@inproceedings{TheiselWeinkaufHegeetal.2004, author = {Theisel, Holger and Weinkauf, Tino and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Grid-independent detection of closed stream lines in 2D vector fields}, booktitle = {Proc. Vision, Modeling and Visualization 2004}, address = {Stanford, U.S.A.}, pages = {421 -- 428}, year = {2004}, language = {en} } @inproceedings{WeinkaufSahnerTheiseletal.2007, author = {Weinkauf, Tino and Sahner, Jan and Theisel, Holger and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {A unified feature extraction architecture}, booktitle = {Active Flow Control}, publisher = {Springer Berlin/Heidelberg}, doi = {10.1007/978-3-540-71439-2_8}, pages = {119 -- 133}, year = {2007}, language = {en} } @inproceedings{KaehlerWiseAbeletal.2006, author = {K{\"a}hler, Ralf and Wise, John and Abel, Tom and Hege, Hans-Christian}, title = {A framework for interactive, high-quality volume rendering of cosmological simulations}, booktitle = {Proc. Int. Workshop on Volume Graphics (VG06)}, publisher = {Eurographics / IEEE VGTC 2006}, address = {Boston}, pages = {103 -- 110}, year = {2006}, language = {en} } @article{BrandtRohlfingRybaketal.2005, author = {Brandt, Robert and Rohlfing, Torsten and Rybak, J{\"u}rgen and Krofczik, Sabine and Maye, Alexander and Westerhoff, Malte and Hege, Hans-Christian and Menzel, Randolf}, title = {A three-dimensional average-shape atlas of the honeybee brain and its applications}, volume = {492(1)}, journal = {Journal of Comparative Neurology}, pages = {1 -- 19}, year = {2005}, language = {en} } @misc{StallingWesterhoffHege2005, author = {Stalling, Detlev and Westerhoff, Malte and Hege, Hans-Christian}, title = {Amira: A highly interactive system for visual data analysis}, journal = {The Visualization Handbook}, editor = {Hansen, Charles and Johnson, Christopher}, publisher = {Elsevier}, doi = {10.1016/B978-012387582-2/50040-X}, pages = {749 -- 767}, year = {2005}, language = {en} } @article{TheiselWeinkaufHegeetal.2005, author = {Theisel, Holger and Weinkauf, Tino and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Topological methods for 2D time-dependent vector fields based on stream lines and path lines}, volume = {11}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {4}, doi = {10.1109/TVCG.2005.68}, year = {2005}, language = {en} } @article{GoubergritsTimmelAffeldetal.2006, author = {Goubergrits, Leonid and Timmel, Tobias and Affeld, Klaus and Petz, Christoph and Stalling, Detlev and Hege, Hans-Christian}, title = {Characterization of an artificial valve flow using the numerical dye washout visualization technique}, volume = {30(8)}, journal = {Artificial Organs}, pages = {642 -- 650}, year = {2006}, language = {en} } @inproceedings{BaumHege2006, author = {Baum, Daniel and Hege, Hans-Christian}, title = {A Point-matching based algorithm for 3D surface alignment of drug-sized molecules}, volume = {4216}, booktitle = {Computational Life Sciences II, Second International Symposium, CompLife 2006, Cambridge (UK), Sept. 2006}, publisher = {Springer}, doi = {10.1007/11875741_18}, pages = {183 -- 193}, year = {2006}, language = {en} } @inproceedings{ShiTheiselWeinkaufetal.2006, author = {Shi, Kuangyu and Theisel, Holger and Weinkauf, Tino and Hauser, Helwig and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Path line oriented topology for periodic 2D time-dependent vector fields}, booktitle = {Proc. Eurographics / IEEE VGTC Symposium on Visualization}, address = {Lisbon, Portugal}, pages = {139 -- 146}, year = {2006}, language = {en} } @article{WeinkaufTheiselHegeetal.2006, author = {Weinkauf, Tino and Theisel, Holger and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Topological structures in two-parameter-dependent 2D vector fields}, volume = {25 (3)}, journal = {Computer Graphics Forum}, doi = {10.1111/j.1467-8659.2006.00980.x}, pages = {607 -- 616}, year = {2006}, language = {en} } @inproceedings{CoconuDeussenHege2006, author = {Coconu, Liviu and Deussen, Oliver and Hege, Hans-Christian}, title = {Real-time pen-and-ink illustration of landscapes}, booktitle = {NPAR '06: Proceedings of the 3rd International Symposium on Non-photorealistic Animation and Rendering}, publisher = {ACM press}, address = {New York, NY, USA}, doi = {10.1145/1124728.1124734}, pages = {27 -- 35}, year = {2006}, language = {en} } @inproceedings{KaehlerProhaskaHutanuetal.2005, author = {K{\"a}hler, Ralf and Prohaska, Steffen and Hutanu, Andrei and Hege, Hans-Christian}, title = {Visualization of time-dependent remote adaptive mesh refinement data}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, doi = {10.1109/VISUAL.2005.1532793}, pages = {175 -- 182}, year = {2005}, language = {en} } @inproceedings{WeinkaufTheiselShietal.2005, author = {Weinkauf, Tino and Theisel, Holger and Shi, Kuangyu and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Topological simplification of 3D vector fields and extracting higher order critical points}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, pages = {631 -- 638}, year = {2005}, language = {en} } @inproceedings{SahnerWeinkaufHege2005, author = {Sahner, Jan and Weinkauf, Tino and Hege, Hans-Christian}, title = {Galilean invariant extraction and iconic representation of vortex core lines}, booktitle = {Proc. Eurographics / IEEE VGTC Symposium on Visualization (EuroVis '05)}, editor = {Brodlie, K. and Duke, D. and Joy, K.}, address = {Leeds, UK}, doi = {10.2312/VisSym/EuroVis05/151-160}, pages = {151 -- 160}, year = {2005}, language = {en} } @inproceedings{TheiselSahnerWeinkaufetal.2005, author = {Theisel, Holger and Sahner, Jan and Weinkauf, Tino and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Extraction of parallel vector surfaces in 3D time-dependent fields and application to vortex core line tracking}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, pages = {559 -- 566}, year = {2005}, language = {en} } @misc{PetzWeinkaufStreckwalletal.2006, author = {Petz, Christoph and Weinkauf, Tino and Streckwall, Heinrich and Salvatore, Franceso and Noack, Bernd R. and Hege, Hans-Christian}, title = {Vortex Structures at a Rotating Ship Propeller}, publisher = {Presented at the 24th Annual Gallery of Fluid Motion exhibit, held at the 59th Annual Meeting of the American Physical Society, Division of Fluid Dynamics, Tampa Bay}, year = {2006}, language = {en} } @article{ZieglerHegeDuda2005, author = {Ziegler, G{\"u}nter M. and Hege, Hans-Christian and Duda, Georg}, title = {Neue Bilder f{\"u}r die Medizin?}, volume = {13(3)}, journal = {DFN-Mitteilungen}, pages = {163 -- 167}, year = {2005}, language = {en} } @misc{Hege2005, author = {Hege, Hans-Christian}, title = {Hintergrundinformationen zum Artikel 'Neue Bilder f{\"u}r die Medizin?'}, publisher = {DFG-Research Center Matheon, Report, 19 pages}, year = {2005}, language = {en} } @incollection{DeussenColditzCoconuetal.2005, author = {Deussen, Oliver and Colditz, Carsten and Coconu, Liviu and Hege, Hans-Christian}, title = {Efficient modelling and rendering of landscapes}, booktitle = {Visualization in Landscape and Environmental Planning}, editor = {Bishop, Ian and Lange, Eckart}, publisher = {Spon Press}, address = {London}, pages = {56 -- 61}, year = {2005}, language = {en} } @incollection{ColditzCoconuDeussenetal.2005, author = {Colditz, Carsten and Coconu, Liviu and Deussen, Oliver and Hege, Hans-Christian}, title = {Real-time rendering of complex photorealistic landscapes using hybrid level-of-detail approaches}, booktitle = {Trends in Real-Time Landscape Visualization and Participation}, editor = {Buhmann, Erich and Paar, Philip and Bishop, Ian and Lange, Eckart}, publisher = {Wichmann Verlag}, pages = {97 -- 106}, year = {2005}, language = {en} } @incollection{CoconuColditzHegeetal.2005, author = {Coconu, Liviu and Colditz, Carsten and Hege, Hans-Christian and Deussen, Oliver}, title = {Seamless integration of stylized renditions in computer-generated landscape visualization}, booktitle = {Trends in Real-Time Landscape Visualization and Participation}, editor = {Buhmann, Erich and Paar, Philip and Bishop, Ian and Lange, Eckart}, publisher = {Wichmann Verlag}, address = {Heidelberg}, pages = {88 -- 96}, year = {2005}, language = {en} } @incollection{ClasenHege2005, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Realistic illumination of vegetation in real-time environments}, booktitle = {Trends in Real-Time Landscape Visualization and Participation}, editor = {Buhmann, Erich and Paar, Philip and Bishop, Ian and Lange, Eckart}, publisher = {Wichmann Verlag}, pages = {107 -- 114}, year = {2005}, language = {en} } @article{WernerDeussenDoellneretal.2005, author = {Werner, Armin and Deussen, Oliver and D{\"o}llner, J{\"u}rgen and Hege, Hans-Christian and Paar, Philip and Rekittke, J{\"o}rg}, title = {Lenn{\´e} 3D walking through landscape plan}, journal = {Trends in Real-Time Landscape Visualization and Participation}, editor = {Buhmann, Erich and Paar, Philip and Bishop, Ian and Lange, Eckart}, publisher = {Wichmann Verlag}, pages = {48 -- 59}, year = {2005}, language = {en} } @article{EggerDercksenUdvaryetal.2014, author = {Egger, Robert and Dercksen, Vincent J. and Udvary, Daniel and Hege, Hans-Christian and Oberlaender, Marcel}, title = {Generation of dense statistical connectomes from sparse morphological data}, volume = {8}, journal = {Frontiers in Neuroanatomy}, number = {129}, doi = {10.3389/fnana.2014.00129}, year = {2014}, language = {en} } @misc{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51194}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @incollection{PfisterKaynigBothaetal.2014, author = {Pfister, Hanspeter and Kaynig, Verena and Botha, Charl P. and Bruckner, Stefan and Dercksen, Vincent J. and Hege, Hans-Christian and Roerdink, Jos B.T.M.}, title = {Visualization in Connectomics}, booktitle = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization}, editor = {Hansen, Charles D. and Chen, Min and Johnson, Christopher R. and Kaufman, Arie E. and Hagen, Hans}, publisher = {Springer}, isbn = {978-1-4471-6496-8}, arxiv = {http://arxiv.org/abs/1206.1428}, doi = {10.1007/978-1-4471-6497-5_21}, pages = {221 -- 245}, year = {2014}, abstract = {Connectomics is a branch of neuroscience that attempts to create a connectome, i.e., a complete map of the neuronal system and all connections between neuronal structures. This representation can be used to understand how functional brain states emerge from their underlying anatomical structures and how dysfunction and neuronal diseases arise. We review the current state-of-the-art of visualization and image processing techniques in the field of connectomics and describe a number of challenges. After a brief summary of the biological background and an overview of relevant imaging modalities, we review current techniques to extract connectivity information from image data at macro-, meso- and microscales. We also discuss data integration and neural network modeling, as well as the visualization, analysis and comparison of brain networks.}, language = {en} } @incollection{BonneauHegeJohnsonetal.2014, author = {Bonneau, Georges-Pierre and Hege, Hans-Christian and Johnson, Chris R. and Oliveira, Manuel M. and Potter, Kristin and Rheingans, Penny and Schultz, Thomas}, title = {Overview and State-of-the-Art of Uncertainty Visualization}, booktitle = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization}, publisher = {Springer}, isbn = {978-1-4471-6496-8}, doi = {10.1007/978-1-4471-6497-5_1}, pages = {3 -- 27}, year = {2014}, abstract = {The goal of visualization is to effectively and accurately communicate data. Visualization research has often overlooked the errors and uncertainty which accompany the scientific process and describe key characteristics used to fully understand the data. The lack of these representations can be attributed, in part, to the inherent difficulty in defining, characterizing, and controlling this uncertainty, and in part, to the difficulty in including additional visual metaphors in a well designed, potent display. However, the exclusion of this information cripples the use of visualization as a decision making tool due to the fact that the display is no longer a true representation of the data. This systematic omission of uncertainty commands fundamental research within the visualization community to address, integrate, and expect uncertainty information. In this chapter, we outline sources and models of uncertainty, give an overview of the state-of-the-art, provide general guidelines, outline small exemplary applications, and finally, discuss open problems in uncertainty visualization.}, language = {en} } @misc{OPUS4-5228, title = {Visualization in Medicine and Life Sciences II}, editor = {Linsen, Lars and Hagen, Hans and Hamann, Bernd and Hege, Hans-Christian}, publisher = {Springer}, address = {Berlin}, isbn = {978-3-642-21607-7}, doi = {10.1007/978-3-642-21608-4}, pages = {290}, year = {2012}, language = {en} } @article{GoubergritsSpulerSchalleretal.2014, author = {Goubergrits, Leonid and Spuler, Andreas and Schaller, Jens and Wiegmann, Nils and Berthe, Andre and Hege, Hans-Christian and Affeld, Klaus and Kertzscher, Ulrich}, title = {In vitro study of hemodynamic treatment improvement: Hunterian ligation of a fenestrated basilar artery aneurysm after coiling}, volume = {37}, journal = {The International Journal of Artificial Organs}, number = {4}, doi = {10.5301/ijao.5000314}, pages = {325 -- 335}, year = {2014}, abstract = {Hunterian ligation affecting hemodynamics in vessels was proposed to avoid rebleeding in a case of a fenestrated basilar artery aneurysm after incomplete coil occlusion. We studied the hemodynamics in vitro to predict the hemodynamic changes near the aneurysm remnant caused by Hunterian ligation. A transparent model was fabricated based on three-dimensional rotational angiography imaging. Arteries were segmented and reconstructed. Pulsatile flow in the artery segments near the partially occluded (coiled) aneurysm was investigated by means of particle image velocimetry. The hemodynamic situation was investigated before and after Hunterian ligation of either the left or the right vertebral artery (LVA/RVA). Since post-ligation flow rate in the basilar artery was unknown, reduced and retained flow rates were simulated for both ligation options. Flow in the RVA and in the corresponding fenestra vessel is characterized by a vortex at the vertebrobasilar junction, whereas the LVA exhibits undisturbed laminar flow. Both options (RVA or LVA ligation) cause a significant flow reduction near the aneurysm remnant with a retained flow rate. The impact of RVA ligation is, however, significantly higher. This in vitro case study shows that flow reduction near the aneurysm remnant can be achieved by Hunterian ligation and that this effect depends largely on the selection of the ligated vessel. Thus the ability of the proposed in vitro pipe-line to improve hemodynamic impact of the proposed therapy was successfully proved.}, language = {en} } @inproceedings{StoppelHegeWiebel2014, author = {Stoppel, Sergej and Hege, Hans-Christian and Wiebel, Alexander}, title = {Visibility-driven depth determination of surface patches in direct volume rendering}, booktitle = {EuroVis - Short Papers 2014}, doi = {10.2312/eurovisshort.20141164}, pages = {97 -- 101}, year = {2014}, abstract = {This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a visible and typically rather smooth surface. In the last step the selected surface is displayed. We provide examples for results using artificially generated and real-world data sets.}, language = {en} } @article{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, volume = {20}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2014.2346404}, pages = {2486 -- 2495}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @article{GoubergritsSchallerKertzscheretal.2013, author = {Goubergrits, Leonid and Schaller, Jens and Kertzscher, Ulrich and Petz, Christoph and Hege, Hans-Christian and Spuler, Andreas}, title = {Reproducibility of Image-Based Analysis of Cerebral Aneurysm Geometry and Hemodynamics: An In-Vitro Study of Magnetic Resonance Imaging, Computed Tomography, and Three-Dimensional Rotational Angiography}, volume = {74}, journal = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, number = {5}, doi = {10.1055/s-0033-1342937}, pages = {294 -- 302}, year = {2013}, language = {en} } @article{SipsKothurUngeretal.2012, author = {Sips, Mike and Kothur, Patrick and Unger, Andrea and Hege, Hans-Christian and Dransch, Doris}, title = {A Visual Analytics Approach to Multiscale Exploration of Environmental Time Series}, volume = {18}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2012.191}, pages = {2899 -- 2907}, year = {2012}, abstract = {We present a Visual Analytics approach that addresses the detection of interesting patterns in numerical time series, specifically from environmental sciences. Crucial for the detection of interesting temporal patterns are the time scale and the starting points one is looking at. Our approach makes no assumption about time scale and starting position of temporal patterns and consists of three main steps: an algorithm to compute statistical values for all possible time scales and starting positions of intervals, visual identification of potentially interesting patterns in a matrix visualization, and interactive exploration of detected patterns. We demonstrate the utility of this approach in two scientific scenarios and explain how it allowed scientists to gain new insight into the dynamics of environmental systems.}, language = {en} } @article{WeinkaufHegeTheisel2012, author = {Weinkauf, Tino and Hege, Hans-Christian and Theisel, Holger}, title = {Advected Tangent Curves: A General Scheme for Characteristic Curves of Flow Fields}, volume = {31}, journal = {Computer Graphics Forum}, number = {2pt4}, doi = {10.1111/j.1467-8659.2012.03063.x}, pages = {825 -- 834}, year = {2012}, abstract = {We present the first general scheme to describe all four types of characteristic curves of flow fields - stream, path, streak, and time lines - as tangent curves of a derived vector field. Thus, all these lines can be obtained by a simple integration of an autonomous ODE system. Our approach draws on the principal ideas of the recently introduced tangent curve description of streak lines. We provide the first description of time lines as tangent curves of a derived vector field, which could previously only be constructed in a geometric manner. Furthermore, our scheme gives rise to new types of curves. In particular, we introduce advected stream lines as a parameter-free variant of the time line metaphor. With our novel mathematical description of characteristic curves, a large number of feature extraction and analysis tools becomes available for all types of characteristic curves, which were previously only available for stream and path lines. We will highlight some of these possible applications including the computation of time line curvature fields and the extraction of cores of swirling advected stream lines.}, language = {en} } @inproceedings{HellerWurlPerkaetal.2012, author = {Heller, Markus O. and Wurl, Alexander and Perka, Carsten and Hege, Hans-Christian}, title = {In vivo gluteus medius volume and shape variations across gender and disease status}, volume = {45, Suppl. 1}, booktitle = {Journal of Biomechanics}, doi = {10.1016/S0021-9290(12)70359-7}, pages = {S358}, year = {2012}, language = {en} } @misc{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, year = {2015}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @inproceedings{Hege2014, author = {Hege, Hans-Christian}, title = {Visual analysis of molecular dynamics data using geometric and topological methods}, volume = {57}, booktitle = {Forum "Math for Industry" 2014}, publisher = {Institute of Mathematics for Industry, Kyushu University}, address = {Fukuoka, Japan}, pages = {45 -- 46}, year = {2014}, language = {en} } @article{HeinzeDipankarHenkenetal.2017, author = {Heinze, Rieke and Dipankar, Anurag and Henken, Cintia Carbajal and Moseley, Christopher and Sourdeval, Odran and Tr{\"o}mel, Silke and Xie, Xinxin and Adamidis, Panos and Ament, Felix and Baars, Holger and Barthlott, Christian and Behrendt, Andreas and Blahak, Ulrich and Bley, Sebastian and Brdar, Slavko and Brueck, Matthias and Crewell, Susanne and Deneke, Hartwig and Di Girolamo, Paolo and Evaristo, Raquel and Fischer, J{\"u}rgen and Frank, Christopher and Friederichs, Petra and G{\"o}cke, Tobias and Gorges, Ksenia and Hande, Luke and Hanke, Moritz and Hansen, Akio and Hege, Hans-Christian and Hose, Corinna and Jahns, Thomas and Kalthoff, Norbert and Klocke, Daniel and Kneifel, Stefan and Knippertz, Peter and Kuhn, Alexander and van Laar, Thriza and Macke, Andreas and Maurer, Vera and Mayer, Bernhard and Meyer, Catrin I. and Muppa, Shravan K. and Neggers, Roeland A. J. and Orlandi, Emiliano and Pantillon, Florian and Pospichal, Bernhard and R{\"o}ber, Niklas and Scheck, Leonhard and Seifert, Axel and Seifert, Patric and Senf, Fabian and Siligam, Pavan and Simmer, Clemens and Steinke, Sandra and Stevens, Bjorn and Wapler, Kathrin and Weniger, Michael and Wulfmeyer, Volker and Z{\"a}ngl, G{\"u}nther and Zhang, Dan and Quaas, Johannes}, title = {Large-eddy simulations over Germany using ICON: a comprehensive evaluation}, volume = {143}, journal = {Quarterly Journal of the Royal Meteorological Society}, number = {702}, doi = {10.1002/qj.2947}, pages = {69 -- 100}, year = {2017}, abstract = {Large-eddy simulations (LES) with the new ICOsahedral Non-hydrostatic atmosphere model (ICON) covering Germany are evaluated for four days in spring 2013 using observational data from various sources. Reference simulations with the established Consortium for Small-scale Modelling (COSMO) numerical weather prediction model and further standard LES codes are performed and used as a reference. This comprehensive evaluation approach covers multiple parameters and scales, focusing on boundary-layer variables, clouds and precipitation. The evaluation points to the need to work on parametrizations influencing the surface energy balance, and possibly on ice cloud microphysics. The central purpose for the development and application of ICON in the LES configuration is the use of simulation results to improve the understanding of moist processes, as well as their parametrization in climate models. The evaluation thus aims at building confidence in the model's ability to simulate small- to mesoscale variability in turbulence, clouds and precipitation. The results are encouraging: the high-resolution model matches the observed variability much better at small- to mesoscales than the coarser resolved reference model. In its highest grid resolution, the simulated turbulence profiles are realistic and column water vapour matches the observed temporal variability at short time-scales. Despite being somewhat too large and too frequent, small cumulus clouds are well represented in comparison with satellite data, as is the shape of the cloud size spectrum. Variability of cloud water matches the satellite observations much better in ICON than in the reference model. In this sense, it is concluded that the model is fit for the purpose of using its output for parametrization development, despite the potential to improve further some important aspects of processes that are also parametrized in the high-resolution model.}, language = {en} } @article{KozlikovaKroneFalketal.2016, author = {Kozl{\´i}kov{\´a}, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art Revisited}, volume = {36}, journal = {Computer Graphics Forum}, number = {8}, doi = {10.1111/cgf.13072}, pages = {178 -- 204}, year = {2016}, abstract = {Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.}, language = {en} } @misc{GuentherKuhnHegeetal.2016, author = {G{\"u}nther, Tobias and Kuhn, Alexander and Hege, Hans-Christian and Gross, Markus and Theisel, Holger}, title = {Progressive Monte-Carlo Rendering of Atmospheric Flow Features Across Scales}, journal = {69th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 20-22, 2016, Portland, OR, USA.}, doi = {10.1103/APS.DFD.2016.GFM.P0030}, year = {2016}, abstract = {To improve existing weather prediction and reanalysis capabilities, high-resolution and multi-modal climate data becomes an increasingly important topic. The advent of increasingly dense numerical simulation of atmospheric phenomena, provides new means to better understand dynamic processes and to visualize structural flow patterns that remain hidden otherwise. In the presented illustrations we demonstrate an advanced technique to visualize multiple scales of dense flow fields and Lagrangian patterns therein, simulated by state-of-the-art simulation models for each scale. They provide a deeper insight into the structural differences and patterns that occur on each scale and highlight the complexity of flow phenomena in our atmosphere.}, language = {en} } @inproceedings{KuhnEngelkeFlatkenetal.2017, author = {Kuhn, Alexander and Engelke, Wito and Flatken, Markus and Hege, Hans-Christian and Hotz, Ingrid}, title = {Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions}, booktitle = {Topological Methods in Data Analysis and Visualization IV}, publisher = {Springer}, address = {Cham, Schweiz}, doi = {10.1007/978-3-319-44684-4_2}, pages = {35 -- 50}, year = {2017}, language = {en} } @misc{StoppelHegeWiebel2014, author = {Stoppel, Sergej and Hege, Hans-Christian and Wiebel, Alexander}, title = {Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering}, issn = {1438-0064}, doi = {10.2312/eurovisshort.20141164}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50266}, year = {2014}, abstract = {This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a very visible but relatively smooth surface. In the last step the selected surface is displayed. We provide examples for the results in real-world dataset as well as in artificially generated datasets.}, language = {en} } @misc{PolthierSullivanZiegleretal.2014, author = {Polthier, Konrad and Sullivan, John and Ziegler, G{\"u}nter M. and Hege, Hans-Christian}, title = {Visualization}, journal = {MATHEON - Mathematics for Key Technologies}, editor = {Deuflhard, Peter and et al.,}, publisher = {European Mathematical Society}, isbn = {978-3-03719-137-8}, doi = {10.4171/137}, pages = {335 -- 339}, year = {2014}, language = {en} } @article{KastenReininghausHotzetal.2016, author = {Kasten, Jens and Reininghaus, Jan and Hotz, Ingrid and Hege, Hans-Christian and Noack, Bernd and Daviller, Guillaume and Morzyński, Marek}, title = {Acceleration feature points of unsteady shear flows}, volume = {68}, journal = {Archives of Mechanics}, number = {1}, pages = {55 -- 80}, year = {2016}, abstract = {A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2.}, language = {en} } @misc{KastenReininghausHotzetal.2015, author = {Kasten, Jens and Reininghaus, Jan and Hotz, Ingrid and Hege, Hans-Christian and Noack, Bernd and Daviller, Guillaume and Morzyński, Marek}, title = {Acceleration feature points of unsteady shear flows}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58397}, year = {2015}, abstract = {A framework is proposed for extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance. The minima of the acceleration magnitude, i.e. a superset of the acceleration zeros, are extracted and discriminated into vortices and saddle points --- based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These features are tracked in time with a robust algorithm for tracking features. Thus a space-time hierarchy of the minima is built and vortex merging events are detected. The acceleration feature extraction strategy is applied to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of pressure field and minima of λ2.}, language = {en} } @inproceedings{JacomeEggelerPoethkowetal.2015, author = {J{\´a}come, Leonardo Agudo and Eggeler, Gunter and P{\"o}thkow, Kai and Paetsch, Olaf and Hege, Hans-Christian}, title = {Three-Dimensional Characterization of Superdislocation Interactions in the High Temperature and Low Stress Creep Regime of Ni-Base Superalloy Single Crystals}, booktitle = {Proceedings of CREEP 2015 - 13th International Conference on Creep and Fracture of Engineering Materials and Structures, May 31 - June 4, 2015, Toulouse, France}, pages = {16 -- 17}, year = {2015}, abstract = {Monocrystaline Ni-base superalloys are the material of choice for first row blades in jet engine gas turbines. Using a novel visualization tool for 3D reconstruction and visualization of dislocation line segments from stereo-pairs of scanning transmission electron microscopies, the superdislocation substructures in Ni-base superalloy LEK 94 (crept to ε = 26\%) are characterized. Probable scenarios are discussed, how these dislocation substructures form.}, language = {en} } @misc{BojarovskiHegeLieetal.2015, author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, year = {2015}, abstract = {Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models.}, language = {en} } @article{GoubergritsOsmanMevertetal.2016, author = {Goubergrits, Leonid and Osman, Jan and Mevert, Ricardo and Kertzscher, Ulrich and P{\"o}thkow, Kai and Hege, Hans-Christian}, title = {Turbulence in blood damage modeling}, volume = {39}, journal = {The International Journal of Artificial Organs}, number = {4}, doi = {10.5301/ijao.5000476}, pages = {147 -- 210}, year = {2016}, abstract = {Purpose: To account for the impact of turbulence in blood damage modeling, a novel approach based on the generation of instantaneous flow fields from RANS simulations is proposed. Methods: Turbulent flow in a bileaflet mechanical heart valve was simulated using RANS-based (SST k-ω) flow solver using FLUENT 14.5. The calculated Reynolds shear stress (RSS) field is transformed into a set of divergence-free random vector fields representing turbulent velocity fluctuations using procedural noise functions. To consider the random path of the blood cells, instantaneous flow fields were computed for each time step by summation of RSS-based divergence-free random and mean velocity fields. Using those instantaneous flow fields, instantaneous pathlines and corresponding point-wise instantaneous shear stresses were calculated. For a comparison, averaged pathlines based on mean velocity field and respective viscous shear stresses together with RSS values were calculated. Finally, the blood damage index (hemolysis) was integrated along the averaged and instantaneous pathlines using a power law approach and then compared. Results: Using RSS in blood damage modeling without a correction factor overestimates damaging stress and thus the blood damage (hemolysis). Blood damage histograms based on both presented approaches differ. Conclusions: A novel approach to calculate blood damage without using RSS as a damaging parameter is established. The results of our numerical experiment support the hypothesis that the use of RSS as a damaging parameter should be avoided.}, language = {en} } @article{WilliePapPerkaetal.2015, author = {Willie, Bettina M. and Pap, Thomas and Perka, Carsten and Schmidt, Carsten Oliver and Eckstein, Felix and Arampatzis, Adamantios and Hege, Hans-Christian and Madry, Henning and Vortkamp, Andrea and Duda, Georg}, title = {OVERLOAD - Rolle der Gelenk{\"u}berlastung in der prim{\"a}ren Arthrose - Die Krankheitsprogression verstehen und vermeiden}, volume = {74}, journal = {Zeitschrift f{\"u}r Rheumatologie}, doi = {10.1007/s00393-014-1561-2}, pages = {618 -- 621}, year = {2015}, abstract = {Intakte Gelenke sind eine Voraussetzung f{\"u}r das Funktionieren des Skeletts und die Mobilit{\"a}t im Lebensalltag. Ein gesunder Bewegungsapparat ist die Grundlage f{\"u}r die Funktionsf{\"a}higkeit des Herz-Kreislauf-Systems wie auch der Immunabwehr. Bewegungs- und Physiotherapie sowie verschiedene Formen der Patientenaktivit{\"a}t stellen essenzielle klinische Ans{\"a}tze in der Behandlung von neurodegenerativen Erkrankungen, Schlaganfall, Diabetes und Krebs dar. Kommt es zu degenerativen Ver{\"a}nderungen von Gelenken, bedeutet dies eine wesentliche Beeintr{\"a}chtigung der Mobilit{\"a}t. N{\"a}chtliche Schmerzen und Schlafst{\"o}rungen treten in fortgeschrittenen Stadien auf und sind besonders belastend. Arthrose wird auch als degenerative Gelenkerkrankung bezeichnet. Sie geht mit Ver{\"a}nderungen in der Struktur und Zusammensetzung des Gelenkknorpels wie auch des verkalkten Knorpels, der subchondralen Kortikalis, der subchondralen Spongiosa, des Meniskus, der Gelenkkapsel und der Synovialis einher, was schließlich zur Degeneration dieser Gewebe f{\"u}hrt, aus denen sich die Synovialgelenke zusammensetzen.}, language = {de} } @misc{SieberKuhnHegeetal.2015, author = {Sieber, Moritz and Kuhn, Alexander and Hege, Hans-Christian and Paschereit, C. Oliver and Oberleithner, Kilian}, title = {A Graphical Representation of the Spectral Proper Orthogonal Decomposition}, journal = {68th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 22-24, 2015, Boston, MA, USA.}, year = {2015}, abstract = {We consider the spectral proper orthogonal decomposition (SPOD) for experimental data of a turbulent swirling jet. This newly introduced method combines the advantages of spectral methods, such as Fourier decomposition or dynamic mode decomposition, with the energy-ranked proper orthogonal decomposition (POD). This poster visualizes how the modal energy spectrum transitions from the spectral purity of Fourier space to the sparsity of POD space. The transition is achieved by changing a single parameter - the width of the SPOD filter. Each dot in the 3D space corresponds to an SPOD mode pair, where the size and color indicates its spectral coherence. What we notice is that neither the Fourier nor the POD spectrum achieves a clear separation of the dynamic phenomena. Scanning through the graph from the front plane (Fourier) to the back plane (POD), we observe how three highly coherent SPOD modes emerge from the dispersed Fourier spectrum and later branch out into numerous POD modes. The spatial properties of these three individual SPOD modes are displayed in the back of the graph using line integral convolution colored by vorticity. The first two modes correspond to single-helical global instabilities that are well known for these flows. Their coexistence, however, has not been observed until now. The third mode is of double- helical shape and has not been observed so far. For this considered data set and many others, the SPOD is superior in identification of coherent structures in turbulent flows. Hopefully, it gives access to new fluid dynamic phenomena and enriches the available methods.}, language = {en} } @article{FroehlerElberfeldMoelleretal.2020, author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres}, volume = {35}, journal = {Nondestructive Testing and Evaluation}, number = {3}, doi = {10.1080/10589759.2020.1774583}, pages = {328 -- 341}, year = {2020}, abstract = {We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres.}, language = {en} } @misc{SagnolHegeWeiser2016, author = {Sagnol, Guillaume and Hege, Hans-Christian and Weiser, Martin}, title = {Using sparse kernels to design computer experiments with tunable precision}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59605}, year = {2016}, abstract = {Statistical methods to design computer experiments usually rely on a Gaussian process (GP) surrogate model, and typically aim at selecting design points (combinations of algorithmic and model parameters) that minimize the average prediction variance, or maximize the prediction accuracy for the hyperparameters of the GP surrogate. In many applications, experiments have a tunable precision, in the sense that one software parameter controls the tradeoff between accuracy and computing time (e.g., mesh size in FEM simulations or number of Monte-Carlo samples). We formulate the problem of allocating a budget of computing time over a finite set of candidate points for the goals mentioned above. This is a continuous optimization problem, which is moreover convex whenever the tradeoff function accuracy vs. computing time is concave. On the other hand, using non-concave weight functions can help to identify sparse designs. In addition, using sparse kernel approximations drastically reduce the cost per iteration of the multiplicative weights updates that can be used to solve this problem.}, language = {en} }