@article{TitschackBaumDePolHolzetal.2015, author = {Titschack, J{\"u}rgen and Baum, Daniel and De Pol-Holz, Ricardo and L{\´o}pez Correa, Matthias and Forster, Nina and Fl{\"o}gel, Sascha and Hebbeln, Dierk and Freiwald, Andr{\´e}}, title = {Aggradation and carbonate accumulation of Holocene Norwegian cold-water coral reefs}, volume = {62}, journal = {Sedimentology}, number = {7}, publisher = {Wiley}, doi = {10.1111/sed.12206}, pages = {1873 -- 1898}, year = {2015}, language = {en} } @article{EggerDercksenUdvaryetal.2014, author = {Egger, Robert and Dercksen, Vincent J. and Udvary, Daniel and Hege, Hans-Christian and Oberlaender, Marcel}, title = {Generation of dense statistical connectomes from sparse morphological data}, volume = {8}, journal = {Frontiers in Neuroanatomy}, number = {129}, doi = {10.3389/fnana.2014.00129}, year = {2014}, language = {en} } @misc{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51194}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @incollection{PfisterKaynigBothaetal.2014, author = {Pfister, Hanspeter and Kaynig, Verena and Botha, Charl P. and Bruckner, Stefan and Dercksen, Vincent J. and Hege, Hans-Christian and Roerdink, Jos B.T.M.}, title = {Visualization in Connectomics}, booktitle = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization}, editor = {Hansen, Charles D. and Chen, Min and Johnson, Christopher R. and Kaufman, Arie E. and Hagen, Hans}, publisher = {Springer}, isbn = {978-1-4471-6496-8}, arxiv = {http://arxiv.org/abs/1206.1428}, doi = {10.1007/978-1-4471-6497-5_21}, pages = {221 -- 245}, year = {2014}, abstract = {Connectomics is a branch of neuroscience that attempts to create a connectome, i.e., a complete map of the neuronal system and all connections between neuronal structures. This representation can be used to understand how functional brain states emerge from their underlying anatomical structures and how dysfunction and neuronal diseases arise. We review the current state-of-the-art of visualization and image processing techniques in the field of connectomics and describe a number of challenges. After a brief summary of the biological background and an overview of relevant imaging modalities, we review current techniques to extract connectivity information from image data at macro-, meso- and microscales. We also discuss data integration and neural network modeling, as well as the visualization, analysis and comparison of brain networks.}, language = {en} } @incollection{BonneauHegeJohnsonetal.2014, author = {Bonneau, Georges-Pierre and Hege, Hans-Christian and Johnson, Chris R. and Oliveira, Manuel M. and Potter, Kristin and Rheingans, Penny and Schultz, Thomas}, title = {Overview and State-of-the-Art of Uncertainty Visualization}, booktitle = {Scientific Visualization - Uncertainty, Multifield, Biomedical, and Scalable Visualization}, publisher = {Springer}, isbn = {978-1-4471-6496-8}, doi = {10.1007/978-1-4471-6497-5_1}, pages = {3 -- 27}, year = {2014}, abstract = {The goal of visualization is to effectively and accurately communicate data. Visualization research has often overlooked the errors and uncertainty which accompany the scientific process and describe key characteristics used to fully understand the data. The lack of these representations can be attributed, in part, to the inherent difficulty in defining, characterizing, and controlling this uncertainty, and in part, to the difficulty in including additional visual metaphors in a well designed, potent display. However, the exclusion of this information cripples the use of visualization as a decision making tool due to the fact that the display is no longer a true representation of the data. This systematic omission of uncertainty commands fundamental research within the visualization community to address, integrate, and expect uncertainty information. In this chapter, we outline sources and models of uncertainty, give an overview of the state-of-the-art, provide general guidelines, outline small exemplary applications, and finally, discuss open problems in uncertainty visualization.}, language = {en} } @phdthesis{Kuhn2013, author = {Kuhn, Alexander}, title = {Lagrangian Methods for Visualization and Analysis of Time-dependent Vector Fields}, url = {http://nbn-resolving.de/urn:nbn:de:gbv:ma9:1-4177}, pages = {179}, year = {2013}, abstract = {Time-dependent vector fields are of high relevance to describe a wide range of physical phenomena based on particle motion, including stall effects in technical engineering, blood flow anomalies, and atmospheric mass trans- port. The efficient analysis and fundamental understanding of intrinsic field properties can lead to significant improvements when interacting with such phenomena based on the available field data. So called Lagrangian methods are a particularly established technique for this purpose. They are based on the evaluation of time-dependent particle trajectories. This work will present an overview of the state of the art in time-dependent vector field analysis and visualization, with special focus on topology-oriented and Lagrangian methods. The first core aspect of this work is the introduction of a novel concept for a more objective and qualitative benchmark of existing Lagrangian approaches. Based on this benchmark, this work contributes and evaluates a set of novel concepts, that offer new perspectives towards established approaches with respect to computational handling, quality and efficiency. The second core aspect is the empirical application and validation of Lagrangian methods with respect to practically relevant analysis scenarios. Each application case includes an introduction into the underlying problem statement and an efficient solution using Lagrangian methods. The validation focuses on the comparison with existing flow analysis concepts and aspects of the quantitative evaluation in each case. Together, both topics of this work contribute towards a more consistent formalization, but also to the improved applicability of Lagrangian methods.}, language = {en} } @misc{OPUS4-5228, title = {Visualization in Medicine and Life Sciences II}, editor = {Linsen, Lars and Hagen, Hans and Hamann, Bernd and Hege, Hans-Christian}, publisher = {Springer}, address = {Berlin}, isbn = {978-3-642-21607-7}, doi = {10.1007/978-3-642-21608-4}, pages = {290}, year = {2012}, language = {en} } @phdthesis{Zoeckler2006, author = {Z{\"o}ckler, Maja}, title = {Modellgebundene Cranioplastie - Operationstechnik zur Umformung fr{\"u}hkindlicher Sch{\"a}deldeformit{\"a}ten unter Verwendung dreidimensionaler Standardformmodelle aus MRT-basierten Rekonstruktionen nicht deformierter Kinder}, year = {2006}, language = {de} } @misc{vonHafePerezFerreiradaSilva2014, type = {Master Thesis}, author = {von Hafe P{\´e}rez Ferreira da Silva, Maria Isabel}, title = {Computational Left-Ventricle Reconstruction from MRI Data for Patient-specific Cardiac Simulations}, pages = {105}, year = {2014}, language = {en} } @phdthesis{Kubiack2013, author = {Kubiack, Kim}, title = {Erstellung eines statistischen Formmodells des Mittelgesichts zur Planung individueller Templates f{\"u}r die navigationsgest{\"u}tzte Rekonstruktion des Mittelgesichtssch{\"a}dels}, year = {2013}, language = {de} } @phdthesis{Hildebrandt2011, author = {Hildebrandt, Thomas}, title = {Das Konzept der Rhinorespiratorischen Hom{\"o}ostase - ein neuer theoretischer Ansatz f{\"u}r die Diskussion physiologischer und physikalischer Zusammenh{\"a}nge bei der Nasenatmung}, year = {2011}, language = {de} } @article{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0113222}, pages = {e113222}, year = {2014}, language = {en} } @article{TodtLameckerRammetal.2014, author = {Todt, Ingo and Lamecker, Hans and Ramm, Heiko and Frenzel, Henning and Wollenberg, Barbara and Beleites, Thomas and Zahnert, Thomas and Thomas, Jan Peter and Dazert, Stefan and Ernst, Arneborg}, title = {Entwicklung eines CT-Daten-basierten Vibrant-Bonebridge-Viewers}, volume = {62}, journal = {HNO}, publisher = {Springer}, doi = {10.1007/s00106-014-2851-3}, pages = {439 -- 442}, year = {2014}, abstract = {Die Positionierung des B-FMT der Vibrant Bonebridge kann aufgrund der anatomischen Verh{\"a}ltnisse des Mastoids und der Gr{\"o}ße des Aktuators ohne eine vorherige Beurteilung der individuellen Computertomographie (CT) des Felsenbeins problematisch sein. Die Entwicklung eines einfach zu bedienenden Viewers, welcher eine Positionierung des B-FMT im Felsenbeinmodell erm{\"o}glicht und hier auf individuelle potenzielle anatomische Konflikte hinweist sowie L{\"o}sungsm{\"o}glichkeiten anbietet, kann ein hilfreiches Werkzeug zur pr{\"a}operativen Positionierung sein. Ziel der Arbeit war die Definition von Anforderungen und die Anfertigung eines Prototyps eines Vibrant-Bonebridge-Viewers. Auf der Basis einer ZIBAmira-Software-Version und der Inklusion eines B-FMT-Modells unter Erstellung eines Felsenbeinmodells, welches die intuitive Beurteilung von Konflikten erm{\"o}glicht, erfolgte die Erstellung des Prototyps eines Vibrant-Bonebridge-Viewers.Ergebnisse. Die Segmentierungszeit der individuellen DICOM-Daten („digital imaging and communications in medicine") betr{\"a}gt etwa 5 min. Eine Positionierung im individuellen 3-D-Felsenbeinmodell erm{\"o}glicht die quantitative und qualitative Beurteilung von Konflikten (Sinus sigmoideus, mittlere Sch{\"a}delgrube) und das Aufsuchen einer bevorzugten Position. Das Anheben des B-FMT mittels virtueller Unterlegscheiben kann simuliert werden. Der erstellte Vibrant-Bonebridge-Viewer erm{\"o}glicht verl{\"a}sslich eine Simulation der B-FMT-Positionierung. Die klinische Anwendbarkeit muss evaluiert werden.}, language = {de} } @article{CampoliBakaKapteinetal.2014, author = {Campoli, Gianni and Baka, Nora and Kaptein, Bart and Valstar, Edward and Zachow, Stefan and Weinans, Harrie and Zadpoor, Amir Abbas}, title = {Relationship between the shape and density distribution of the femur and its natural frequencies of vibration}, volume = {47}, journal = {Journal of Biomechanics}, publisher = {Elsevier}, doi = {10.1016/j.jbiomech.2014.08.008}, pages = {3334 -- 3343}, year = {2014}, abstract = {It has been recently suggested that mechanical loads applied at frequencies close to the natural frequencies of bone could enhance bone apposition due to the resonance phenomenon. Other applications of bone modal analysis are also suggested. For the above-mentioned applications, it is important to understand how patient-specific bone shape and density distribution influence the natural frequencies of bones. We used finite element models to study the effects of bone shape and density distribution on the natural frequencies of the femur in free boundary conditions. A statistical shape and appearance model that describes shape and density distribution independently was created, based on a training set of 27 femora. The natural frequencies were then calculated for different shape modes varied around the mean shape while keeping the mean density distribution, for different appearance modes around the mean density distribution while keeping the mean bone shape, and for the 27 training femora. Single shape or appearance modes could cause up to 15\% variations in the natural frequencies with certain modes having the greatest impact. For the actual femora, shape and density distribution changed the natural frequencies by up to 38\%. First appearance mode that describes the general cortical bone thickness and trabecular bone density had one of the strongest impacts. The first appearance mode could therefore provide a sensitive measure of general bone health and disease progression. Since shape and density could cause large variations in the calculated natural frequencies, patient-specific FE models are needed for accurate estimation of bone natural frequencies.}, language = {en} } @article{TodtLameckerRammetal.2014, author = {Todt, Ingo and Lamecker, Hans and Ramm, Heiko and Ernst, Arneborg}, title = {A computed tomographic data-based vibrant bonebridge visualization tool}, volume = {15}, journal = {Cochlear Implants International}, number = {S1}, doi = {10.1179/1467010014Z.000000000155}, pages = {72 -- 74}, year = {2014}, abstract = {Information about the temporal bone size and variations of anatomical structures are crucial for a safe positioning of the Vibrant Bonebridge B-FMT. A radiological based preoperative planning of the surgical procedure decreases the surgical time and minimizes the risk of complications. We developed a software tool, which allows a catch up of foreign DICOM data based CT temporal bone scans. The individual CT scan is transmitted into a 3D reconstructed pattern of the temporal bone. In this 3D reconstruction the individually favored position of the B- FMT should be found. The software allows a determination of a safe B-FMT position by identifying the individual relation of middle fossa, jugular bulb and external auditory canal. Skull thickness and screw length are contained parameters for the surgical planning. An easy to handle software tool allows a radiologically data based safe and fast surgical positioning of the B-FMT.}, language = {en} } @misc{RedemannWeberMoelleretal.2014, author = {Redemann, Stefanie and Weber, Britta and M{\"o}ller, Marit and Verbavatz, Jean-Marc and Hyman, Anthony and Baum, Daniel and Prohaska, Steffen and M{\"u}ller-Reichert, Thomas}, title = {The Segmentation of Microtubules in Electron Tomograms Using Amira}, journal = {Mitosis: Methods and Protocols}, publisher = {Springer}, doi = {10.1007/978-1-4939-0329-0_12}, pages = {261 -- 278}, year = {2014}, language = {en} } @misc{CostaOstrovskyMantonetal.2015, author = {Costa, Marta and Ostrovsky, Aaron D. and Manton, James D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, journal = {bioRxiv preprint}, doi = {10.1101/006346}, year = {2015}, language = {en} } @misc{Amiranashvili2014, type = {Master Thesis}, author = {Amiranashvili, Tamaz}, title = {Fitting Smooth Strips to Rough Surfaces}, year = {2014}, language = {en} } @masterthesis{Kirschner2013, type = {Bachelor Thesis}, author = {Kirschner, Bruno}, title = {Interaktives Planungstool zur 3D Rekonstruktion von Knochenresektion}, year = {2013}, language = {de} } @article{HochfeldLameckerThomaleetal.2014, author = {Hochfeld, Mascha and Lamecker, Hans and Thomale, Ulrich W. and Schulz, Matthias and Zachow, Stefan and Haberl, Hannes}, title = {Frame-based cranial reconstruction}, volume = {13}, journal = {Journal of Neurosurgery: Pediatrics}, number = {3}, doi = {10.3171/2013.11.PEDS1369}, pages = {319 -- 323}, year = {2014}, abstract = {The authors report on the first experiences with the prototype of a surgical tool for cranial remodeling. The device enables the surgeon to transfer statistical information, represented in a model, into the disfigured bone. The model is derived from a currently evolving databank of normal head shapes. Ultimately, the databank will provide a set of standard models covering the statistical range of normal head shapes, thus providing the required template for any standard remodeling procedure as well as customized models for intended overcorrection. To date, this technique has been used in the surgical treatment of 14 infants (age range 6-12 months) with craniosynostosis. In all 14 cases, the designated esthetic result, embodied by the selected model, has been achieved, without morbidity or mortality. Frame-based reconstruction provides the required tools to precisely realize the surgical reproduction of the model shape. It enables the establishment of a self-referring system, feeding back postoperative growth patterns, recorded by 3D follow-up, into the model design.}, language = {en} } @misc{Sniegula2014, type = {Master Thesis}, author = {Sniegula, Erik}, title = {Histogram-based Visualization and Analysis of Vector Fields using Stream Line Projection Plots}, pages = {71}, year = {2014}, abstract = {Field lines in vector fields, e.g. stream lines, path lines, streak lines or time lines, play an important role in the analysis of vector fields. They improve the classification of flow features and its characteristics in particular. Because of the variety of structural information in field lines the effective processing, analysis and visualization play an important role. More effective techniques may contribute to an improved understanding of struc- tural phenomena in a wide range of applications of vector field visualization, such as gaseous flow (e.g. development of cars and aircrafts), design of machines (e.g. turbines), chemistry (e.g. simulation of molecules) and fluid flow in technical or medical applications (e.g. bloodvessel and ocean simulations). This master thesis focuses on the histogram-based visualization and analysis of vec- tor fields using field line projection plots, stream lines in particular. The goal of this work is to develop a hand full of selection criteria to answer specific applica- tion relevant questions about the characteristics and structures of their vector fields. Therefore we present a powerful analysis tool for vector fields or more precisely for their field lines.}, language = {en} } @article{GoubergritsSpulerSchalleretal.2014, author = {Goubergrits, Leonid and Spuler, Andreas and Schaller, Jens and Wiegmann, Nils and Berthe, Andre and Hege, Hans-Christian and Affeld, Klaus and Kertzscher, Ulrich}, title = {In vitro study of hemodynamic treatment improvement: Hunterian ligation of a fenestrated basilar artery aneurysm after coiling}, volume = {37}, journal = {The International Journal of Artificial Organs}, number = {4}, doi = {10.5301/ijao.5000314}, pages = {325 -- 335}, year = {2014}, abstract = {Hunterian ligation affecting hemodynamics in vessels was proposed to avoid rebleeding in a case of a fenestrated basilar artery aneurysm after incomplete coil occlusion. We studied the hemodynamics in vitro to predict the hemodynamic changes near the aneurysm remnant caused by Hunterian ligation. A transparent model was fabricated based on three-dimensional rotational angiography imaging. Arteries were segmented and reconstructed. Pulsatile flow in the artery segments near the partially occluded (coiled) aneurysm was investigated by means of particle image velocimetry. The hemodynamic situation was investigated before and after Hunterian ligation of either the left or the right vertebral artery (LVA/RVA). Since post-ligation flow rate in the basilar artery was unknown, reduced and retained flow rates were simulated for both ligation options. Flow in the RVA and in the corresponding fenestra vessel is characterized by a vortex at the vertebrobasilar junction, whereas the LVA exhibits undisturbed laminar flow. Both options (RVA or LVA ligation) cause a significant flow reduction near the aneurysm remnant with a retained flow rate. The impact of RVA ligation is, however, significantly higher. This in vitro case study shows that flow reduction near the aneurysm remnant can be achieved by Hunterian ligation and that this effect depends largely on the selection of the ligated vessel. Thus the ability of the proposed in vitro pipe-line to improve hemodynamic impact of the proposed therapy was successfully proved.}, language = {en} } @inproceedings{StoppelHegeWiebel2014, author = {Stoppel, Sergej and Hege, Hans-Christian and Wiebel, Alexander}, title = {Visibility-driven depth determination of surface patches in direct volume rendering}, booktitle = {EuroVis - Short Papers 2014}, doi = {10.2312/eurovisshort.20141164}, pages = {97 -- 101}, year = {2014}, abstract = {This paper presents an algorithm called surfseek for selecting surfaces on the most visible features in direct volume rendering (DVR). The algorithm is based on a previously published technique (WYSIWYP) for picking 3D locations in DVR. The new algorithm projects a surface patch on the DVR image, consisting of multiple rays. For each ray the algorithm uses WYSIWYP or a variant of it to find the candidates for the most visible locations along the ray. Using these candidates the algorithm constructs a graph and computes a minimum cut on this graph. The minimum cut represents a visible and typically rather smooth surface. In the last step the selected surface is displayed. We provide examples for results using artificially generated and real-world data sets.}, language = {en} } @article{LindowBaumHege2014, author = {Lindow, Norbert and Baum, Daniel and Hege, Hans-Christian}, title = {Ligand Excluded Surface: A New Type of Molecular Surface}, volume = {20}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2014.2346404}, pages = {2486 -- 2495}, year = {2014}, abstract = {The most popular molecular surface in molecular visualization is the solvent excluded surface (SES). It provides information about the accessibility of a biomolecule for a solvent molecule that is geometrically approximated by a sphere. During a period of almost four decades, the SES has served for many purposes - including visualization, analysis of molecular interactions and the study of cavities in molecular structures. However, if one is interested in the surface that is accessible to a molecule whose shape differs significantly from a sphere, a different concept is necessary. To address this problem, we generalize the definition of the SES by replacing the probe sphere with the full geometry of the ligand defined by the arrangement of its van der Waals spheres. We call the new surface ligand excluded surface (LES) and present an efficient, grid-based algorithm for its computation. Furthermore, we show that this algorithm can also be used to compute molecular cavities that could host the ligand molecule. We provide a detailed description of its implementation on CPU and GPU. Furthermore, we present a performance and convergence analysis and compare the LES for several molecules, using as ligands either water or small organic molecules.}, language = {en} } @masterthesis{Zoufahl2012, type = {Bachelor Thesis}, author = {Zoufahl, Andre}, title = {Explorative Analysis of Vortex Structures in 2D Flows}, year = {2012}, language = {en} } @misc{Bressler2012, type = {Master Thesis}, author = {Bressler, David}, title = {Pattern Analysis for Flow Visualization}, year = {2012}, language = {en} } @misc{Stoppel2013, type = {Master Thesis}, author = {Stoppel, Sergej}, title = {Visibility-Driven Depth Determination of Surface Patches in Direct Volume Rendering}, year = {2013}, language = {en} } @article{GoubergritsSchallerKertzscheretal.2013, author = {Goubergrits, Leonid and Schaller, Jens and Kertzscher, Ulrich and Petz, Christoph and Hege, Hans-Christian and Spuler, Andreas}, title = {Reproducibility of Image-Based Analysis of Cerebral Aneurysm Geometry and Hemodynamics: An In-Vitro Study of Magnetic Resonance Imaging, Computed Tomography, and Three-Dimensional Rotational Angiography}, volume = {74}, journal = {Journal of Neurological Surgery, Part A: Central European Neurosurgery}, number = {5}, doi = {10.1055/s-0033-1342937}, pages = {294 -- 302}, year = {2013}, language = {en} } @article{SipsKothurUngeretal.2012, author = {Sips, Mike and Kothur, Patrick and Unger, Andrea and Hege, Hans-Christian and Dransch, Doris}, title = {A Visual Analytics Approach to Multiscale Exploration of Environmental Time Series}, volume = {18}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, doi = {10.1109/TVCG.2012.191}, pages = {2899 -- 2907}, year = {2012}, abstract = {We present a Visual Analytics approach that addresses the detection of interesting patterns in numerical time series, specifically from environmental sciences. Crucial for the detection of interesting temporal patterns are the time scale and the starting points one is looking at. Our approach makes no assumption about time scale and starting position of temporal patterns and consists of three main steps: an algorithm to compute statistical values for all possible time scales and starting positions of intervals, visual identification of potentially interesting patterns in a matrix visualization, and interactive exploration of detected patterns. We demonstrate the utility of this approach in two scientific scenarios and explain how it allowed scientists to gain new insight into the dynamics of environmental systems.}, language = {en} } @article{WeinkaufHegeTheisel2012, author = {Weinkauf, Tino and Hege, Hans-Christian and Theisel, Holger}, title = {Advected Tangent Curves: A General Scheme for Characteristic Curves of Flow Fields}, volume = {31}, journal = {Computer Graphics Forum}, number = {2pt4}, doi = {10.1111/j.1467-8659.2012.03063.x}, pages = {825 -- 834}, year = {2012}, abstract = {We present the first general scheme to describe all four types of characteristic curves of flow fields - stream, path, streak, and time lines - as tangent curves of a derived vector field. Thus, all these lines can be obtained by a simple integration of an autonomous ODE system. Our approach draws on the principal ideas of the recently introduced tangent curve description of streak lines. We provide the first description of time lines as tangent curves of a derived vector field, which could previously only be constructed in a geometric manner. Furthermore, our scheme gives rise to new types of curves. In particular, we introduce advected stream lines as a parameter-free variant of the time line metaphor. With our novel mathematical description of characteristic curves, a large number of feature extraction and analysis tools becomes available for all types of characteristic curves, which were previously only available for stream and path lines. We will highlight some of these possible applications including the computation of time line curvature fields and the extraction of cores of swirling advected stream lines.}, language = {en} } @inproceedings{HellerWurlPerkaetal.2012, author = {Heller, Markus O. and Wurl, Alexander and Perka, Carsten and Hege, Hans-Christian}, title = {In vivo gluteus medius volume and shape variations across gender and disease status}, volume = {45, Suppl. 1}, booktitle = {Journal of Biomechanics}, doi = {10.1016/S0021-9290(12)70359-7}, pages = {S358}, year = {2012}, language = {en} } @misc{Josten2012, type = {Master Thesis}, author = {Josten, Jan-Martin}, title = {{\"O}strogenit{\"a}ts-Approximation mittels physikochemischem Oberfl{\"a}chenvergleich}, year = {2012}, language = {de} } @article{LemanisZachowFusseisetal.2015, author = {Lemanis, Robert and Zachow, Stefan and Fusseis, Florian and Hoffmann, Ren{\´e}}, title = {A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells}, volume = {41}, journal = {Paleobiology}, number = {2}, publisher = {Cambridge University Press}, address = {Cambridge}, doi = {10.1017/pab.2014.17}, pages = {313 -- 329}, year = {2015}, abstract = {The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell.}, language = {en} } @article{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, volume = {34}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley}, doi = {10.1111/cgf.12652}, pages = {401 -- 410}, year = {2015}, abstract = {The current characterization methods of the Bulk Heterojunction (BHJ) - the main material of the new Organic Photovoltaic solar cells - are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual charac- terization and exploration of local structure-performance correlations. We propose a new formula that correlates the structural features to the performance bottlenecks. Since research into BHJ materials is highly multidisci- plinary, we enable a visual feedback strategy that allows the scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characteri- zations. We furthermore show that our approach could reduce the previous work-flow time from days to minutes.}, language = {en} } @misc{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, year = {2015}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @misc{EggerDercksenUdvaryetal.2014, author = {Egger, Robert and Dercksen, Vincent J. and Udvary, Daniel and Hege, Hans-Christian and Oberlaender, Marcel}, title = {Generation of dense statistical connectomes from sparse morphological data}, issn = {1438-0064}, doi = {10.3389/fnana.2014.00129}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53075}, year = {2014}, abstract = {Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and sub-cellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results.}, language = {en} } @article{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, volume = {56}, journal = {Connective Tissue Research}, number = {2}, publisher = {Taylor \& Francis}, doi = {10.3109/03008207.2015.1005210}, pages = {133 -- 143}, year = {2015}, language = {en} } @article{CourniaAllenAndricioaeietal.2015, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and H{\´e}nin, J{\´e}r{\^o}me and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta}, title = {Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory}, volume = {248}, journal = {Journal of Membrane Biology}, number = {4}, doi = {10.1007/s00232-015-9802-0}, pages = {611 -- 640}, year = {2015}, language = {en} } @article{MuecklichWebelAboulfadletal.2014, author = {M{\"u}cklich, Frank and Webel, Johannes and Aboulfadl, Hisham and Lindow, Norbert and Hege, Hans-Christian}, title = {Correlative Tomography - Extraction of Reliable Information with Adequate Resolution from mm Scale Down to Sub-nm Scale}, volume = {20}, journal = {Microsc. Microanal.}, number = {Suppl 3}, doi = {10.1017/S1431927614005911}, pages = {838 -- 839}, year = {2014}, language = {en} } @misc{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54353}, year = {2015}, abstract = {Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time.}, language = {en} } @misc{Knoetel2014, type = {Master Thesis}, author = {Kn{\"o}tel, David}, title = {Segmentation of ray and shark tesserae}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54429}, year = {2014}, abstract = {Rays and sharks are cartilaginous fishes. Most of the cartilaginous skeleton is covered with calcified tiles to improve the stability of the skeleton. These tiles are called tesserae and enclose areas of uncalcified cartilage. Because of the special properties of the tesserae, biologists are interested to understand shape and structure of tessellated cartilage. This thesis presents a segmentation pipeline for the separation of tesserae on the cartilaginous skeleton of rays and sharks. The segmentation pipeline consists of an automatic initial segmentation step followed by manual error corrections by the user. The initial segmentation is based on the contour tree data structure that tracks the evolution of level sets in a dataset during iso-value changes. The presented segmentation concepts are not limited to the segmentation of tesserae but also viable for similar kinds of tiled structures. The input datasets are given as micro-CT scans. The contribution of this thesis is the development of a segmentation pipeline. The pipeline uses a newly developed fast version of the contour-tree-based segmentation algorithm that, after a preprocessing step, does not need to iterate over all voxels in the dataset. Visualizations and computations are done with the software system ZIBAmira. Used algorithms are either implemented as new ZIBAmira modules or they extend already existing ZIBAmira modules.}, language = {en} } @misc{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, issn = {1438-0064}, doi = {10.1371/journal.pone.0113222}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52958}, year = {2014}, abstract = {Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.}, language = {en} } @inproceedings{Hege2014, author = {Hege, Hans-Christian}, title = {Visual analysis of molecular dynamics data using geometric and topological methods}, volume = {57}, booktitle = {Forum "Math for Industry" 2014}, publisher = {Institute of Mathematics for Industry, Kyushu University}, address = {Fukuoka, Japan}, pages = {45 -- 46}, year = {2014}, language = {en} } @inproceedings{EhlkeFrenzelRammetal.2015, author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Shandiz, Mohsen Akbari and Anglin, Carolyn and Zachow, Stefan}, title = {Towards Robust Measurement Of Pelvic Parameters From AP Radiographs Using Articulated 3D Models}, booktitle = {Computer Assisted Radiology and Surgery (CARS)}, year = {2015}, abstract = {Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph.}, language = {en} } @misc{EhlkeFrenzelRammetal.2015, author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Shandiz, Mohsen Akbari and Anglin, Carolyn and Zachow, Stefan}, title = {Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53707}, year = {2015}, abstract = {Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph.}, language = {en} } @inproceedings{KratzSchoeneichZobeletal.2014, author = {Kratz, Andrea and Sch{\"o}neich, Marc and Zobel, Valentin and Burgeth, Bernhard and Scheuermann, Gerik and Hotz, Ingrid and Stommel, Markus}, title = {Tensor Visualization Driven Mechanical Component Design}, booktitle = {Proc. IEEE Pacific Visualization Symposium 2014}, doi = {10.1109/PacificVis.2014.51}, pages = {145 -- 152}, year = {2014}, language = {en} } @article{SchoeneichStommelKratzetal.2014, author = {Sch{\"o}neich, Marc and Stommel, Markus and Kratz, Andrea and Zobel, Valentin and Scheuermann, Gerik and Hotz, Ingrid and Burgeth, Bernhard}, title = {Optimization strategy for the design of ribbed plastic components}, journal = {International Journal of Plastics Technology}, number = {10}, pages = {160 -- 175}, year = {2014}, language = {en} } @misc{WilsonBuecherGreweetal.2015, author = {Wilson, David and B{\"u}cher, Pia and Grewe, Carl Martin and Mocanu, Valentin and Anglin, Carolyn and Zachow, Stefan and Dunbar, Michael}, title = {Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Data}, journal = {Orthopedic Research Society Annual Meeting}, address = {Las Vegas, Nevada}, year = {2015}, language = {en} } @inproceedings{DeanSeidelKnoeteletal.2016, author = {Dean, Mason N. and Seidel, R. and Kn{\"o}tel, David and Lyons, K. and Baum, Daniel and Weaver, James C. and Fratzl, Peter}, title = {To build a shark: 3D tiling laws of tessellated cartilage}, volume = {56 (suppl 1)}, booktitle = {Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA}, year = {2016}, abstract = {The endoskeleton of sharks and rays (elasmobranchs) is comprised of a cartilaginous core, covered by thousands of mineralized tiles, called tesserae. Characterizing the relationship between tesseral morphometrics, skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. We integrate material property, histology, electron microscopy and synchrotron and laboratory µCT scans of skeletal elements from an ontogenetic series of round stingray Urobatis halleri, to gain insights into the generation and maintenance of a natural tessellated system. Using a custom-made semiautomatic segmentation algorithm, we present the first quantitative and 3d description of tesserae across whole skeletal elements. The tessellation is not interlocking or regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick- or disc-shaped tesserae are found in planar/flatter areas. Comparison of the tessellation across ontogeny, shows that in younger animals, the forming tesseral network is less densely packed, appearing as a covering of separate, poorly mineralized islands that grow together with age to form a complete surface. Some gaps in the tessellation are localized to specific regions in all samples, indicating they are real features, perhaps either regions of delayed mineralization or of tendon insertion. We will use the structure of elasmobranch skeletons as a road map for understanding shark and ray skeletal mechanics, but also to extract fundamental engineering principles for tiled composite materials.}, language = {en} } @phdthesis{Lindow2016, author = {Lindow, Norbert}, title = {Visual Analysis of Atomic Structures Based on the Hard-Sphere Model}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63190}, year = {2016}, abstract = {Visualization and Analysis of atomic compositions is essential to understand the structure and functionality of molecules. There exist versatile areas of applications, from fundamental researches in biophysics and materials science to drug development in pharmaceutics. For most applications, the hard-sphere model is the most often used molecular model. Although the model is a quite simple approximation of reality, it enables investigating important physical properties in a purely geometrical manner. Furthermore, large data sets with thousands up to millions of atoms can be visualized and analyzed. In addition to an adequate and efficient visualization of the data, the extraction of important structures plays a major role. For the investigation of biomolecules, such as proteins, especially the analysis of cavities and their dynamics is of high interest. Substrates can bind in cavities, thereby inducing changes in the function of the protein. Another example is the transport of substrates through membrane proteins by the dynamics of the cavities. For both, the visualization as well as the analysis of cavities, the following contributions will be presented in this thesis: 1. The rendering of smooth molecular surfaces for the analysis of cavities is accelerated and visually improved, which allows showing dynamic proteins. On the other hand, techniques are proposed to interactively render large static biological structures and inorganic materials up to atomic resolution for the first time. 2. A Voronoi-based method is presented to extract molecular cavities. The procedure comes with a high geometrical accuracy by a comparatively fast computation time. Additionally, new methods are presented to visualize and highlight the cavities within the molecular structure. In a further step, the techniques are extended for dynamic molecular data to trace cavities over time and visualize topological changes. 3. To further improve the accuracy of the approaches mentioned above, a new molecular surface model is presented that shows the accessibility of a substrate. For the first time, the structure and dynamics of the substrate as hard-sphere model is considered for the accessibility computation. In addition to the definition of the surface, an efficient algorithm for its computation is proposed, which additionally allows extracting cavities. The presented algorithms are demonstrated on different molecular data sets. The data sets are either the result of physical or biological experiments or molecular dynamics simulations.}, language = {en} } @article{GuentherKuhnHegeetal.2016, author = {G{\"u}nther, Tobias and Kuhn, Alexander and Hege, Hans-Christian and Theisel, Holger}, title = {MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields}, volume = {35}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.12914}, pages = {381 -- 390}, year = {2016}, language = {en} }