@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} } @inproceedings{LameckerZoecklerHaberletal.2005, author = {Lamecker, Hans and Z{\"o}ckler, Maja and Haberl, Hannes and Zachow, Stefan and Hege, Hans-Christian}, title = {Statistical shape modeling for craniosynostosis planning}, booktitle = {2nd International Conference Advanced Digital Technology in Head and Neck Reconstruction 2005, Abstract Volume}, address = {Banff, Alberta}, pages = {64}, 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{ZachowHegeDeuflhard2005, author = {Zachow, Stefan and Hege, Hans-Christian and Deuflhard, Peter}, title = {Maxillofacial surgery planning with 3D soft tissue prediction - modeling, planning, simulation}, journal = {2. Int. Conf. on Advanced Digital Technology in Head and Neck Reconstruction, Abstract 33}, address = {Banff, Alberta, CA}, pages = {64}, 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{LameckerWenckebachHege2006, author = {Lamecker, Hans and Wenckebach, Thomas and Hege, Hans-Christian}, title = {Atlas-based 3D-shape reconstruction from x-ray images}, volume = {Volume I}, booktitle = {Proc. Int. Conf. of Pattern Recognition (ICPR2006)}, publisher = {IEEE Computer Society}, doi = {10.1109/ICPR.2006.279}, pages = {371 -- 374}, year = {2006}, language = {en} } @inproceedings{ClasenHege2006, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Terrain rendering using spherical clipmaps}, booktitle = {EuroVis 2006 - Eurographics / IEEE VGTC Symposium on Visualization}, pages = {91 -- 98}, year = {2006}, language = {en} } @inproceedings{LameckerWenckebachHegeetal.2006, author = {Lamecker, Hans and Wenckebach, Thomas and Hege, Hans-Christian and N. Duda, Georg and Heller, Markus}, title = {Atlas-basierte 3D-Rekonstruktion des Beckens aus 2D-Projektionsbildern}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2006: Algorithmen - Systeme - Anwendungen}, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/3-540-32137-3_6}, pages = {26 -- 30}, 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{SchmidtEhrenbergHege2005, author = {Schmidt-Ehrenberg, Johannes and Hege, Hans-Christian}, title = {Visual analysis of molecular conformations by means of a dynamic density mixture model}, volume = {3695}, booktitle = {Computational Life Sciences: First International Symposium, CompLife 2005}, publisher = {Springer}, address = {Konstanz, Germany}, pages = {229 -- 240}, year = {2005}, 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} } @inproceedings{KraemerHerrmannBoethetal.2015, author = {Kr{\"a}mer, Martin and Herrmann, Karl-Heinz and Boeth, Heide and Tycowicz, Christoph von and K{\"o}nig, Christian and Zachow, Stefan and Ehrig, Rainald and Hege, Hans-Christian and Duda, Georg and Reichenbach, J{\"u}rgen}, title = {Measuring 3D knee dynamics using center out radial ultra-short echo time trajectories with a low cost experimental setup}, booktitle = {ISMRM (International Society for Magnetic Resonance in Medicine), 23rd Annual Meeting 2015, Toronto, Canada}, year = {2015}, 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} } @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} } @misc{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}, issn = {1438-0064}, doi = {10.3389/fnana.2014.00129}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53075}, year = {2014}, abstract = {Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and sub-cellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results.}, language = {en} } @article{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}, volume = {56}, journal = {Connective Tissue Research}, number = {2}, publisher = {Taylor \& Francis}, doi = {10.3109/03008207.2015.1005210}, pages = {133 -- 143}, year = {2015}, language = {en} } @article{CourniaAllenAndricioaeietal.2015, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and H{\´e}nin, J{\´e}r{\^o}me and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta}, title = {Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory}, volume = {248}, journal = {Journal of Membrane Biology}, number = {4}, doi = {10.1007/s00232-015-9802-0}, pages = {611 -- 640}, year = {2015}, language = {en} } @article{MuecklichWebelAboulfadletal.2014, author = {M{\"u}cklich, Frank and Webel, Johannes and Aboulfadl, Hisham and Lindow, Norbert and Hege, Hans-Christian}, title = {Correlative Tomography - Extraction of Reliable Information with Adequate Resolution from mm Scale Down to Sub-nm Scale}, volume = {20}, journal = {Microsc. Microanal.}, number = {Suppl 3}, doi = {10.1017/S1431927614005911}, pages = {838 -- 839}, year = {2014}, 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{GuentherKuhnHegeetal.2016, author = {G{\"u}nther, Tobias and Kuhn, Alexander and Hege, Hans-Christian and Theisel, Holger}, title = {MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields}, volume = {35}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.12914}, pages = {381 -- 390}, year = {2016}, language = {en} } @inproceedings{SagnolHegeWeiser2016, author = {Sagnol, Guillaume and Hege, Hans-Christian and Weiser, Martin}, title = {Using sparse kernels to design computer experiments with tunable precision}, booktitle = {22nd Intern. Conf. on Computational Statistics - COMPSTAT 2016, Oviedo, Spain, 23-26 August 2016, Proceedings ISBN 978-90-73592-36-0}, pages = {397 -- 408}, year = {2016}, language = {en} } @inproceedings{CoconuHege2017, author = {Coconu, Liviu and Hege, Hans-Christian}, title = {devEyes: Tangible Devices on Augmented Passive Surfaces}, booktitle = {TEI '17 Proceedings of the Eleventh International Conference on Tangible, Embedded, and Embodied Interaction, Yokohama, Japan, March 20 - 23, 2017}, doi = {10.1145/3024969.3025065}, pages = {409 -- 411}, year = {2017}, abstract = {We present a novel approach to turn smartphones/ tablets into tangible near-surface devices with augmented reality (AR) capability on virtually any passive surface, like desks, tables and wallboards. A low-cost optoelectronic add-on for the device back camera enables position tracking on an almost invisible printable fiducial marker grid. This approach is promising in terms of adoption potential because it can be used anywhere with existing devices, requires no dedicated hardware installations and is applicable to a broad range of real-world applications.}, 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{ArltLindowBaumetal.2016, author = {Arlt, Tobias and Lindow, Norbert and Baum, Daniel and Hilger, Andre and Mahnke, Ingo and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Mahnke, Heinz.Eberhard}, title = {Virtual Access to Hidden Texts - Study of Ancient Papyri}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, year = {2016}, abstract = {When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.}, language = {en} } @inproceedings{KuhnHege2017, author = {Kuhn, Alexander and Hege, Hans-Christian}, title = {Object-based visualization and evaluation of cloud-resolving simulations}, booktitle = {Book of Abstracts, SCCS 2017 - Scaling Cascades in Complex Systems, Mar 27-29, 2017, Berlin, Germany}, year = {2017}, abstract = {Recent advances in high-resolution, cloud resolving simulation models pose several challenges towards respective analysis methodologies. To enable efficient comparison and validation of such models efficient, scalable, and informative diagnostic procedures are mandatory. In this talk, an object-based evaluation scheme based on the notion of scalar field topology will be presented. The presentation will cover the application of topological clustering procedures for object identification, tracking, and the retrieval of object-based statistics. The pro-posed methodology is shown to enable an advanced in-depth evaluation and visualization of high cloud-resolving models. Using a newly developed large-scale high-resolution model (i.e., HD(CP)2 ICON), it will be demonstrated that the presented procedures are applicable to assess the model performance compared to measurements (e.g., radar, satellite) and standard operational models (COSMO) at different domains and spatial scales.}, 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} }