@inproceedings{PoethkeGoubergritsKertzscheretal.2008, author = {Poethke, Jens and Goubergrits, Leonid and Kertzscher, Ulrich and Spuler, Andreas and Petz, Christoph and Hege, Hans-Christian}, title = {Impact of imaging modality for analysis of a cerebral aneurysm: Comparison between CT, MRI and 3DRA}, series = {Proceedings of the 4th European Conference of the International Federation for Medical and Biological Engineering}, booktitle = {Proceedings of the 4th European Conference of the International Federation for Medical and Biological Engineering}, editor = {Jos Vander Sloten, Pascal and Haueisen, Jens}, publisher = {Springer-Verlag}, address = {Antwerp, Belgium}, doi = {10.1007/978-3-540-89208-3}, pages = {1889 -- 1893}, year = {2008}, language = {en} } @article{HellerMatziolisKoenigetal.2007, author = {Heller, Markus O. and Matziolis, Georg and K{\"o}nig, Christian and Taylor, William R. and Hinterwimmer, S. and Graichen, H. and Hege, Hans-Christian and Bergmann, G. and Perka, Carsten and Duda, G. N.}, title = {Muskuloskelettale Biomechanik des Kniegelenks - Grundlagen f{\"u}r die pr{\"a}operative Planung von Umstellung und Gelenkersatz}, series = {Der Orthop{\"a}de}, volume = {36}, journal = {Der Orthop{\"a}de}, number = {7}, doi = {10.1007/s00132-007-1115-2}, pages = {628 -- 634}, year = {2007}, language = {en} } @inproceedings{KaehlerAbelHege2007, author = {K{\"a}hler, Ralf and Abel, Tom and Hege, Hans-Christian}, title = {Simultaneous GPU-Assisted Raycasting of Unstructured Point Sets and Volumetric Grid Data}, series = {Proceedings of IEEE/EG International Symposium on Volume Graphics 2007}, booktitle = {Proceedings of IEEE/EG International Symposium on Volume Graphics 2007}, publisher = {A K Peters}, address = {Prague, Czech Republic}, pages = {49 -- 56}, year = {2007}, language = {en} } @inproceedings{ClasenHege2007, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Clipmap-based Terrain Data Synthesis}, series = {Proc. SimVis 2007}, booktitle = {Proc. SimVis 2007}, editor = {Schulze, Thomas and Preim, Bernhard and Schumann, Heidrun}, publisher = {SCS Publishing House e.V.}, pages = {385 -- 398}, year = {2007}, language = {en} } @inproceedings{ZachowZilskeHege2007, author = {Zachow, Stefan and Zilske, Michael and Hege, Hans-Christian}, title = {3D Reconstruction of Individual Anatomy from Medical Image Data: Segmentation and Geometry Processing}, series = {25. ANSYS Conference \& CADFEM Users' Meeting}, booktitle = {25. ANSYS Conference \& CADFEM Users' Meeting}, address = {Dresden}, year = {2007}, language = {en} } @inproceedings{NeubertLameckerHegeetal.2007, author = {Neubert, Kerstin and Lamecker, Hans and Hege, Hans-Christian and Menzel, Randolf and Rybak, J{\"u}rgen}, title = {Model-based autosegmentation of brain structures in the honeybee using statistical shape models}, series = {Proc. 8th Int. Congr. of Neuroethology (ICN)}, booktitle = {Proc. 8th Int. Congr. of Neuroethology (ICN)}, year = {2007}, language = {en} } @misc{ShiTheiselWeinkaufetal.2007, author = {Shi, Kuangyu and Theisel, Holger and Weinkauf, Tino and Hauser, Helwig and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Extracting separation surfaces of path line oriented topology in periodic 2D time-dependent vector fields}, pages = {75 -- 82}, year = {2007}, language = {en} } @inproceedings{ShiTheiselHauseretal.2009, author = {Shi, Kuangyu and Theisel, Holger and Hauser, Helwig and Weinkauf, Tino and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Path Line Attributes - an Information Visualization Approach to Analyzing the Dynamic Behavior of 3D Time-Dependent Flow Fields}, series = {Topology-Based Methods in Visualization II}, booktitle = {Topology-Based Methods in Visualization II}, publisher = {Springer}, address = {Berlin}, doi = {10.1007/978-3-540-88606-8_6}, pages = {75 -- 88}, year = {2009}, language = {en} } @article{HegeWeinkaufProhaskaetal.2005, author = {Hege, Hans-Christian and Weinkauf, Tino and Prohaska, Steffen and Hutanu, Andrei}, title = {Towards distributed visualization and analysis of large flow data}, series = {JSME International Journal, Series B}, volume = {48 (2)}, journal = {JSME International Journal, Series B}, pages = {241 -- 246}, year = {2005}, language = {en} } @inproceedings{DercksenProhaskaHege2005, author = {Dercksen, Vincent J. and Prohaska, Steffen and Hege, Hans-Christian}, title = {Fast cross-sectional display of large data sets}, series = {IAPR Conference on Machine Vision Applications}, booktitle = {IAPR Conference on Machine Vision Applications}, address = {Tsukuba, Japan}, pages = {336 -- 339}, year = {2005}, 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}, series = {Journal of Comparative Neurology}, volume = {492(1)}, journal = {Journal of Comparative Neurology}, pages = {1 -- 19}, year = {2005}, language = {en} } @inproceedings{WenckebachLameckerHege2005, author = {Wenckebach, Thomas and Lamecker, Hans and Hege, Hans-Christian}, title = {Capturing anatomical shape variability using B-spline registration}, series = {Information Processing in Medical Imaging: 19th International Conference (IPMI 2005)}, volume = {3565/2005}, booktitle = {Information Processing in Medical Imaging: 19th International Conference (IPMI 2005)}, editor = {Christensen, Gary and Sonka, Milan}, publisher = {Springer-Verlag GmbH}, address = {Glenwood Springs, CO, USA}, doi = {10.1007/b137723}, pages = {578 -- 590}, 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}, series = {Visualization in Landscape and Environmental Planning}, 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} } @inproceedings{SchmidtEhrenbergHege2005, author = {Schmidt-Ehrenberg, Johannes and Hege, Hans-Christian}, title = {Visual analysis of molecular conformations by means of a dynamic density mixture model}, series = {Computational Life Sciences: First International Symposium, CompLife 2005}, 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}, series = {Proc. IEEE Visualization 2005}, 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}, series = {Proc. IEEE Visualization 2005}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, pages = {631 -- 638}, year = {2005}, language = {en} } @inproceedings{KussHegeKrofcziketal.2007, author = {Kuß, Anja and Hege, Hans-Christian and Krofczik, Sabine and B{\"o}rner, Jana}, title = {Pipeline for the creation of surface-based averaged brain atlases}, series = {Proceedings of WSCG 2007 - the 15-th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision}, volume = {15}, booktitle = {Proceedings of WSCG 2007 - the 15-th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision}, address = {Plzen, Czech Republic}, pages = {17 -- 24}, year = {2007}, language = {en} } @misc{SahnerWeinkaufTeuberetal.2007, author = {Sahner, Jan and Weinkauf, Tino and Teuber, Nathalie and Hege, Hans-Christian}, title = {Vortex and strain skeletons in Eulerian and Lagrangian frames}, doi = {10.1109/TVCG.2007.1053}, pages = {980 -- 990}, year = {2007}, language = {en} } @incollection{WeinkaufTheiselHegeetal.2007, author = {Weinkauf, Tino and Theisel, Holger and Hege, Hans-Christian and Seidel, Hans-Peter}, title = {Feature Flow Fields in Out-of-Core Settings}, series = {Topology-based Methods in Visualization}, booktitle = {Topology-based Methods in Visualization}, publisher = {Springer}, pages = {51 -- 64}, year = {2007}, language = {en} } @article{WeinkaufSahnerTheiseletal.2007, author = {Weinkauf, Tino and Sahner, Jan and Theisel, Holger and Hege, Hans-Christian}, title = {Cores of Swirling Particle Motion in Unsteady Flows}, series = {IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2007)}, volume = {13}, journal = {IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization 2007)}, number = {6}, doi = {10.1109/TVCG.2007.70545}, pages = {1759 -- 1766}, year = {2007}, language = {en} } @inproceedings{GuentherThielePetzetal.2007, author = {G{\"u}nther, Bert and Thiele, Frank and Petz, Ralf and Nitsche, Wolfgang and Sahner, Jan and Weinkauf, Tino and Hege, Hans-Christian}, title = {Control of Separation on the Flap of a Three-Element High-Lift Configuration}, series = {45th AIAA Aerospace Sciences Meeting and Exhibit}, booktitle = {45th AIAA Aerospace Sciences Meeting and Exhibit}, address = {Reno, NV, U.S.A.}, year = {2007}, 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}, series = {Active Flow Control}, 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{ClasenHege2006, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Terrain rendering using spherical clipmaps}, series = {EuroVis 2006 - Eurographics / IEEE VGTC Symposium on Visualization}, 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}, series = {Bildverarbeitung f{\"u}r die Medizin 2006: Algorithmen - Systeme - Anwendungen}, 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}, series = {Proc. Eurographics / IEEE VGTC Symposium on Visualization}, 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}, series = {Computer Graphics Forum}, 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}, series = {NPAR '06: Proceedings of the 3rd International Symposium on Non-photorealistic Animation and Rendering}, 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} } @article{LameckerZachowWittmersetal.2006, author = {Lamecker, Hans and Zachow, Stefan and Wittmers, Antonia and Weber, Britta and Hege, Hans-Christian and Elsholtz, Barbara and Stiller, Michael}, title = {Automatic segmentation of mandibles in low-dose CT-data}, series = {Int. J. Computer Assisted Radiology and Surgery}, volume = {1(1)}, journal = {Int. J. Computer Assisted Radiology and Surgery}, pages = {393 -- 395}, year = {2006}, language = {en} } @article{LameckerZachowHegeetal.2006, author = {Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian and Z{\"o}ckler, Maja}, title = {Surgical treatment of craniosynostosis based on a statistical 3D-shape model}, series = {Int. J. Computer Assisted Radiology and Surgery}, volume = {1(1)}, journal = {Int. J. Computer Assisted Radiology and Surgery}, doi = {10.1007/s11548-006-0024-x}, pages = {253 -- 254}, year = {2006}, language = {en} } @inproceedings{BengerHege2006, author = {Benger, Werner and Hege, Hans-Christian}, title = {Analysing curved spacetimes with tensor splats}, series = {Proceedings of the Tenth Marcel Grossmann Meeting in Theoretical and Experimental General Relativity, Gravitation and Relativistic Field Theories}, volume = {3}, booktitle = {Proceedings of the Tenth Marcel Grossmann Meeting in Theoretical and Experimental General Relativity, Gravitation and Relativistic Field Theories}, publisher = {World Scientific}, address = {Singapore}, doi = {10.1142/9789812704030_0164}, pages = {1619 -- 1624}, year = {2006}, language = {en} } @article{BengerHege2006, author = {Benger, Werner and Hege, Hans-Christian}, title = {Strategies for direct visualization of second-rank tensor fields}, series = {Visualization and Processing of Tensor Fields}, journal = {Visualization and Processing of Tensor Fields}, publisher = {Springer Verlag}, doi = {10.1007/3-540-31272-2_11}, pages = {191 -- 214}, year = {2006}, language = {en} } @article{ZachowHegeDeuflhard2006, author = {Zachow, Stefan and Hege, Hans-Christian and Deuflhard, Peter}, title = {Computer assisted planning in cranio-maxillofacial surgery}, series = {Journal of Computing and Information Technology}, volume = {14(1)}, journal = {Journal of Computing and Information Technology}, pages = {53 -- 64}, year = {2006}, language = {en} } @article{BengerBartschHegeetal.2006, author = {Benger, Werner and Bartsch, Hauke and Hege, Hans-Christian and Kitzler, Hagen and Shumilina, Anna and Werner, Annett}, title = {Visualizing neuronal structures in the human brain via Diffusion Tensor MRI}, series = {Int. Journal of Neuroscience}, volume = {116(4)}, journal = {Int. Journal of Neuroscience}, pages = {461 -- 514}, year = {2006}, language = {en} } @article{MayeWenckebachHege2006, author = {Maye, Alexander and Wenckebach, Thomas and Hege, Hans-Christian}, title = {Visualization, reconstruction, and integration of neuronal structures in digital brain atlases}, series = {Int. Journal of Neuroscience}, volume = {116(4)}, journal = {Int. Journal of Neuroscience}, pages = {431 -- 459}, year = {2006}, 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?}, series = {DFN-Mitteilungen}, 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} } @inproceedings{SahnerWeinkaufHege2005, author = {Sahner, Jan and Weinkauf, Tino and Hege, Hans-Christian}, title = {Galilean invariant extraction and iconic representation of vortex core lines}, series = {Proc. Eurographics / IEEE VGTC Symposium on Visualization (EuroVis '05)}, 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}, series = {Proc. IEEE Visualization 2005}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, pages = {559 -- 566}, 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}, series = {Trends in Real-Time Landscape Visualization and Participation}, 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}, series = {Trends in Real-Time Landscape Visualization and Participation}, 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}, series = {Trends in Real-Time Landscape Visualization and Participation}, 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}, series = {Trends in Real-Time Landscape Visualization and Participation}, 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{Hege, author = {Hege, Hans-Christian}, title = {Visual analysis of molecular dynamics data using geometric and topological methods}, series = {Forum "Math for Industry" 2014}, volume = {57}, booktitle = {Forum "Math for Industry" 2014}, publisher = {Institute of Mathematics for Industry, Kyushu University}, address = {Fukuoka, Japan}, pages = {45 -- 46}, 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}, series = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable 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{GoubergritsSchallerKertzscheretal., 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}, series = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, volume = {74}, journal = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, number = {5}, doi = {10.1055/s-0033-1342937}, pages = {294 -- 302}, 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}, series = {IEEE Transactions on Visualization and Computer Graphics}, 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}, series = {Computer Graphics Forum}, 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., 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}, series = {Journal of Biomechanics}, volume = {45, Suppl. 1}, booktitle = {Journal of Biomechanics}, doi = {10.1016/S0021-9290(12)70359-7}, pages = {S358}, 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}, series = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization}, 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}, 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} } @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}, series = {The International Journal of Artificial Organs}, 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{StoppelHegeWiebel, author = {Stoppel, Sergej and Hege, Hans-Christian and Wiebel, Alexander}, title = {Visibility-driven depth determination of surface patches in direct volume rendering}, series = {EuroVis - Short Papers 2014}, booktitle = {EuroVis - Short Papers 2014}, doi = {10.2312/eurovisshort.20141164}, pages = {97 -- 101}, 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{GoubergritsHellmeierBrueningetal., author = {Goubergrits, Leonid and Hellmeier, Florian and Bruening, Jan Joris and Spuler, Andreas and Hege, Hans-Christian and Voss, Samuel and Janiga, G{\´a}bor and Saalfeld, Sylvia and Beuing, Oliver and Berg, Philipp}, title = {Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters}, series = {BioMedical Engineering OnLine}, volume = {18}, journal = {BioMedical Engineering OnLine}, number = {35}, doi = {10.1186/s12938-019-0657-y}, abstract = {Background Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures. Materials 26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values. Results A large variability of relative uncertainties in the range between 3.9 and 179.8\% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6\% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80\% were found for some curvature parameters. Conclusions Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models.}, language = {en} } @article{FroehlerElberfeldMoelleretal., author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and Weissenb{\"o}ck, Johannes and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science}, series = {Computer Graphics Forum}, volume = {38}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.13688}, pages = {273 -- 283}, abstract = {We present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list-based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber-reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well-considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis-)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis.}, language = {en} } @misc{NavaYazdaniHegevonTycowicz, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Geodesic Mixed Effects Model in Kendall's Shape Space}, series = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, journal = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74621}, abstract = {In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and apply the approach for the estimation of group trends and statistical testing of 3D shapes derived from an open access longitudinal imaging study on osteoarthritis.}, language = {en} } @inproceedings{HanikHegevonTycowicz, author = {Hanik, Martin and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {Bi-invariant Two-Sample Tests in Lie Groups for Shape Analysis}, series = {Shape in Medical Imaging}, booktitle = {Shape in Medical Imaging}, publisher = {Springer International Publishing}, address = {Cham}, doi = {10.1007/978-3-030-61056-2_4}, pages = {44 -- 54}, abstract = {We propose generalizations of the T²-statistics of Hotelling and the Bhattacharayya distance for data taking values in Lie groups. A key feature of the derived measures is that they are compatible with the group structure even for manifolds that do not admit any bi-invariant metric. This property, e.g., assures analysis that does not depend on the reference shape, thus, preventing bias due to arbitrary choices thereof. Furthermore, the generalizations agree with the common definitions for the special case of flat vector spaces guaranteeing consistency. Employing a permutation test setup, we further obtain nonparametric, two-sample testing procedures that themselves are bi-invariant and consistent. We validate our method in group tests revealing significant differences in hippocampal shape between individuals with mild cognitive impairment and normal controls.}, language = {en} } @inproceedings{HanikHegeHennemuthetal., author = {Hanik, Martin and Hege, Hans-Christian and Hennemuth, Anja and von Tycowicz, Christoph}, title = {Nonlinear Regression on Manifolds for Shape Analysis using Intrinsic B{\´e}zier Splines}, series = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI)}, booktitle = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI)}, publisher = {Springer International Publishing}, address = {Cham}, doi = {10.1007/978-3-030-59719-1_60}, pages = {617 -- 626}, abstract = {Intrinsic and parametric regression models are of high interest for the statistical analysis of manifold-valued data such as images and shapes. The standard linear ansatz has been generalized to geodesic regression on manifolds making it possible to analyze dependencies of random variables that spread along generalized straight lines. Nevertheless, in some scenarios, the evolution of the data cannot be modeled adequately by a geodesic. We present a framework for nonlinear regression on manifolds by considering Riemannian splines, whose segments are B{\´e}zier curves, as trajectories. Unlike variational formulations that require time-discretization, we take a constructive approach that provides efficient and exact evaluation by virtue of the generalized de Casteljau algorithm. We validate our method in experiments on the reconstruction of periodic motion of the mitral valve as well as the analysis of femoral shape changes during the course of osteoarthritis, endorsing B{\´e}zier spline regression as an effective and flexible tool for manifold-valued regression.}, language = {en} } @article{NavaYazdaniHegeSullivanetal., author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and Sullivan, T. J. and von Tycowicz, Christoph}, title = {Geodesic Analysis in Kendall's Shape Space with Epidemiological Applications}, series = {Journal of Mathematical Imaging and Vision}, volume = {62}, journal = {Journal of Mathematical Imaging and Vision}, number = {4}, doi = {10.1007/s10851-020-00945-w}, pages = {549 -- 559}, abstract = {We analytically determine Jacobi fields and parallel transports and compute geodesic regression in Kendall's shape space. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and thereby reduce the computational expense by several orders of magnitude over common, nonlinear constrained approaches. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As an example application we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative (OAI). Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data alone.}, language = {en} } @inproceedings{NavaYazdaniHegevonTycowicz, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Geodesic Mixed Effects Model in Kendall's Shape Space}, series = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, volume = {11846}, booktitle = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, doi = {10.1007/978-3-030-33226-6_22}, pages = {209 -- 218}, abstract = {In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and apply the approach for the estimation of group trends and statistical testing of 3D shapes derived from an open access longitudinal imaging study on osteoarthritis.}, language = {en} } @article{AgudoJacomeHegePaetschetal., author = {Agudo J{\´a}come, Leonardo and Hege, Hans-Christian and Paetsch, Olaf and P{\"o}thkow, Kai}, title = {Three-dimensional reconstruction and quantification of dislocation substructures from transmission electron microscopy stereo pairs}, series = {Ultramicroscopy}, volume = {195}, journal = {Ultramicroscopy}, doi = {10.1016/j.ultramic.2018.08.015}, pages = {157 -- 170}, abstract = {A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (>300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3\% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed.}, language = {en} } @inproceedings{PapazovHege, author = {Papazov, Chavdar and Hege, Hans-Christian}, title = {Blue-noise Optimized Point Sets Based on Procrustes Analysis}, series = {SIGGRAPH Asia 2017 Technical Briefs}, booktitle = {SIGGRAPH Asia 2017 Technical Briefs}, doi = {10.1145/3145749.3149442}, pages = {20:1 -- 20:4}, language = {en} } @article{OeltzeJaffraMeuschkeNeugebaueretal., author = {Oeltze-Jaffra, Steffen and Meuschke, Monique and Neugebauer, Mathias and Saalfeld, Sylvia and Lawonn, Kai and Janiga, Gabor and Hege, Hans-Christian and Zachow, Stefan and Preim, Bernhard}, title = {Generation and Visual Exploration of Medical Flow Data: Survey, Research Trends, and Future Challenges}, series = {Computer Graphics Forum}, volume = {38}, journal = {Computer Graphics Forum}, number = {1}, publisher = {Wiley}, doi = {10.1111/cgf.13394}, pages = {87 -- 125}, abstract = {Simulations and measurements of blood and air flow inside the human circulatory and respiratory system play an increasingly important role in personalized medicine for prevention, diagnosis, and treatment of diseases. This survey focuses on three main application areas. (1) Computational Fluid Dynamics (CFD) simulations of blood flow in cerebral aneurysms assist in predicting the outcome of this pathologic process and of therapeutic interventions. (2) CFD simulations of nasal airflow allow for investigating the effects of obstructions and deformities and provide therapy decision support. (3) 4D Phase-Contrast (4D PC) Magnetic Resonance Imaging (MRI) of aortic hemodynamics supports the diagnosis of various vascular and valve pathologies as well as their treatment. An investigation of the complex and often dynamic simulation and measurement data requires the coupling of sophisticated visualization, interaction, and data analysis techniques. In this paper, we survey the large body of work that has been conducted within this realm. We extend previous surveys by incorporating nasal airflow, addressing the joint investigation of blood flow and vessel wall properties, and providing a more fine-granular taxonomy of the existing techniques. From the survey, we extract major research trends and identify open problems and future challenges. The survey is intended for researchers interested in medical flow but also more general, in the combined visualization of physiology and anatomy, the extraction of features from flow field data and feature-based visualization, the visual comparison of different simulation results, and the interactive visual analysis of the flow field and derived characteristics.}, language = {en} } @misc{SakuraiHegeKuhnetal., author = {Sakurai, Daisuke and Hege, Hans-Christian and Kuhn, Alexander and Rust, Henning and Kern, Bastian and Breitkopf, Tom-Lukas}, title = {An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-72617}, abstract = {In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features - which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data.}, language = {en} } @inproceedings{FroehlerdaCunhaMeloWeissenboecketal., author = {Fr{\"o}hler, Bernhard and da Cunha Melo, Lucas and Weissenb{\"o}ck, Johannes and Kastner, Johann and M{\"o}ller, Torsten and Hege, Hans-Christian and Gr{\"o}ller, Eduard M. and Sanctorum, Jonathan and De Beenhouwer, Jan and Sijbers, Jan and Heinzl, Christoph}, title = {Tools for the analysis of datasets from X-ray computed tomography based on Talbot-Lau grating interferometry}, series = {Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy - iCT 2019, February 13-15, 2019)}, booktitle = {Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy - iCT 2019, February 13-15, 2019)}, number = {paper 52}, pages = {8}, abstract = {This work introduces methods for analyzing the three imaging modalities delivered by Talbot-Lau grating interferometry X-ray computed tomography (TLGI-XCT). The first problem we address is providing a quick way to show a fusion of all three modal- ities. For this purpose the tri-modal transfer function widget is introduced. The widget controls a mixing function that uses the output of the transfer functions of all three modalities, allowing the user to create one customized fused image. A second problem prevalent in processing TLGI-XCT data is a lack of tools for analyzing the segmentation process of such multimodal data. We address this by providing methods for computing three types of uncertainty: From probabilistic segmentation algorithms, from the voxel neighborhoods as well as from a collection of results. We furthermore introduce a linked views interface to explore this data. The techniques are evaluated on a TLGI-XCT scan of a carbon-fiber reinforced dataset with impact damage. We show that the transfer function widget accelerates and facilitates the exploration of this dataset, while the uncertainty analysis methods give insights into how to tweak and improve segmentation algorithms for more suitable results.}, language = {en} } @inproceedings{CoconuUllmerPaaretal.2018, author = {Coconu, Liviu and Ullmer, Brygg and Paar, Philip and Liu, Jing and Konkel, Miriam and Hege, Hans-Christian}, title = {A smartphone-based tangible interaction approach for landscape visualization.}, series = {PerDis '18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, booktitle = {PerDis '18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/3205873.3210707}, pages = {no. 23}, year = {2018}, abstract = {The use of tangible interfaces for navigation of landscape scenery - for example, lost places re-created in 3D - has been pursued and articulated as a promising, impactful application of interactive visualization. In this demonstration, we present a modern, low-cost implementation of a previously-realized multimodal gallery installation. Our demonstration centers upon the versatile usage of a smartphone for sensing, navigating, and (optionally) displaying element on a physical surface in tandem with a larger, more immersive display.}, language = {en} } @inproceedings{UllmerPaarCoconuetal.2018, author = {Ullmer, Brygg and Paar, Philip and Coconu, Liviu and Liu, Jing and Konkel, Miriam and Hege, Hans-Christian}, title = {An 1834 mediterranean garden in Berlin - engaged from 2004, 2018, 2032, and 2202}, series = {PerDis '18 - 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, booktitle = {PerDis '18 - 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018}, publisher = {ACM}, address = {New York, NY, USA}, doi = {10.1145/3205873.3205894}, pages = {no. 12}, year = {2018}, abstract = {In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as "italienisches Kunstst{\"u}ck" (Italian legerdemain) by Peter Joseph Lenn{\´e}. The park was originally realized on the grounds of Schloss Sanssouci in Potsdam, Germany. The installation centered on highly detailed renderings of hundreds of plants projected upon a panoramic display. Interactivity was expressed with a tangible interface which (while presently dated) we believe remains without near-precedent then or since. We present the installation (experienced by roughly 20,000 visitors), focusing on the interaction aspects. We introduce new book and table/door-format mockups. Drawing upon a heuristic of the scientist-philosopher Freeman Dyson, we consider grounded future prospect variations in the contexts of 2018, 2032, and 2202. We see this exercise as prospectively generalizing to a variety of similar and widely diverse application domains.}, language = {en} } @misc{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-68468}, abstract = {In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.}, language = {en} } @inproceedings{LindowBaumHege, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Atomic Accessibility Radii for Molecular Dynamics Analysis}, series = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, booktitle = {Workshop on Molecular Graphics and Visual Analysis of Molecular Data}, publisher = {The Eurographics Association}, isbn = {978-3-03868-061-1}, doi = {10.2312/molva.20181101}, abstract = {In molecular structure analysis and visualization, the molecule's atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius', that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely.}, language = {en} } @misc{LindowBaumLeborgneetal., author = {Lindow, Norbert and Baum, Daniel and Leborgne, Morgan and Hege, Hans-Christian}, title = {Interactive Visualization of RNA and DNA Structures}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69704}, abstract = {The analysis and visualization of nucleic acids (RNA and DNA) play an increasingly important role due to the growing number of known 3-dimensional structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. For the first time, we present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.}, language = {en} } @article{LindowBaumLeborgneetal., author = {Lindow, Norbert and Baum, Daniel and Leborgne, Morgan and Hege, Hans-Christian}, title = {Interactive Visualization of RNA and DNA Structures}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {25}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {1}, doi = {10.1109/TVCG.2018.2864507}, pages = {967 -- 976}, abstract = {The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization.}, language = {en} } @misc{AgudoJacomeHegePaetschetal., author = {Agudo J{\´a}come, Leonardo and Hege, Hans-Christian and Paetsch, Olaf and P{\"o}thkow, Kai}, title = {Three-Dimensional Reconstruction and Quantification of Dislocation Substructures from Transmission Electron Microscopy Stereo-Pairs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70339}, abstract = {A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 \% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed.}, language = {en} } @misc{EhlkeRammLameckeretal., author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, language = {en} } @misc{NavaYazdaniHegevonTycowiczetal., author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph and Sullivan, T. J.}, title = {A Shape Trajectories Approach to Longitudinal Statistical Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-69759}, abstract = {For Kendall's shape space we determine analytically Jacobi fields and parallel transport, and compute geodesic regression. Using the derived expressions, we can fully leverage the geometry via Riemannian optimization and reduce the computational expense by several orders of magnitude. The methodology is demonstrated by performing a longitudinal statistical analysis of epidemiological shape data. As application example we have chosen 3D shapes of knee bones, reconstructed from image data of the Osteoarthritis Initiative. Comparing subject groups with incident and developing osteoarthritis versus normal controls, we find clear differences in the temporal development of femur shapes. This paves the way for early prediction of incident knee osteoarthritis, using geometry data only.}, language = {en} } @misc{GuentherKuhnHegeetal., 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}, issn = {1438-0064}, doi = {10.1111/cgf.12914}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59054}, abstract = {Traditionally, Lagrangian fields such as finite-time Lyapunov exponents (FTLE) are precomputed on a discrete grid and are ray casted afterwards. This, however, introduces both grid discretization errors and sampling errors during ray marching. In this work, we apply a progressive, view-dependent Monte Carlo-based approach for the visualization of such Lagrangian fields in time-dependent flows. Our ap- proach avoids grid discretization and ray marching errors completely, is consistent, and has a low memory consumption. The system provides noisy previews that con- verge over time to an accurate high-quality visualization. Compared to traditional approaches, the proposed system avoids explicitly predefined fieldline seeding structures, and uses a Monte Carlo sampling strategy named Woodcock tracking to distribute samples along the view ray. An acceleration of this sampling strategy requires local upper bounds for the FTLE values, which we progressively acquire during the rendering. Our approach is tailored for high-quality visualizations of complex FTLE fields and is guaranteed to faithfully represent detailed ridge surface structures as indicators for Lagrangian coherent structures (LCS). We demonstrate the effectiveness of our approach by using a set of analytic test cases and real-world numerical simulations.}, language = {en} } @misc{KuhnEngelkeFlatkenetal., 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}, issn = {1438-0064}, doi = {10.1007/978-3-319-44684-4_2}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57043}, abstract = {Many scientific applications deal with data from a multitude of different sources, e.g., measurements, imaging and simulations. Each source provides an additional perspective on the phenomenon of interest, but also comes with specific limitations, e.g. regarding accuracy, spatial and temporal availability. Effectively combining and analyzing such multimodal and partially incomplete data of limited accuracy in an integrated way is challenging. In this work, we outline an approach for an integrated analysis and visualization of the atmospheric impact of volcano eruptions. The data sets comprise observation and imaging data from satellites as well as results from numerical particle simulations. To analyze the clouds from the volcano eruption in the spatiotemporal domain we apply topological methods. Extremal structures reveal structures in the data that support clustering and comparison. We further discuss the robustness of those methods with respect to different properties of the data and different parameter setups. Finally we outline open challenges for the effective integrated visualization using topological methods.}, language = {en} } @misc{WiebelVosHege, author = {Wiebel, Alexander and Vos, Frans M. and Hege, Hans-Christian}, title = {Perception-Oriented Picking of Structures in Direct Volumetric Renderings}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-14343}, number = {11-45}, abstract = {Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques.}, language = {en} } @misc{BaumLindowHegeetal., author = {Baum, Daniel and Lindow, Norbert and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Kutz, Frank and Mahlow, Kristin and Mahnke, Heinz-Eberhard}, title = {Revealing hidden text in rolled and folded papyri}, issn = {1438-0064}, doi = {10.1007/s00339-017-0808-6}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-61826}, abstract = {Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds.}, language = {en} } @misc{PapazovHege, author = {Papazov, Chavdar and Hege, Hans-Christian}, title = {Blue-noise Optimized Point Sets Based on Procrustes Analysis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-65356}, abstract = {In this paper, we propose a new method for optimizing the blue noise characteristics of point sets. It is based on Procrustes analysis, a technique for adjusting shapes to each other by applying optimal elements of an appropriate transformation group. We adapt this technique to the problem at hand and introduce a very simple, efficient and provably convergent point set optimizer.}, language = {en} } @misc{KlindtBaumProhaskaetal., author = {Klindt, Marco and Baum, Daniel and Prohaska, Steffen and Hege, Hans-Christian}, title = {iCon.text - a customizable iPad app for kiosk applications in museum exhibitions}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-17731}, abstract = {We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar. The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage. The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer. The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".}, language = {en} } @misc{EggerDercksenUdvaryetal., 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}, 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} } @misc{DercksenHegeOberlaender2013, author = {Dercksen, Vincent J. and Hege, Hans-Christian and Oberlaender, Marcel}, title = {The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology}, issn = {1438-0064}, doi = {10.1007/s12021-013-9213-2}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43157}, year = {2013}, abstract = {Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named 'Filament Editor', for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator.}, language = {en} } @misc{StoppelHegeWiebel, 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}, 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{WiebelPreisVosetal., author = {Wiebel, Alexander and Preis, Philipp and Vos, Frans M. and Hege, Hans-Christian}, title = {Computation and Application of 3D Strokes on Visible Structures in Direct Volume Rendering}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-18070}, abstract = {In this paper we describe VisiTrace, a novel technique to draw 3D lines in 3D volume rendered images. It allows to draw strokes in the 2D space of the screen to produce 3D lines that run on top or in the center of structures actually visible in the volume rendering. It can handle structures that only shortly occlude the structure that has been visible at the starting point of the stroke and is able to ignore such structures. For this purpose a shortest path algorithm finding the optimal curve in a specially designed graph data structure is employed. We demonstrate the usefulness of the technique by applying it to MRI data from medicine and engineering, and show how the method can be used to mark or analyze structures in the example data sets, and to automatically obtain good views toward the selected structures.}, language = {en} } @article{MahnkeArltBaumetal., author = {Mahnke, Heinz-Eberhard and Arlt, Tobias and Baum, Daniel and Hege, Hans-Christian and Herter, Felix and Lindow, Norbert and Manke, Ingo and Siopi, Tzulia and Menei, Eve and Etienne, Marc and Lepper, Verena}, title = {Virtual unfolding of folded papyri}, series = {Journal of Cultural Heritage}, volume = {41}, journal = {Journal of Cultural Heritage}, publisher = {Elsevier}, doi = {10.1016/j.culher.2019.07.007}, pages = {264 -- 269}, abstract = {The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Mus{\´e}e du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for "Lord".}, language = {en} } @misc{MahnkeArltBaumetal., author = {Mahnke, Heinz-Eberhard and Arlt, Tobias and Baum, Daniel and Hege, Hans-Christian and Herter, Felix and Lindow, Norbert and Manke, Ingo and Siopi, Tzulia and Menei, Eve and Etienne, Marc and Lepper, Verena}, title = {Virtual unfolding of folded papyri}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74338}, abstract = {The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Mus{\´e}e du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for "Lord".}, language = {en} } @misc{HoerthBaumKnoeteletal., 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}, 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} } @article{WilliePapPerkaetal., 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}, series = {Zeitschrift f{\"u}r Rheumatologie}, volume = {74}, journal = {Zeitschrift f{\"u}r Rheumatologie}, doi = {10.1007/s00393-014-1561-2}, pages = {618 -- 621}, 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} } @article{WilliePapPerkaetal., 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 of joints and its role in osteoarthritis - Towards understanding and preventing progression of primary osteoarthritis}, series = {Zeitschrift f{\"u}r Rheumatologie}, volume = {76}, journal = {Zeitschrift f{\"u}r Rheumatologie}, number = {Suppl. 1}, doi = {10.1007/s00393-014-1561-2}, pages = {1 -- 4}, abstract = {Intact joints are necessary for skeletal function and mobility in daily life. A healthy musculoskeletal system is the basis for a functional cardiovascular system as well as an intact immune system. Locomotion, physiotherapy, and various forms of patient activity are essential clinical therapies used in the treatment of neurodegeneration, stroke, diabetes, and cancer. Mobility is substantially impaired with degeneration of joints and, in advanced stages, nighttime pain and sleep disturbance are particularly cumbersome. Osteoarthritis (OA) is also known as degenerative joint disease. OA involves structural and compositional changes in the articular cartilage, as well as in the calcified cartilage, subchondral cortical bone, subchondral cancellous bone, meniscus, joint capsular tissue, and synovium; which eventually lead to degeneration of these tissues comprising synovial joints.}, language = {en} } @inproceedings{KraemerHerrmannBoethetal., 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}, series = {ISMRM (International Society for Magnetic Resonance in Medicine), 23rd Annual Meeting 2015, Toronto, Canada}, booktitle = {ISMRM (International Society for Magnetic Resonance in Medicine), 23rd Annual Meeting 2015, Toronto, Canada}, language = {en} } @inproceedings{CoconuHege2002, author = {Coconu, Liviu and Hege, Hans-Christian}, title = {Hardware-Accelerated Point-Based Rendering of Complex Scenes}, series = {Proceedings of the 13th Eurographics Workshop on Rendering Techniques}, booktitle = {Proceedings of the 13th Eurographics Workshop on Rendering Techniques}, editor = {Gibson, Simon and Debevec, Paul}, address = {Pisa, Italy}, pages = {43 -- 52}, year = {2002}, language = {en} } @article{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, series = {IEEE Transactions on Visualization and Computer Graphics}, journal = {IEEE Transactions on Visualization and Computer Graphics}, doi = {10.1109/TVCG.2023.3243668}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @article{HoerthBaumKnoeteletal., 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}, series = {Connective Tissue Research}, volume = {56}, journal = {Connective Tissue Research}, number = {2}, publisher = {Taylor \& Francis}, doi = {10.3109/03008207.2015.1005210}, pages = {133 -- 143}, language = {en} } @misc{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89932}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @misc{NavaYazdaniHegevonTycowicz, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85187}, abstract = {In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends.}, language = {en} } @article{MikulaDoerffelBaumetal.2022, author = {Mikula, Natalia and D{\"o}rffel, Tom and Baum, Daniel and Hege, Hans-Christian}, title = {An Interactive Approach for Identifying Structure Definitions}, series = {Computer Graphics Forum}, volume = {41}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.14543}, pages = {321 -- 332}, year = {2022}, abstract = {Our ability to grasp and understand complex phenomena is essentially based on recognizing structures and relating these to each other. For example, any meteorological description of a weather condition and explanation of its evolution recurs to meteorological structures, such as convection and circulation structures, cloud fields and rain fronts. All of these are spatiotemporal structures, defined by time-dependent patterns in the underlying fields. Typically, such a structure is defined by a verbal description that corresponds to the more or less uniform, often somewhat vague mental images of the experts. However, a precise, formal definition of the structures or, more generally, concepts is often desirable, e.g., to enable automated data analysis or the development of phenomenological models. Here, we present a systematic approach and an interactive tool to obtain formal definitions of spatiotemporal structures. The tool enables experts to evaluate and compare different structure definitions on the basis of data sets with time-dependent fields that contain the respective structure. Since structure definitions are typically parameterized, an essential part is to identify parameter ranges that lead to desired structures in all time steps. In addition, it is important to allow a quantitative assessment of the resulting structures simultaneously. We demonstrate the use of the tool by applying it to two meteorological examples: finding structure definitions for vortex cores and center lines of temporarily evolving tropical cyclones. Ideally, structure definitions should be objective and applicable to as many data sets as possible. However, finding such definitions, e.g., for the common atmospheric structures in meteorology, can only be a long-term goal. The proposed procedure, together with the presented tool, is just a first systematic approach aiming at facilitating this long and arduous way.}, language = {en} } @article{FroehlerElberfeldMoelleretal., 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}, series = {Nondestructive Testing and Evaluation}, volume = {35}, journal = {Nondestructive Testing and Evaluation}, number = {3}, doi = {10.1080/10589759.2020.1774583}, pages = {328 -- 341}, 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} } @inproceedings{HanikHegevonTycowicz, author = {Hanik, Martin and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Nonlinear Hierarchical Model for Longitudinal Data on Manifolds}, series = {2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)}, booktitle = {2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)}, doi = {10.1109/ISBI52829.2022.9761465}, pages = {1 -- 5}, abstract = {Large longitudinal studies provide lots of valuable information, especially in medical applications. A problem which must be taken care of in order to utilize their full potential is that of correlation between intra-subject measurements taken at different times. For data in Euclidean space this can be done with hierarchical models, that is, models that consider intra-subject and between-subject variability in two different stages. Nevertheless, data from medical studies often takes values in nonlinear manifolds. Here, as a first step, geodesic hierarchical models have been developed that generalize the linear ansatz by assuming that time-induced intra-subject variations occur along a generalized straight line in the manifold. However, this is often not the case (e.g., periodic motion or processes with saturation). We propose a hierarchical model for manifold-valued data that extends this to include trends along higher-order curves, namely B{\´e}zier splines in the manifold. To this end, we present a principled way of comparing shape trends in terms of a functional-based Riemannian metric. Remarkably, this metric allows efficient, yet simple computations by virtue of a variational time discretization requiring only the solution of regression problems. We validate our model on longitudinal data from the osteoarthritis initiative, including classification of disease progression.}, language = {en} } @article{UdvaryHarthMackeetal., author = {Udvary, Daniel and Harth, Philipp and Macke, Jakob H. and Hege, Hans-Christian and de Kock, Christiaan P. J. and Sakmann, Bert and Oberlaender, Marcel}, title = {The Impact of Neuron Morphology on Cortical Network Architecture}, series = {Cell Reports}, volume = {39}, journal = {Cell Reports}, number = {2}, doi = {10.1016/j.celrep.2022.110677}, abstract = {The neurons in the cerebral cortex are not randomly interconnected. This specificity in wiring can result from synapse formation mechanisms that connect neurons depending on their electrical activity and genetically defined identity. Here, we report that the morphological properties of the neurons provide an additional prominent source by which wiring specificity emerges in cortical networks. This morphologically determined wiring specificity reflects similarities between the neurons' axo-dendritic projections patterns, the packing density and cellular diversity of the neuropil. The higher these three factors are the more recurrent is the topology of the network. Conversely, the lower these factors are the more feedforward is the network's topology. These principles predict the empirically observed occurrences of clusters of synapses, cell type-specific connectivity patterns, and nonrandom network motifs. Thus, we demonstrate that wiring specificity emerges in the cerebral cortex at subcellular, cellular and network scales from the specific morphological properties of its neuronal constituents.}, language = {en} } @inproceedings{HarthVohraUdvaryetal., author = {Harth, Philipp and Vohra, Sumit and Udvary, Daniel and Oberlaender, Marcel and Hege, Hans-Christian and Baum, Daniel}, title = {A Stratification Matrix Viewer for Analysis of Neural Network Data}, series = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM)}, address = {Vienna, Austria}, doi = {10.2312/vcbm.20221194}, abstract = {The analysis of brain networks is central to neurobiological research. In this context the following tasks often arise: (1) understand the cellular composition of a reconstructed neural tissue volume to determine the nodes of the brain network; (2) quantify connectivity features statistically; and (3) compare these to predictions of mathematical models. We present a framework for interactive, visually supported accomplishment of these tasks. Its central component, the stratification matrix viewer, allows users to visualize the distribution of cellular and/or connectional properties of neurons at different levels of aggregation. We demonstrate its use in four case studies analyzing neural network data from the rat barrel cortex and human temporal cortex.}, language = {en} } @misc{DercksenOberlaenderSakmannetal.2012, author = {Dercksen, Vincent J. and Oberlaender, Marcel and Sakmann, Bert and Hege, Hans-Christian}, title = {Interactive Visualization - a Key Prerequisite for Reconstruction of Anatomically Realistic Neural Networks}, series = {Visualization in Medicine and Life Sciences II}, journal = {Visualization in Medicine and Life Sciences II}, editor = {Linsen, Lars and Hagen, Hans and Hamann, Bernd and Hege, Hans-Christian}, publisher = {Springer, Berlin}, pages = {27 -- 44}, year = {2012}, language = {en} }