Jens Petersen

Postdoc

University of Copenhagen

Sigurdsgade 41

2200 København N

Email:	phup@di.ku.dk
Office:	1.10b

Short CV

Jens Petersen received a B.Sc. in 2005 and a M.Sc. in 2010 both in Computer Science at the University of Copenhagen in Denmark. 2010 to 2014 was spent as a Ph.D. student in Medical Image Analysis, also at the University of Copenhagen, with a four month stay as a visiting researcher at the Centre for Medical Image Computing at University College London, England. Since getting his Ph.D. in May of 2014, Jens has been employed as a postdoc in the Image Group.

Research Interests

Medical image analysis, image segmentation, image registration, chronic obstructive pulmonary disease, graph cuts, and optimal surface methods.

Software

• Opfront C++ Library, this open source software provides functionality to segment three-dimensional images with repeated use of optimal surfaces resulting in moving fronts, which adapts to structures within the images.

• Meshing C++ Library, this open source software based on the CGAL library provides functionality to generate and visualize triangular and tetrahedral meshes.

Publications

Journal papers

• Nina Amenta, Manasi Datar, Asger Dirksen, Marleen de Bruijne, Aasa Feragen, Xiaoyin Ge, Jesper H. Pedersen, Marylesa Howard, Megan Owen, Jens Petersen, Jie Shi, and Qiuping Xu: Quantification and visualization of variation in anatomical trees. Research in shape modeling (Association for Women in Mathematics Series, Vol. 1), 57-79, 2015
• Aasa Feragen*, Jens Petersen*, Megan Owen, Pechin Lo, Mathilde M. W. Wille, Laura H. Thomsen, Asger Dirksen, and Marleen de Bruijne: Geodesic Atlas-based Labeling of Anatomical Trees: Application and Evaluation on Airways Extracted from CT. IEEE Trans Med Imag, 34(6):1212-1226, 2015
• Mathilde M. W. Wille, Laura H. Thomsen, Jens Petersen, Marleen de Bruijne, Asger Dirksen, Jesper H. Pedersen, Saher B. Shaker: Visual assessment of early emphysema and interstitial abnormalities on CT is useful in lung cancer risk analysis European Radiology, 2015 (in press)
• Jens Petersen, Mathilde M. W. Wille, Lars L. Rakêt, Aasa Feragen, Jesper H. Pedersen, Mads Nielsen, and Marleen de Bruijne: Effect of Inspiration on Airway Dimensions Measured in Maximal Inspiration CT Images of Subjects without Airflow Limitation. European Radiology, 24(9):2319–2325, 2014
• Mathilde M. W. Wille, Laura H. Thomsen, Asger Dirksen, Jens Petersen, Jesper H. Pedersen, and Saher B. Shaker: Emphysema Progression is Visually Detectable in Low-dose CT in Continuous but Not in Former Smokers. European Radiology, 24(11):2692–2699, 2014
• Jens Petersen, Mads Nielsen, Pechin Lo, Lars H. Nordenmark, Jesper H. Pedersen, Mathild M. W. Wille, Asger Dirksen, and Marleen de Bruijne: Optimal Surface Segmentation using Flow Lines to Quantify Airway Abnormalties in Chronic Obstructive Pulmonary Disease. Med Image Anal, 18(3):531–541, 2014.

Conference papers

• Aasa Feragen, Niklas Kasenburg, Jens Petersen, Marleen de Bruijne, and Karsten Borgwardt: Scalable Kernels for Graphs with Continuous Attributes. Neural Information Processing Systems (NIPS 2013), volume 26, 216–224, 2013.
• Jens Petersen, Marc Modat, Manuel J. Cardoso, Asger Dirksen, Sebastien Ourselin, Marleen and de Bruijne:, Quantitative Airway Analysis in Longitudinal Studies using Groupwise Registration and 4D Optimal Surfaces. Med Image Comput Assist Interv - MICCAI 2013, Lecture Notes in Computer Science, 287–294, 2013.
• Andres Arias, Diego Carvalho, Jens Petersen, Anouk C. van Dijk, Aad van der Lugt, Wiro J. Niessen, Stefan Klein, and Marleen de Bruijne: Carotid Artery Lumen Segmentation on 3D Free-Hand Ultrasound Images using Surface Graph cuts. Med Image Comput Assist Interv - MICCAI 2013, Lecture Notes in Computer Science, 542–549, 2013.
• Aasa Feragen, Megan Owen, Jens Petersen, Mathilde M. W. Wille, Laura H. Thomsen, Asger Dirksen, and Marleen de Bruijne: Tree-Space Statistics and Approximations for Large-Scale Analysis of Anatomical Trees, Information Processing in Medical Imaging, Lecture Notes in Computer Science, 74–85, 2013.
• Aasa Feragen, Jens Petersen, Dominik Grimm, Asger Dirksen, Jesper H. Pedersen, Karsten Borgwardt, and Marleen de Bruijne: Geometric tree kernels: Classification of COPD from airway tree geometry. Information Processing in Medical Imaging, Lecture Notes in Computer Science, 171–183, 2013.
• Aasa Feragen, Jens Petersen, Megan Owen, Pechin Lo, Laura H. Thomsen, Mathilde M. W. Wille, Asger Dirksen, and Marleen de Bruijne: A Hierarchical Scheme for Geodesic Anatomical Labeling of Airway Trees. Med Image Comput Assist Interv - MICCAI 2012, Lecture Notes in Computer Science, 147–155, 2012.
• Andres Arias, Jens Petersen, Arna van Engelen, Hui Tang, Mariana Selwaness, Jacqueline C. M. Witteman, Aad van der Lugt, Wiro J. Niessen, and Marleen de Bruijne: Carotid Artery Wall Segmentation by Coupled Surface Graph Cuts. Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging, 38–47, 2012.
• Jens Petersen, Vladlena Gorbunova, Mads Nielsen, Asger Dirksen, Pechin Lo, and Marleen de Bruijne: Longitudinal Analysis of Airways using Registration. Fourth International Workshop on Pulmonary Image Analysis, 11–22, 2011.
• Lauge Sørensen, Pechin Lo, Jens Petersen, Asger Dirksen, and Marleen de Bruijne: Dissimilarity-based Classification of Anatomical Tree structures. Information Processing in Medical Imaging, Lecture Notes in Computer Science, 475–485, 2011.
• Jens Petersen, Mads Nielsen, Pechin Lo, Zaigham Saghir, Asger Dirksen, and Marleen de Bruijne: Optimal Graph Based Segmentation using Flow Lines with Application to Airway Wall Segmentation. Information Processing in Medical Imaging, Lecture Notes in Computer Science, 49–60, 2011.
• Jens Petersen, Pechin Lo, Mads Nielsen, Goutham Edula, Haseem Ashraf, Asger Dirksen, and Marleen de Bruijne: Quantitative Analysis of Airway Abnormalities in CT. Medical Imaging: Computer-Aided Diagnosis, Proceedings of SPIE 7624, 76241S–76241S–12, 2010.

Abstracts

• Adria Perez-Rovira, Wieying Kuo, Jens Petersen, Harm A. W. M. Tiddens, and Marleen de Bruijne: Automated Quantification of Bronchiectasis, Airway Wall Thickening and Lumen Tapering in Chest CT. ECR - Annual meeting of the European Society of Radiology (Accepted)
• Mathilde M. W. Wille, Jens Petersen, Asger Dirksen, and Marleen de Bruijne: Airway Distensibility in Chronic Obstructive Pulmonary Disease - Evaluation by CT Airway Segmentation and Lung Density Measurement Based on the Danish Lung Cancer Screening Trial. American Thoracic Society International Conference (ATS), 2013
• Jens Petersen, Aasa Feragen, Megan Owen, Mathilde M. W. Wille, Laura H. Thomsen, Asger Dirksen, and Marleen de Bruijne: An Automatic System for Segmentation, Longitudinal Matching, Anatomical Labeling and Measurements of Airways from CT Images. Novel Technology that Shapes Radiology: EIBIR presents IMAGINE, 2013
• Jens Petersen, Aasa Feragen, Laura H. Thomsen, Mathilde M. W. Wille, Asger Dirksen, and Marleen de Bruijne:. Manual Airway Labeling has Limited Reproducibility. ECR - Annual meeting of the European Society of Radiology, 2013
• Jens Petersen, Mathilde M. W. Wille, Laura H. Thomsen, Aasa Feragen, Asger Dirksen, and Marleen de Bruijne: The Effect of Inspiration on Airway Dimensions Measured in CT Images from the Danish Lung Cancer Screening Trial. ECR - Annual Meeting of the European Society of Radiology, 2013
• Mathilde M. W. Wille, Laura H. Thomsen, Jens Petersen, Saher B. Shaker, Asger Dirksen, and Jesper H. Pedersen: Interobserver Variability in Visual Evaluation of Thoracic CT Scans and Comparison with Automatic Computer Measurements of CT Lung Density. European Respiratory Society, Annual Congres, Vienna, 2013

Theses

• Jens Petersen: Analysis of Airways in Computed Tomography. Phd, Department of Computer Science, University of Copenhagen, Denmark, 2014
• Jens Petersen: Three-dimensional Graph Cuts for Human Airway Analysis. Master’s thesis, Department of Computer Science, University of Copenhagen, Denmark, 2010