Prof. Dr. Benjamin Berkels

Prof. Dr. Benjamin Berkels

Faculty

Mathematical Image and Signal Processing

Mathematics, Computer Science and Natural Sciences

Member

Junior Research Group Leader, Steering Committee Member

Research

Image Processing, Computer Vision, Variational Methods

Contact

Aachen Institute for Advanced Study in Computational Engineering Science (AICES)
RWTH Aachen University
Schinkelstr. 2
52062 Aachen
Germany

Room: 124
Phone: +49-241-8099123
Fax: +49-241-80628498
email: berkels@aices.rwth-aachen.de

Job openings

I'm currently looking for a PhD student for project A08 Sparse exit wave reconstruction via deep unfolding in the CRC 1481. Details can be found here.

Education

Dr. rer. nat in Mathematics, University of Bonn, Germany, 2010
Dipl.-Math., University of Duisburg-Essen, Germany, 2005

Professional experience

Research Interests

Image Processing, Computer Vision
Variational Methods, Joint Methods, Registration, Segmentation, Medical Image Processing

Publications

[1] Karina Ruzaeva, Katharina Nöh, and Benjamin Berkels. Polar space based shape averaging for star-shaped biological objects. In Eurographics Workshop on Visual Computing for Biology and Medicine. The Eurographics Association, 2021. [ DOI ]
[2] Thomas Pinetz, Erich Kobler, Christian Doberstein, Benjamin Berkels, and Alexander Effland. Total deep variation for noisy exit wave reconstruction in transmission electron microscopy. In Eighth International Conference on Scale Space and Variational Methods in Computer Vision, volume 12679 of Lecture Notes in Computer Science, pages 491--502. Springer, 2021. [ DOI ]
[3] Marcin Copik, Tobias Grosser, Torsten Hoefler, Paolo Bientinesi, and Benjamin Berkels. Work-stealing prefix scan: Addressing load imbalance in large-scale image registration. IEEE Transactions on Parallel and Distributed Systems, 2021. [ DOI | arXiv ]
[4] Johanna C. Clauser, Judith Maas, Jutta Arens, Thomas Schmitz-Rode, Ulrich Steinseifer, and Benjamin Berkels. Hemocompatibility evaluation of biomaterials -- the crucial impact of analyzed area. ACS Biomaterials Science & Engineering, 7(2):553--561, January 2021. [ DOI ]
[5] Johanna C. Clauser, Judith Maas, Jutta Arens, Thomas Schmitz-Rode, Ulrich Steinseifer, and Benjamin Berkels. Automation of hemocompatibility analysis using image segmentation and supervised classification. Engineering Applications of Artificial Intelligence, 97:104009, January 2021. [ DOI | arXiv ]
[6] Chenyu Zhang, Jie Feng, Andrew B. Yankovich, Alexander Kvit, Benjamin Berkels, and Paul M. Voyles. Optimizing nonrigid registration for scanning transmission electron microscopy image series. Microscopy and Microanalysis, 27(1):90--98, November 2020. [ DOI ]
[7] Florian Wellmann and Benjamin Berkels. Detecting subsurface interfaces with a physics-based level-set segmentation and additional geological constraints. In EGU General Assembly 2020, May 2020. [ DOI ]
[8] Niklas Mevenkamp, Katherine MacArthur, Vasiliki Tileli, Philipp Ebert, Leslie J. Allen, Benjamin Berkels, and Martial Duchamp. Multi-modal and multi-scale non-local means method to analyze spectroscopic datasets. Ultramicroscopy, 209, February 2020. [ DOI ]
[9] Benjamin Berkels and Christian H. Liebscher. Joint non-rigid image registration and reconstruction for quantitative atomic resolution scanning transmission electron microscopy. Ultramicroscopy, 198:49--57, March 2019. [ DOI | arXiv ]
[10] Sebastian J. Schröders, Stefanie Sandlöbes, Benjamin Berkels, and Sandra Korte-Kerzel. On the structure of defects in the Fe7Mo6 μ-phase. Acta Materialia, 167:257--266, 2019. [ DOI | arXiv ]
[11] Sönke Reiche, Benjamin Berkels, and Benedikt Weiß. Automated static and moveout corrections of high-resolution seismic data from the Baltic Sea. Near Surface Geophysics, 2019. in press. [ DOI ]
[12] Christian Doberstein and Benjamin Berkels. A least-squares functional for joint exit wave reconstruction and image registration. Inverse Problems, 35(5), 2019. [ DOI | arXiv ]
[13] Sönke Reiche and Benjamin Berkels. Automated stacking of seismic reflection data based on non-rigid image matching. Geophysics, 83(3):V171--V183, May 2018. [ DOI ]
[14] Zhicheng Wu, Stefanie Sandlöbes, Jing Rao, James S.K.-L. Gibson, Benjamin Berkels, and Sandra Korte-Kerzel. Local mechanical properties and plasticity mechanisms in a Zn-Al eutectic alloy. Materials and Design, 157:337--350, 2018. [ DOI ]
[15] Zhicheng Wu, Stefanie Sandlöbes, Jing Rao, James S.K.-L. Gibson, Benjamin Berkels, and Sandra Korte-Kerzel. Data on measurement of the strain partitioning in a multiphase Zn-Al eutectic alloy. Data in Brief, 20:1639--1644, 2018. [ DOI ]
[16] Rosalia Tatano, Benjamin Berkels, Eva E. Ehrlich, Thomas M. Deserno, and Ulrike B. Fritz. Spatial agreement of demineralisations in quantitative light-induced fluorescence images and digital photographs. Dentomaxillofacial Radiology, 47(8), 2018. [ DOI ]
[17] Kai Schüller, Benjamin Berkels, and Julia Kowalski. Integrated modeling and validation for phase change with natural convection. In Recent Advances in Computational Engineering, Proceedings of the 4th International Conference on Computational Engineering (ICCE 2017), volume 124 of Lecture Notes in Computational Science and Engineering, pages 127--144. Springer, 2018. [ DOI | arXiv ]
[18] Lan Nguyen, Teruo Hashimoto, Dmitri N. Zakharov, Eric A. Stach, Aidan P. Rooney, Benjamin Berkels, George E. Thompson, Sarah J. Haigh, and Tim L. Burnett. Atomic-scale insights into the oxidation of aluminum. ACS Applied Materials & Interfaces, 10(3):2230--2235, 2018. [ DOI ]
[19] Christian H. Liebscher, Mengji Yao, Poulumi Dey, Marta Lipinska-Chwalek, Benjamin Berkels, Baptiste Gault, Tilmann Hickel, Michael Herbig, Joachim Mayer, Jörg Neugebauer, Dierk Raabe, Gerhard Dehm, and Christina Scheu. Tetragonal fcc-Fe induced by κ-carbide precipitates: Atomic scale insights from correlative electron microscopy, atom probe tomography and density functional theory. Physical Review Materials, 2:023804--1--023804--6, 2018. [ DOI ]
[20] Markus Frings, Benjamin Berkels, Marek Behr, and Stefanie Elgeti. Comparison of optimization algorithms for the slow shot phase in HPDC. In Proceedings of the 21st International ESAFORM Conference on Material Forming (ESAFORM 2018), volume 1960 of AIP Conference Proceedings, 2018. [ DOI ]
[21] Dzmitry S. Firaha, Malte Döntgen, Benjamin Berkels, and Kai Leonhard. Pressure-dependent rate constant predictions utilizing the inverse Laplace transform: A victim of deficient input data. ACS Omega, 3(7):8212--8219, 2018. [ DOI ]
[22] Rosalia Tatano, Benjamin Berkels, and Thomas M. Deserno. Mesh-to-raster based non-rigid registration of multi-modal images. Journal of Medical Imaging, 4(4):044002--1--044002--14, October 2017. [ DOI | arXiv ]
[23] Rosalia Tatano, Eva E. Ehrlich, Benjamin Berkels, Ekaterina Sirazitdinova, Thomas M. Deserno, and Ulrike B. Fritz. Reproducibility of manually marked demineralisations in quantitative light-induced fluorescence (QLF) images and digital photographs. Journal of Orofacial Orthopedics, 78(2):137--143, March 2017. [ DOI ]
[24] Chenyu Zhang, Benjamin Berkels, Benedikt Wirth, and Paul M. Voyles. Joint denoising and distortion correction for atomic column detection in scanning transmission electron microscopy images. In Microscopy and Microanalysis, volume 23 (Supplement S1), pages 164--165, 2017. [ DOI ]
[25] Yi Wang, Lewys Jones, Benjamin Berkels, Wilfried Sigle, and Peter A. van Aken. Measuring the cation and oxygen atomic column displacement at picometer precision. In Microscopy and Microanalysis, volume 23 (Supplement S1), pages 1612--1613, 2017. [ DOI ]
[26] Niklas Mevenkamp, Benjamin Berkels, and Martial Duchamp. Denoising electron-energy loss data using non-local means filters. In Microscopy and Microanalysis, volume 23 (Supplement S1), pages 106--107, 2017. [ DOI ]
[27] Benjamin Berkels and Benedikt Wirth. Joint denoising and distortion correction of atomic scale scanning transmission electron microscopy images. Inverse Problems, 33(9):095002, 2017. [ DOI | arXiv ]
[28] Benjamin Berkels, Alexander Effland, and Martin Rumpf. A posteriori error control for the binary Mumford-Shah model. Math. Comp., 86(306):1769--1791, 2017. [ DOI | arXiv | .pdf ]
[29] Benjamin Berkels, Michael Buchner, Alexander Effland, Martin Rumpf, and Steffen Schmitz-Valckenberg. GPU based image geodesics for optical coherence tomography. In Bildverarbeitung für die Medizin, Informatik aktuell, pages 68--73. Springer, 2017. [ DOI | .pdf ]
[30] Niklas Mevenkamp and Benjamin Berkels. Variational multi-phase segmentation using high-dimensional local features. In IEEE Winter Conference on Applications of Computer Vision (WACV 2016). IEEE, 2016. [ DOI | arXiv ]
[31] Niklas Mevenkamp and Benjamin Berkels. Non-local averaging in em: decreasing the required electron dose in crystal image reconstruction without losing spatial resolution. In European Microscopy Congress 2016: Proceedings, 2016. [ DOI ]
[32] András P. Keszei, Benjamin Berkels, and Thomas M. Deserno. Survey of non-rigid registration tools in medicine. Journal of Digital Imaging, pages 1--15, 2016. [ DOI | http ]
[33] Chen Huang, Benjamin Berkels, and Angus Kirkland. Non-rigid image registration of low-dose image series of zeolite materials. In European Microscopy Congress 2016: Proceedings, 2016. [ DOI ]
[34] Benjamin Berkels and Niklas Mevenkamp. Denoising of atomic-scale images based on automatic grain segmentation, unsupervised primitive unit cell extraction and periodic block-matching. In Microscopy and Microanalysis, volume 22 (Supplement S3), pages 1404--1405, 2016. [ DOI ]
[35] Benjamin Berkels, Thomas M. Deserno, Eva E. Ehrlich, Ulrike B. Fritz, Ekaterina Sirazitdinova, and Rosalia Tatano. Non-rigid contour-to-pixel registration of photographic and quantitative light-induced fluorescence imaging of decalcified teeth. In Proceedings of SPIE - Medical Imaging, volume 9784, pages 97840Z--1--97840Z--7, 2016. [ DOI ]
[36] Benjamin Berkels, Thomas M. Deserno, Eva E. Ehrlich, Ulrike B. Fritz, Ekaterina Sirazitdinova, and Rosalia Tatano. Curve-to-image based non-rigid registration of digital photos and quantitative light-induced fluorescence images in dentistry. In Bildverarbeitung für die Medizin 2016, Informatik aktuell, pages 80--85. Springer, 2016. [ DOI ]
[37] Niklas Mevenkamp and Benjamin Berkels. Unsupervised and accurate extraction of primitive unit cells from crystal images. In Proceedings of the 37th German Conference on Pattern Recognition (GCPR), volume 9358 of Lecture Notes in Computer Science, pages 105--116. Springer, November 2015. [ DOI ]
[38] Andrew B. Yankovich, Benjamin Berkels, Wolfgang Dahmen, Peter Binev, and Paul M. Voyles. High-precision scanning transmission electron microscopy at coarse pixel sampling for reduced electron dose. Advanced Structural and Chemical Imaging, 1, 2015. [ DOI ]
[39] Niklas Mevenkamp, Peter Binev, Wolfgang Dahmen, Paul M. Voyles, Andrew B. Yankovich, and Benjamin Berkels. Poisson noise removal from high-resolution STEM images based on periodic block-matching. Advanced Structural and Chemical Imaging, 1, 2015. [ DOI ]
[40] Rolf E. Isele-Holder, Benjamin Berkels, and Ahmed E. Ismail. Smoothing of contact lines in spreading droplets by trisiloxane surfactants and its relevance for superspreading. Soft Matter, 2015. [ DOI ]
[41] Stefan Heldmann, Alexander Derksen, Thomas Polzin, and Benjamin Berkels. An image registration framework for sliding motion with piecewise smooth deformations. In Fifth International Conference on Scale Space and Variational Methods in Computer Vision, Lecture Notes in Computer Science, pages 335--347, 2015. [ DOI ]
[42] Alexander Derksen, Stefan Heldmann, Thomas Polzin, and Benjamin Berkels. Image registration with sliding motion constraints for 4D CT motion correction. In Bildverarbeitung für die Medizin 2015, Informatik aktuell, pages 335--340. Springer, 2015. [ DOI ]
[43] Kanglin Chen, Alexander Derksen, Stefan Heldmann, Marc Hallmann, and Benjamin Berkels. Deformable image registration with automatic non-correspondence detection. In Fifth International Conference on Scale Space and Variational Methods in Computer Vision, Lecture Notes in Computer Science, pages 360--371, 2015. [ DOI ]
[44] Benjamin Berkels, Alexander Effland, and Martin Rumpf. Time discrete geodesic paths in the space of images. SIAM J. Imaging Sci., 8(3):1457--1488, 2015. [ DOI | arXiv | .pdf ]
[45] Andrew B. Yankovich, Benjamin Berkels, Wolfgang Dahmen, Peter Binev, Sergio I. Sanchez, Steven A. Bradley, Ao Li, Izabela Szlufarska, and Paul M. Voyles. Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts. Nature Communications, 5, June 2014. [ DOI ]
[46] Benjamin Berkels, Ivan Cabrilo, Sven Haller, Martin Rumpf, and Karl Schaller. Co-registration of intra-operative brain surface photographs and pre-operative MR images. International Journal of Computer Assisted Radiology and Surgery, 9(3):387--400, May 2014. [ DOI | .pdf ]
[47] Benjamin Berkels, Peter Binev, Douglas A. Blom, Wolfgang Dahmen, Robert C. Sharpley, and Thomas Vogt. Optimized imaging using non-rigid registration. Ultramicroscopy, 138:46--56, March 2014. [ DOI | arXiv | .pdf ]
[48] Anna K. Trull, Benjamin Berkels, and Jan Modersitzki. Glomerular filtration rate estimation from dynamic contrast-enhanced MRI using a separable compartment model and parameter elimination. In Bildverarbeitung für die Medizin 2014, Informatik aktuell, pages 30--35. Springer, 2014. [ DOI ]
[49] Niklas Mevenkamp, Andrew B. Yankovich, Paul M. Voyles, and Benjamin Berkels. Non-local means for scanning transmission electron microscopy images and poisson noise based on adaptive periodic similarity search and patch regularization. In Jan Bender, Arjan Kuijper, Tatiana von Landesberger, Holger Theisel, and Philipp Urban, editors, Vision, Modeling and Visualization, pages 63--70. Eurographics Association, 2014. [ DOI ]
[50] Constantin Heck, Lars Ruthotto, Jan Modersitzki, and Benjamin Berkels. Model-based parameterestimation in DCE-MRI without an arterial input function. In Bildverarbeitung für die Medizin 2014, Informatik aktuell, pages 246--251. Springer, 2014. [ DOI ]
[51] Benjamin Berkels, Sebastian Bauer, Svenja Ettl, Oliver Arold, Joachim Hornegger, and Martin Rumpf. Joint surface reconstruction and 4D deformation estimation from sparse data and prior knowledge for marker-less respiratory motion tracking. Medical Physics, 40(9):091703, September 2013. [ DOI ]
[52] Andrew B. Yankovich, Benjamin Berkels, Wolfgang Dahmen, Robert C. Sharpley, Peter Binev, and Paul M. Voyles. Measuring surface atom bond length contraction in Au and Pt nanoparticles using high-precision STEM imaging. In Microscopy and Microanalysis, volume 19 (Supplement 2), pages 1688--1689. Cambridge University Press, August 2013. [ DOI ]
[53] José Iglesias, Benjamin Berkels, Martin Rumpf, and Otmar Scherzer. A thin shell approach to the registration of implicit surfaces. In Michael Bronstein, Jean Favre, and Kai Hormann, editors, Vision, Modeling and Visualization, pages 89--96. Eurographics Association, 2013. [ DOI | .pdf ]
[54] Benjamin Berkels, P. Thomas Fletcher, Behrend Heeren, Martin Rumpf, and Benedikt Wirth. Discrete geodesic regression in shape space. In Proc. of International Conference on Energy Minimization Methods in Computer Vision and Pattern Recognition, volume 8081 of Lecture Notes in Computer Science, pages 108--122. Springer, 2013. [ DOI | .pdf ]
[55] Benjamin Berkels, Ivan Cabrilo, Sven Haller, Martin Rumpf, and Karl Schaller. Co-registration of intra-operative photographs and pre-operative MR images. In Bildverarbeitung für die Medizin 2013, Informatik aktuell, pages 122--127. Springer, 2013. [ DOI | .pdf ]
[56] Benjamin Berkels, Andrew B. Yankovich, Fengyuan Shi, Paul M. Voyles, Wolfgang Dahmen, Robert C. Sharpley, and Peter Binev. High precision STEM imaging by non-rigid alignment and averaging of a series of short exposures. In Microscopy and Microanalysis, volume 18 (Supplement 2), pages 300--301, 2012. [ DOI | .pdf ]
[57] Sebastian Bauer, Benjamin Berkels, Svenja Ettl, Oliver Arold, Joachim Hornegger, and Martin Rumpf. Marker-less reconstruction of dense 4-d surface motion fields using active laser triangulation from sparse measurements for respiratory motion management. In Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 7510 of Lecture Notes in Computer Science, pages 414--421. Springer, 2012. [ DOI | .pdf ]
[58] Benjamin Berkels, Marc Kotowski, Martin Rumpf, and Carlo Schaller. Sulci detection in photos of the human cortex based on learned discriminative dictionaries. In Third International Conference on Scale Space Methods and Variational Methods in Computer Vision, Lecture Notes in Computer Science, pages 326--337. Springer, 2011. [ DOI | .pdf ]
[59] Sebastian Bauer, Benjamin Berkels, Joachim Hornegger, and Martin Rumpf. Joint ToF image denoising and registration with a CT surface in radiation therapy. In Third International Conference on Scale Space Methods and Variational Methods in Computer Vision, Lecture Notes in Computer Science, pages 98--109. Springer, 2011. [ DOI | .pdf ]
[60] Claudia Nieuwenhuis, Benjamin Berkels, Martin Rumpf, and Daniel Cremers. Interactive motion segmentation. In 32nd DAGM Symposium on Pattern Recognition, volume 6376 of Lecture Notes in Computer Science, pages 483--492. Springer, 2010. [ DOI | .pdf ]
[61] Markus Boerdgen, Benjamin Berkels, Martin Rumpf, and Daniel Cremers. Convex relaxation for grain segmentation at atomic scale. In Dieter Fellner, editor, Vision, Modeling and Visualization, pages 179--186. Eurographics Association, 2010. [ DOI | .pdf ]
[62] Benjamin Berkels, Gina Linkmann, and Martin Rumpf. An SL(2) invariant shape median. Journal of Mathematical Imaging and Vision, 37(2):85--97, 2010. [ DOI | .pdf ]
[63] Benjamin Berkels. Joint methods in imaging based on diffuse image representations. Dissertation, University of Bonn, 2010. [ http ]
[64] Benjamin Berkels, Claudia Kondermann, Christoph Garbe, and Martin Rumpf. Reconstructing optical flow fields by motion inpainting. In 7th International Conference on Energy Minimization Methods in Computer Vision and Pattern Recognition, volume 5681 of Lecture Notes in Computer Science, pages 388--400. Springer, 2009. [ DOI | .pdf ]
[65] Benjamin Berkels. An unconstrained multiphase thresholding approach for image segmentation. In Proceedings of the Second International Conference on Scale Space Methods and Variational Methods in Computer Vision (SSVM 2009), volume 5567 of Lecture Notes in Computer Science, pages 26--37. Springer, 2009. [ DOI | .pdf ]
[66] Benjamin Berkels, Andreas Rätz, Martin Rumpf, and Axel Voigt. Extracting grain boundaries and macroscopic deformations from images on atomic scale. Journal of Scientific Computing, 35(1):1--23, April 2008. [ DOI | .pdf ]
[67] Benjamin Berkels, Gina Linkmann, and Martin Rumpf. A shape median based on symmetric area differences. In Oliver Deussen, Daniel Keim, and Dietmar Saupe, editors, Vision, Modeling and Visualization, pages 399--407. AKA Publishing, 2008. [ .pdf ]
[68] Jens F. Acker, Benjamin Berkels, Kristian Bredies, Mamadou S. Diallo, Marc Droske, Christoph S. Garbe, Matthias Holschneider, Jaroslav Hron, Claudia Kondermann, Michail Kulesh, Peter Mass, Nadine Olischläger, Heinz-Otto Peitgen, Tobias Preusser, Martin Rumpf, Karl Schaller, Frank Scherbaum, and Stefan Turek. Mathematical Methods in Time Series Analysis and Digital Image Processing, chapter Inverse Problems and Parameter Identification in Image Processing, pages 111--151. Understanding Complex Systems. Springer, 2008. [ DOI | .pdf ]
[69] Jingfeng Han, Benjamin Berkels, Marc Droske, Joachim Hornegger, Martin Rumpf, Carlo Schaller, Jasmin Scorzin, and Horst Urbach. Mumford-Shah model for one-to-one edge matching. IEEE Transactions on Image Processing, 16(11):2720--2732, November 2007. [ DOI | .pdf ]
[70] Benjamin Berkels, Andreas Rätz, Martin Rumpf, and Axel Voigt. Identification of grain boundary contours at atomic scale. In First International Conference on Scale Space Methods and Variational Methods in Computer Vision, volume 4485 of Lecture Notes in Computer Science, pages 765--776. Springer, 2007. [ DOI | .pdf ]
[71] Leah Bar, Benjamin Berkels, Martin Rumpf, and Guillermo Sapiro. A variational framework for simultaneous motion estimation and restoration of motion-blurred video. In 11th IEEE International Conference on Computer Vision. IEEE, 2007. [ DOI | .pdf ]
[72] Jingfeng Han, Benjamin Berkels, Martin Rumpf, Joachim Hornegger, Marc Droske, Michael Fried, Jasmin Scorzin, and Carlo Schaller. A variational framework for joint image registration, denoising and edge detection. In Bildverarbeitung für die Medizin, pages 246--250. Springer, 2006. [ DOI | .pdf ]
[73] Benjamin Berkels, Martin Burger, Marc Droske, Oliver Nemitz, and Martin Rumpf. Cartoon extraction based on anisotropic image classification. In Vision, Modeling and Visualization, pages 293--300. AKA Publishing, 2006. [ .pdf ]
[74] Benjamin Berkels. Gradientenflussmethoden bei inversen Problemen in der Fernerkennung. Diploma thesis, University of Duisburg-Essen, 2005. [ .pdf ]
[75] Benjamin Berkels, Ulrich Clarenz, Susanne Crewell, Ulrich Löhnert, Martin Rumpf, and Clemens Simmer. A physical temperatur profiling method using gradient flows. In Microwave Radiometry and Remote Sensing Applications, Feb. 2004, Rome, Italy, 2004. [ .pdf ]
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