesion. Medical Image Analysis, 69:101888, 2021.
Pinto A., Amorim J., Hakim A., Alves V., Reyes M., and Silva C. Prediction of stroke lesion at 90-day follow-up by fusing raw dsc-mri with parametric maps using deep learning. IEEE Access, 9:26260–26270, 2021
Richard McKinley, Rik Wepfer, Fabian Aschwanden, Lorenz Grunder, Raphaela Muri, Christian Rummel, Rajeev Verma, Christian Weisstanner, Mauricio Reyes, Anke Salmen, Andrew Chan, Franca Wagner, and Roland Wiest. Simultaneous lesion and brain segmentation in multiple sclerosis using deep neural networks. Scientific Reports, 11(1):1087, 2021.
Georgios S. Ioannidis, Søren Christensen, Katerina Nikiforaki, Eleftherios Trivizakis, Kostas Perisinakis, Adam Hatzidakis, Apostolos Karantanas, Mauricio Reyes, Maarten Lansberg, and Kostas Marias. Cerebral ct perfusion in acute stroke: The effect of lowering the tube load and sampling rate on the reproducibility of parametric maps. Diagnostics, 11(6), 2021.
Jungo A., Scheidegger O., Reyes M., and Balsiger F. pymia: A python package for data handling and evaluation in deep learning-based medical image analysis. Computer Methods and Programs in Biomedicine, 198:105796, 2021.
Reyes M., Meier R., Pereira S., Silva C., Dahlweid FM., von Teng-Kobligk H., Summers R., and Wiest R. On the interpretability of artificial intelligence in radiology: Challenges and opportunities. Radiology: Artificial Intelligence, 2(3):e190043, 2020.
Bjoern Menze, Fabian Isensee, Roland Wiest, Bene Wiestler, Klaus Maier-Hein, Mauricio Reyes, and Spyridon Bakas. Analyzing magnetic resonance imaging data from glioma patients using deep learning. Computerized Medical Imaging and Graphics, page 101828, 2020.
Balsiger F., Jungo A., Scheidegger O., Carlier P., Reyes M., and Marty B. Spatially regularized parametric map reconstruction for fast magnetic resonance fingerprinting. Medical Image Analysis, 64:101741, August 2020.
Suter Y., Knecht U., Alao M., Valenzuela W., Hewer E., Schucht P., Wiest R., and Reyes M. Radiomics for glioblastoma survival analysis in pre-operative mri: Exploring feature robustness, class boundaries, and machine learning techniques. Cancer Imaging, 20(2):1–13, June 2020.
Michael Rebsamen, Christian Rummel, Mauricio Reyes, Roland Wiest, and Richard McKinley. Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation. Human brain mapping, 41(17):4804–4814, 2020.
Zongxin-Jin B., De Stefano P., Petroulia V., Rummel C., Kiefer C., Reyes M., Schindler K., van Mierlo P., Seeck M., and Wiest R. Diagnosis of epilepsy after first seizure. introducing the swiss first study. Clinical and Translational Neuroscience, 4(2):2514183X20939448, 2020.
Ermi¸s E., Jungo A., Poel R., Blatti-Moreno M., Meier R., Knecht U., Aebersold D., Fix M., Manser P., Reyes M., and Herrmann E. Fully automated brain resection cavity delineation for radiation target volume definition in glioblastoma patients using deep learning. Radiation oncology, 15:1–10, 2020.
Hu X., Luo W., Hu J., Guo S., Huang W., Scott M., Wiest R., Dahlweid M., and Reyes M. Brain segnet: 3d local refinement network for brain lesion segmentation. BMC Medical Imaging, 20(1):17, 2020.
Jungo A., Balsiger F., and Reyes M. Analyzing the quality and challenges of uncertainty estimations for brain tumor segmentation. Frontiers in Neuroscience, 14:282, 2020.
McKinley R., Wepfer R., Grunder L., Aschwanden F., Fischer T., Friedli C., Muri R., Rummel C., Verma R.K., Weisstanner C., Wiestler B., Berger C., Eichinger P., Muhlau M., Reyes M., Salmen A., Chan A., Wiest R., and Wagner F. Automatic detection of lesion load change in multiple sclerosis using convolutional neural networks with segmentation confidence. NeuroImage: Clinical, 25:102104, 2020.
Rebsamen M., Suter Y., Wiest R., Reyes M., and Rummel C. Brain morphometry estimation: From hours to seconds using deep learning. Frontiers in Neurology, 11:244, 2020.
Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Reyes M., Gralla J., Wiest R., and Slotboom J. Analysis of metabolic abnormalities in high-grade glioma using mrsi and convex nmf. NMR in Biomedicine, 32(8):e4109, August 2019.
Bozorgtabar B., Mahapatra D., von Teng-Kobligk H., Pollinger A., Ebner L., Thiran JP., and Reyes M. Informative sample generation using class aware generative adversarial networks for classification of chest xrays. Computer Vision and Image Understanding, 184:57–65, 2019.
Meier R., Lux P., Jung S., Fischer U., Gralla J., Reyes M., Wiest R., McKinley R., and Kaesmacher J. Neural network–derived perfusion maps for the assessment of lesions in patients with acute ischemic stroke. Radiology: Artificial Intelligence, 1(5):e190019, 2019.
Pinto A., Mckinley R., Alves V., Wiest R., Silva C., and Reyes M. Stroke lesion outcome prediction based on mri imaging combined with clinical information. Frontiers in Neurology, 9:1060, 2018.
Balsiger F., Steindel C., Arn M., Wagner B., Grunder L., El-Koussy M., Valenzuela W., Reyes M., and Scheidegger O. Segmentation of peripheral nerves from magnetic resonance neurography: A fully-automatic, deep learning-based approach. Frontiers in Neurology, 9:777, 2018.
Habegger S., Wiest R., Weder B., Mordasini P., Gralla J., Haeni L., Jung S., Reyes M., and McKinley R. Relating acute lesion loads to chronic outcome in ischemic stroke–an exploratory comparison of mismatch patterns and predictive modeling. Frontiers in Neurology, 9:737, 2018.
Winzeck S., Hakim A., McKinley R., Pinto J., Alves V., Silva C., Pisov M., Krivov E., Belyaev M., Monteiro M., Oliveira A., Choi Y., Paik M., Kwon Y., Lee H., Kim B., Won J-H, Islam M., Ren H., Robben D., Suetens P., Gong E., Niu Y., Xu J., Pauly J., Lucas C., Heinrich M., Rivera L., Castillo L., Daza L., Beers A., Arbelaezs P., Maier O., Chang K., Brown J., Kalpathy-Cramer J., Zaharchuk G., Wiest R., and Reyes M. Isles 2016 and 2017-benchmarking ischemic stroke lesion outcome prediction based on multispectral mri. Frontiers in Neurology, 9:679, 2018.
Pereira S., Meier R., McKinley R., Wiest R., Alves V., Silva C., and Reyes M. Enhancing interpretability of automatically extracted machine learning features: application to a rbm-random forest system on brain lesion segmentation. Med Image Anal, 44:228–244, Feb 2018.
Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Herrmann E., Schucht P., Reyes M., Gralla J., Wiest R., and Slotboom J. On the relation between mr spectroscopy features and the distance to mri-visible solid tumor in gbm patients. Magn Reson Med, Jun 2018.
Chandran V., Reyes M., and Zysset P. A novel registration-based methodology for prediction of trabecular bone fabric from clinical qct: A comprehensive analysis. PLOS ONE, 12(11):1–23, 11 2017.
Gerber N., Reyes M., Barazzetti L., Kjer H., Vera S., Stauber M., Mistrik P., Ceresa M., Mangado N., Wimmer W., Stark T., Paulsen R., Weber S., Caversaccio M., and Ballester-Gonzalez M. A multiscale imaging and modelling dataset of the human inner ear. Nature Scientific Data, 4:170132 EP –, 09 2017.
Meier R., Porz N., Knecht U., Loosli T., Schucht P., Beck J., Slotboom J., Wiest R., and Reyes M. Automatic estimation of extent of resection and residual tumor volume of patients with glioblastoma. Journal of Neurosurgery, pages 1–9, 2017.
Kellner-Weldon F., Stippich C., Wiest R., Lehmann V., Meier R., Beck J., Schucht P., Raabe A., Reyes M., and Bink A. Comparison of perioperative automated versus manual two-dimensional tumor analysis in glioblastoma patients. Eur J Radiol, 95:75–81, Oct 2017.
Lu P., Barazzetti L., Chandran V., Gavaghan K., Weber S., Gerber N., and Reyes M. Highly accurate facial nerve segmentation refinement from cbct/ct imaging using a super resolution classification approach. IEEE Transactions on Biomedical Engineering, PPs(99):1–1, 2017.
Porz N., Habegger S., Meier R., Verma R.K., Jilch A., Fichtner J., Knecht U., Radina C., Schucht P., Ju¨rgen B., Raabe A., Slotboom J., Reyes M., and Wiest R. Fully automated enhanced tumor compartmentalization: Man vs. machine reloaded. PLoS ONE, 11(11):1–16, 11 2016.
Maier O., Menze B., Wiest R., Handels H., and Reyes M. ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical Image Analysis, 35:250–269, aug 2016.
McKinley R., Haeni L., Gralla J., El-Koussy M., Bauer S., Arnold M., Fischer U., Jung S., Mattmann K., Reyes M., and Wiest R. Fully automated stroke tissue estimation using random forest classifiers (faster). Journal of Cerebral Blood Flow and Metabolism, 37(8):2728–2741, August 2017.
Meier R., Knecht U., Loosli T., Bauer S., Slotboom J., Wiest R., and Reyes M. Clinical evaluation of a fully-automatic segmentation method for longitudinal brain tumor volumetry. Nature Scientific Reports, 6(23376), 2016.
Valenzuela W., Ferguson S., Ignasiak D., Diserens G., Haeni L., Wiest R., Vermathen P., Boesch C., and Reyes M. Fisico: Fast image segmentation correction. PLoS ONE, 11(5):1–17, 05 2016.
Seif M., Mani L., Lu H., Boesch C., Reyes M., Vogt B., and Vermathen P. Diffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering? J Magn Reson Imaging, 44(2):327–334, Feb 2016.
Taghizadeh E., Reyes M., Zysset P., Latypova A., Terrier A., and Buchler P. Biomechanical role of bone anisotropy estimated on clinical ct scans by image registration. Ann Biomed Eng, Jan 2016.
Rios-Velazquez E., Meier R., Dunn W., Alexander B., Wiest R., Bauer S., Gutmann D., Reyes M., and Aerts H. Fully automatic gbm segmentation in the tcga-gbm dataset: Prognosis and correlation with vasari features. Nature Scientific Reports, 5(16822), November 2015.
Menze B., Reyes M., and Van Leemput K. The multimodal brain tumor image segmentation benchmark (brats). IEEE Trans Med Imaging, 34(10), Oct 2015.
Cerrolaza J.J., Reyes M., Summers R.M., Gonz´alez-Ballester M.A., and Linguraru M.G. Automatic multi-resolution shape modeling of multi-organ structures. Medical Image Analysis, 25(1):11–21, April 2015.
V. Chappuis, O. Engel, K. Shahim, M. Reyes, C. Katsaros, and D. Buser. Soft tissue alterations in esthetic postextraction sites: A 3-dimensional analysis. Journal of Dental Research, 94(9 suppl):187S–193S, 2015.
Seif M., Lu H., Boesch C., Reyes M., and Vermathen P. Image registration for triggered and non-triggered dti of the human kidney: Reduced variability of diffusion parameter estimation. J Magn Reson Imaging, 41(5):1228–1235, Jun 2014.
Porz N., Bauer S., Pica A., Schucht P., Beck J., Verma R.K., Slotboom J., Reyes M., and Wiest R. Multi-modal glioblastoma segmentation: Man versus machine. PLoS ONE, 9(5):e96873, May 2014.
Bonaretti S., Seiler C., Boichon C., Reyes M., and Buechler P. Image-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations. Medical Engineering & Physics, 36(12):1626 – 1635, 2014.
Bou-Sleiman H., Paul L., Nolte L.P., and Reyes M. Comparative evaluation of pelvic allograft selection methods. Annals of Biomedical Engineering, 41(5):931–938, May 2013.
Oliveira-Santos T., Baumberger C., Constantinescu M., Olariu R., Nolte L.P., Alaraibi S., and Reyes M. 3d face reconstruction from 2d pictures: First results of a web-based computer aided system for aesthetic procedures. Annals of Biomedical Engineering, 41(5):952–966, May 2013.
Lu H., Beisteiner R., Nolte L.P., and Reyes M. Hierarchical segmentation-assisted multimodal registration for mr brain images. Computerized Medical Imaging and Graphics, 37(3):234–244, April 2013.
Bauer S., Lu H., May C., Nolte L.P., Buechler P., and Reyes M. Integrated segmentation of brain tumor images for radiotherapy and neurosurgery. International Journal of Imaging Systems and Technology, 23(1):59–63, March 2013.
Bou Sleiman H., Iizuka T., Nolte L.P., and Reyes M. Population-based design of mandibular fixation plates with bone quality and morphology considerations. Annals of Biomedical Engineering, 41(2):377–384, February 2013.
Bauer S., Wiest R., Nolte L.P., and Reyes M. A survey of mri-based medical image analysis for brain tumor studies. Physics in Medicine and Biology, 58(13):R97, 2013.
Chappuis V., Engel O., Reyes. M., Shahim K., Nolte L.P., and Buser D. Ridge alterations post-extraction in the esthetic zone a 3d analysis with cbct. Journal of Dental Research, 92(12 suppl):195S–201S, 2013.
Kim B.R., Oh K.M., Cevidanes L.H.S., Park J.E., Sim H.S., Seo S.K., Reyes M., Kim Y.J., and Park Y.H. Analysis of 3d soft tissue changes after 1-and 2-jaw orthognathic surgery in mandibular prognathism patients. Journal of Oral and Maxillofacial Surgery, 71(1):151–161, January 2013.
Seiler C., Pennec X., Nolte L.P., and Reyes M. Capturing the multiscale anatomical shape variability with polyaffine transformation trees. Medical Image Analysis, 16(7):1371–1384, October 2012.
Bauer S., Ritacco L.E., Boesch C., Nolte L.P., and Reyes M. Automatic scan planning for magnetic resonance imaging of the knee joint. Annals of Biomedical Engineering, 40(9):2033–2042, September 2012.
Blanc R., Seiler C., Sz´ekely G., Nolte L.P., and Reyes M. Statistical model based shape prediction from a combination of direct observations and various surrogates. application to orthopaedic research. Medical Image Analysis, 16(6):1156–1166, August 2012.
Seiler C., Gazdhar A., Reyes M., Benneker L.M., Geiser T., Siebenrock K.A., and Gantenbein-Ritter B. Time-lapse microscopy and classification of 2d human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation. Journal of Tissue Engineering and Regenerative Medicine, page In Press, July 2012.
Ritacco L.E., Seiler C., Farfalli G.L., Nolte L., Reyes M., Muscolo D.L., and Tinao L.A. Validity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system. Cell Tissue Bank, 1:1–8, Apr 2012.
de Heras Ciechomski P., Constantinescu M., Garcia J., Olariu R., Dindoyal I., Le Huu S., and Reyes M. Development and implementation of a web-enabled 3d consultation tool for breast augmentation surgery based on 3d-image reconstruction of 2d pictures. Journal of Medical Internet Research, 14(1):e21, 2012.
Lu H., Nolte L.P., and Reyes M. Interest points localization for brain image using landmark-annotated atlas. International Journal of Imaging Systems and Technology, 22(2):145–152, 2012.
Schulz A.P, Reimers N. Nils, Wipf F., Vallotton M., Bonaretti S., Kozic N., Reyes M., and Kienast B.J. Evidence based development of a novel lateral fibula plate (variax fibula) using a real ct bone data based optimization process during device development. Open Orthop J, 6:1–7, January 2012.
Kim Y.J., Oh K.M., Hong J.S., Lee J.H., Kim H.M., Reyes M., Cevidanes L.H.S., and Park Y.H. Do patients treated with bimaxillary surgery have more stable condylar positions than those who have undergone single-jaw surgery? Journal of Oral and Maxillofacial Surgery, 70(9):2143–52, September 2011.
Bauer S., May C., Dionysiou D., Stamatakos G., Buechler P., and Reyes M. Multi-scale modeling for image analysis of brain tumor studies. IEEE Trans Biomed Eng, 59(1):25–29, Aug 2011.
Ju¨rgens P., Klug C., Krol Z., Beinemann J., Kim H., Reyes M., Guevara-Rojas G., Zeilhofer H. F, Ewers R., and Schicho K. Navigation-guided harvesting of autologous iliac crest graft for mandibular reconstruction. J Oral Maxillofac Surg, 69(11):2915–2923, May 2011.
Bou Sleiman H., Ritacco L.E., Aponte-Tinao L., Muscolo D.L., Nolte L.P., and Reyes M. Allograft selection for transepiphyseal tumor resection around the knee using three-dimensional surface registration. Annals of Biomedical Engineering, 39(6):1720–7, March 2011.
Marias K., Dionysiou D., Sakkalis V., Graf N., Bohle RM, Coveney PV, Wan S., Folarin A., Bu¨chler P., Reyes M., et al. Clinically driven design of multi-scale cancer models: the contracancrum project paradigm. Interface Focus, 1(3):450–461, 2011.
Kim H., Ju¨rgens P., Weber S., Nolte L.P., and Reyes M. A new soft-tissue simulation strategy for cranio-maxillofacial surgery using facial muscle template model. Progress in Biophysics and Molecular Biology. Special Issue on Soft Tissue Modelling, 103(2-3):284–291, December 2010.
Tucker S., Cevidanes L., Styner M., Kim H., Reyes M., Proffit W., and Turvey T. Comparison of actual surgical outcomes and 3-dimensional surgical simulations. J Oral Maxillofac Surg, 68(10):2412–2421, Oct 2010.
Kozic N., Weber S., Bu¨chler P., Lutz C., Reimers N., Gonz´alez Ballester MA., and Reyes M. Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets. Medical Image Analysis, 14(3):265–275, June 2010.
Cevidanes L., Tucker S., Styner M., Kim H., Chapuis J., Reyes M., Proffit W., Turvey T., and Jaskolka M. Three-dimensional surgical simulation. American Journal of Orthodontics and Dentofacial Orthopedics, 138(3):361 – 371, 2010.
Kozic N., Weber S., Gonz´alez-Ballester M.A., Abdo G., Rufenacht D.A., Ferguson S., and Reyes M. Automated cement segmentation in vertebroplasty. Comput Aided Surg, 15(1-3):49–55, 2010.
Reyes M., Malandain G., Koulibaly P.M., Gonz´alez-Ballester M.A., and Darcourt J. Model-based respiratory motion compensation for emission tomography image reconstruction. Physics in Medicine and Biology, 52(12):3579–3600, June 2007.
Linguraru M.G., Vercauteren T., Reyes M., Gonz´alez-Ballester M.A., and Ayache N. Segmentation propagation from deformable atlases for brain mapping and analysis. Brain Research Journal, 1(4):269–287, 2007.
Reyes M., Gonz´alez-Ballester M.A., and Linguraru M.G. Statistical bone shape analysis for image free surgery. Acta Universitatis Cibiniensis, Technical Series, Vol, LV:121–129, 2007.
Malandain G. and Reyes M. La tomographie en mouvement. Pour la science, 338:132–137, December 2005.
Reyes M. and Pereda J. Reconstrucci´on virtual de la mano de un embri´on humano, evaluaci´on experimental. Teor´ıa y Metodolog´ıas. Cl´ınica y Ciencia magazine, 1(2), 2001.