TY - CHAP A1 - Heller, Markus O. A1 - Wurl, Alexander A1 - Perka, Carsten A1 - Hege, Hans-Christian T1 - In vivo gluteus medius volume and shape variations across gender and disease status BT - Proceedings of ESB2012 - 18th Congress of the European Society of Biomechanics, Lisbon, Portugal, 1–4 July 2012 T2 - Journal of Biomechanics Y1 - 2012 U6 - https://doi.org/10.1016/S0021-9290(12)70359-7 VL - 45, Suppl. 1 SP - S358 ER - TY - GEN A1 - Hoerth, Rebecca M. A1 - Baum, Daniel A1 - Knötel, David A1 - Prohaska, Steffen A1 - Willie, Bettina M. A1 - Duda, Georg A1 - Hege, Hans-Christian A1 - Fratzl, Peter A1 - Wagermaier, Wolfgang T1 - Registering 2D and 3D Imaging Data of Bone during Healing N2 - 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. T3 - ZIB-Report - 15-01 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53426 SN - 1438-0064 ER - TY - CHAP A1 - Hege, Hans-Christian T1 - Visual analysis of molecular dynamics data using geometric and topological methods T2 - Forum "Math for Industry" 2014 Y1 - 2014 VL - 57 SP - 45 EP - 46 PB - Institute of Mathematics for Industry, Kyushu University CY - Fukuoka, Japan ER - TY - JOUR A1 - Heinze, Rieke A1 - Dipankar, Anurag A1 - Henken, Cintia Carbajal A1 - Moseley, Christopher A1 - Sourdeval, Odran A1 - Trömel, Silke A1 - Xie, Xinxin A1 - Adamidis, Panos A1 - Ament, Felix A1 - Baars, Holger A1 - Barthlott, Christian A1 - Behrendt, Andreas A1 - Blahak, Ulrich A1 - Bley, Sebastian A1 - Brdar, Slavko A1 - Brueck, Matthias A1 - Crewell, Susanne A1 - Deneke, Hartwig A1 - Di Girolamo, Paolo A1 - Evaristo, Raquel A1 - Fischer, Jürgen A1 - Frank, Christopher A1 - Friederichs, Petra A1 - Göcke, Tobias A1 - Gorges, Ksenia A1 - Hande, Luke A1 - Hanke, Moritz A1 - Hansen, Akio A1 - Hege, Hans-Christian A1 - Hose, Corinna A1 - Jahns, Thomas A1 - Kalthoff, Norbert A1 - Klocke, Daniel A1 - Kneifel, Stefan A1 - Knippertz, Peter A1 - Kuhn, Alexander A1 - van Laar, Thriza A1 - Macke, Andreas A1 - Maurer, Vera A1 - Mayer, Bernhard A1 - Meyer, Catrin I. A1 - Muppa, Shravan K. A1 - Neggers, Roeland A. J. A1 - Orlandi, Emiliano A1 - Pantillon, Florian A1 - Pospichal, Bernhard A1 - Röber, Niklas A1 - Scheck, Leonhard A1 - Seifert, Axel A1 - Seifert, Patric A1 - Senf, Fabian A1 - Siligam, Pavan A1 - Simmer, Clemens A1 - Steinke, Sandra A1 - Stevens, Bjorn A1 - Wapler, Kathrin A1 - Weniger, Michael A1 - Wulfmeyer, Volker A1 - Zängl, Günther A1 - Zhang, Dan A1 - Quaas, Johannes T1 - Large-eddy simulations over Germany using ICON: a comprehensive evaluation JF - Quarterly Journal of the Royal Meteorological Society N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1002/qj.2947 VL - 143 IS - 702 SP - 69 EP - 100 ER - TY - JOUR A1 - Conrad, Tim A1 - Karsch, K. A1 - Obermeier, Patrick A1 - Seeber, L. A1 - Chen, X. A1 - Tief, Franziska A1 - Muehlhans, S. A1 - Hoppe, Christian A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Rath, Barbara T1 - Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children JF - The Pediatric Infectious Disease Journal Y1 - 2015 VL - 34 IS - 10 ER - TY - JOUR A1 - Conrad, Tim A1 - Rath, Barbara A1 - Tief, Franziska A1 - Karsch, K. A1 - Muehlhans, S. A1 - Obermeier, Patrick A1 - Adamou, E. A1 - Chen, X. A1 - Seeber, L. A1 - Peiser, Ch. A1 - Hoppe, Christian A1 - von Kleist, Max A1 - Schweiger, Brunhilde T1 - Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir JF - Infectious Disorders - Drug Targets Y1 - 2013 VL - 13 IS - 1 SP - 25 EP - 33 ER - TY - JOUR A1 - Kozlíková, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art Revisited JF - Computer Graphics Forum N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.13072 VL - 36 IS - 8 SP - 178 EP - 204 ER - TY - GEN A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Gross, Markus A1 - Theisel, Holger T1 - Progressive Monte-Carlo Rendering of Atmospheric Flow Features Across Scales T2 - 69th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 20-22, 2016, Portland, OR, USA. N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1103/APS.DFD.2016.GFM.P0030 ER - TY - CHAP A1 - Kuhn, Alexander A1 - Engelke, Wito A1 - Flatken, Markus A1 - Hege, Hans-Christian A1 - Hotz, Ingrid T1 - Topology-based Analysis for Multimodal Atmospheric Data of Volcano Eruptions T2 - Topological Methods in Data Analysis and Visualization IV Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-44684-4_2 SP - 35 EP - 50 PB - Springer CY - Cham, Schweiz ER - TY - GEN A1 - Stoppel, Sergej A1 - Hege, Hans-Christian A1 - Wiebel, Alexander T1 - Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering N2 - 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. T3 - ZIB-Report - 14-11 KW - Interaction Techniques KW - Volume Rendering KW - Picking KW - Surfaces Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50266 SN - 1438-0064 ER - TY - GEN A1 - Polthier, Konrad A1 - Sullivan, John A1 - Ziegler, Günter M. A1 - Hege, Hans-Christian ED - Deuflhard, Peter ED - et al., T1 - Visualization T2 - MATHEON - Mathematics for Key Technologies Y1 - 2014 SN - 978-3-03719-137-8 U6 - https://doi.org/10.4171/137 SP - 335 EP - 339 PB - European Mathematical Society ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Advanced computed tomography analyses of cold-water coral mound cores: new insights into mound formation processes T2 - Poster, 19th International Sedimentological Congress, Geneva, Switzerland, 2014, August 18 - 22 Y1 - 2014 ER - TY - GEN A1 - Titschack, Jürgen A1 - Baum, Daniel T1 - Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals T2 - Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Kraków, Poland Y1 - 2015 ER - TY - JOUR A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Daviller, Guillaume A1 - Morzyński, Marek T1 - Acceleration feature points of unsteady shear flows JF - Archives of Mechanics N2 - 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. Y1 - 2016 VL - 68 IS - 1 SP - 55 EP - 80 ER - TY - GEN A1 - Kasten, Jens A1 - Reininghaus, Jan A1 - Hotz, Ingrid A1 - Hege, Hans-Christian A1 - Noack, Bernd A1 - Daviller, Guillaume A1 - Morzyński, Marek T1 - Acceleration feature points of unsteady shear flows N2 - 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. T3 - ZIB-Report - 15-65 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-58397 SN - 1438-0064 ER - TY - CHAP A1 - Jácome, Leonardo Agudo A1 - Eggeler, Gunter A1 - Pöthkow, Kai A1 - Paetsch, Olaf A1 - Hege, Hans-Christian T1 - Three-Dimensional Characterization of Superdislocation Interactions in the High Temperature and Low Stress Creep Regime of Ni-Base Superalloy Single Crystals T2 - Proceedings of CREEP 2015 – 13th International Conference on Creep and Fracture of Engineering Materials and Structures, May 31 – June 4, 2015, Toulouse, France N2 - 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. Y1 - 2015 SP - 16 EP - 17 ER - TY - GEN A1 - Bojarovski, Stefan A1 - Hege, Hans-Christian A1 - Lie, Han Cheng A1 - Weber, Marcus T1 - Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales T2 - Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany N2 - 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. Y1 - 2015 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Osman, Jan A1 - Mevert, Ricardo A1 - Kertzscher, Ulrich A1 - Pöthkow, Kai A1 - Hege, Hans-Christian T1 - Turbulence in blood damage modeling JF - The International Journal of Artificial Organs N2 - 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. Y1 - 2016 U6 - https://doi.org/10.5301/ijao.5000476 VL - 39 IS - 4 SP - 147 EP - 210 ER - TY - GEN A1 - Sieber, Moritz A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Paschereit, C. Oliver A1 - Oberleithner, Kilian T1 - A Graphical Representation of the Spectral Proper Orthogonal Decomposition T2 - 68th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 22-24, 2015, Boston, MA, USA. N2 - 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. Y1 - 2015 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres JF - Nondestructive Testing and Evaluation N2 - 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. Y1 - 2020 U6 - https://doi.org/10.1080/10589759.2020.1774583 VL - 35 IS - 3 SP - 328 EP - 341 ER -