@misc{BestHege1998, author = {Best, Christoph and Hege, Hans-Christian}, title = {Visualizing conformations in molecular dynamics}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-3859}, number = {SC-98-42}, year = {1998}, abstract = {The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small number of conformations representing essential changes in the shape of the molecule. We present a method to visualize these conformations by point sets in the plane based on a geometrical distance measure between individual configurations. It turns out that different conformations appear as well-separated point sets. The method is further improved by performing a cluster analysis of the data set. The point-cluster representation is used to control a three-dimensional molecule viewer application to show individual configurations and conformational changes. The extraction of essential coordinates and visualization of molecular shape is discussed.}, language = {en} } @misc{KaehlerHege2003, author = {K{\"a}hler, Ralf and Hege, Hans-Christian}, title = {Visualization of Time-Dependent Adaptive Mesh Refinement Data}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7384}, number = {03-16}, year = {2003}, abstract = {Analysis of phenomena that simultaneously occur on quite different spatial and temporal scales require adaptive, hierarchical schemes to reduce computational and storage demands. For data represented as grid functions, the key are adaptive, hierarchical, time-dependent grids that resolve spatio-temporal details without too much redundancy. Here, so-called AMR grids gain increasing popularity. For visualization and feature identification/tracking, the underlying continuous function has to be faithfully reconstructed by spatial and temporal interpolation. Well designed interpolation methods yield better results and help to reduce the amount of data to be stored. We address the problem of temporal interpolation of AMR grid data, e.g.\ for creation of smooth animations or feature tracking. Intermediate grid hierarchies are generated by merging the cells on all refinement levels that are present in the key frames considered. Utilizing a clustering algorithm a structure of nested grids is induced on the resulting collection of cells. The grid functions are mapped to the intermediate hierarchy, thus allowing application of appropriate interpolation techniques.}, language = {en} } @misc{BengerHege2003, author = {Benger, Werner and Hege, Hans-Christian}, title = {Tensor Splats}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7393}, number = {03-17}, year = {2003}, abstract = {An improved general-purpose technique for the visualization of symmetric positive definite tensor fields of rank two is described. It is based on a splatting technique that is built from tiny transparent glyph primitives which are capable to incorporate the full directional information content of a tensor. The result is an information-rich image that allows to read off the preferred directions in a tensor field at each point of a three-dimensional volume or two-dimensional surface. It is useful for analyzing slices or volumes of a three-dimensional tensor field and can be overlayed with standard volume rendering or color mapping. The application of the rendering technique is demonstrated on general relativistic data and the diffusion tensor field of a human brain.}, language = {en} } @misc{HegeHutanuKaehleretal.2003, author = {Hege, Hans-Christian and Hutanu, Andrei and K{\"a}hler, Ralf and Merzky, Andr{\´e} and Radke, Thomas and Seidel, Edward and Ullmer, Brygg}, title = {Progressive Retrieval and Hierarchical Visualization of Large Remote Data}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7623}, number = {03-40}, year = {2003}, abstract = {\noindent The size of data sets produced on remote supercomputer facilities frequently exceeds the processing capabilities of local visualization workstations. This phenomenon increasingly limits scientists when analyzing results of large-scale scientific simulations. That problem gets even more prominent in scientific collaborations, spanning large virtual organizations, working on common shared sets of data distributed in Grid environments. In the visualization community, this problem is addressed by distributing the visualization pipeline. In particular, early stages of the pipeline are executed on resources closer to the initial (remote) locations of the data sets. \noindent This paper presents an efficient technique for placing the first two stages of the visualization pipeline (data access and data filter) onto remote resources. This is realized by exploiting the ``extended retrieve'' feature of GridFTP for flexible, high performance access to very large HDF5 files. We reduce the number of network transactions for filtering operations by utilizing a server side data processing plugin, and hence reduce latency overhead compared to GridFTP partial file access. The paper further describes the application of hierarchical rendering techniques on remote uniform data sets, which make use of the remote data filtering stage.}, language = {en} } @misc{BaumannHegeSchwarzetal.1996, author = {Baumann, Wolfgang and Hege, Hans-Christian and Schwarz, Uwe and St{\"u}ben, Hinnerk}, title = {Netzverteilte Visualisierung und Simulation}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5379}, number = {TR-96-08}, year = {1996}, abstract = {Dieser Bericht beschreibt die Ergebnisse eines Anwendungsprojektes, das parallel zum Aufbau des Berliner Hochgeschwindigkeitsdatennetzes (Berlin Regional Testbed) am ZIB durchgef{\"u}hrt wurde. Es werden allgemeine Werkzeuge und anwendungsspezifische Arbeitsumgebungen zur netzverteilten Visualisierung und Simulation vorgestellt. Die allgemeinen Werkzeuge unterst{\"u}tzen folgende Aufgaben: Kopplung von Simulationen auf (Hochleistungs-)Rechnern an lokale Grafikarbeitspl{\"a}tze, objektorientierte und verteilte Visualisierung, Remote-Videoaufzeichnung, Bilddatenkompression und digitaler Filmschnitt. Die spezifischen Arbeitsumgebungen wurden f{\"u}r Aufgaben aus den Bereichen Numerische Mathematik, Astrophysik, Strukturforschung, Chemie, Polymerphysik und Str{\"o}mungsmechanik entwickelt.}, language = {de} } @misc{DeuflhardHegeSedlmayred1994, author = {Deuflhard, Peter and Hege, Hans-Christian and Sedlmayr(ed.), E.}, title = {Scientific Computing in der Theoretischen Physik. Collected Abstracts.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5068}, number = {TR-94-01}, year = {1994}, abstract = {Die von der DMV-Fachgruppe Scientific Computing in Kooperation mit dem gleichnamigen GAMM-Fachausschuss organisierte Tagung \glqq Scientific Computing in der Theoretischen Physik\grqq~fand vom 16. - 18. M{\"a}rz 1994 am Fachbereich Mathematik und Informatik der Freien Universit{\"a}t Berlin statt. Ziel des Workshops war, die Kontakte zwischen den Fachleuten der Gebiete {\em Computational Physics} und {\em Scientific Computing} zu intensivieren. Schwerpunkte des Workshops waren numerische Simulation von Transportmodellen der Astrophysik und Halbleiterphysik, Multilevel-Methoden f{\"u}r partielle Differentialgleichungen sowie Monte-Carlo-Methoden und molekulardynamische Verfahren f{\"u}r Probleme der Statistischen Physik und Quantenfeldtheorie. Der Workshop fand ein {\"a}usserst positives Echo und f{\"u}hrte {\"u}ber 70 Teilnehmer der verschiedenen Teilgebiete der Theoretischen Physik und ca. 50 Teilnehmer aus dem Bereich der Numerischen Mathematik zusammen. \originalTeX}, language = {en} } @misc{DeuflhardHegeSeebass2000, author = {Deuflhard, Peter and Hege, Hans-Christian and Seebass, Martin}, title = {Progress Towards a Combined MRI/Hyperthermia System}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5755}, number = {00-07}, year = {2000}, abstract = {Regional hyperthermia, a clinical cancer therapy, is the main topic of the Sonderforschungsbereich Hyperthermia: Scientific Methods and Clinical Applications'' at Berlin. In recent years, technological improvements towards a better concentration of heat to the desired target region have been achieved. These include a rather sophisticated integrated software environment for therapy planning and a new hyperthermia applicator. In a next step, a detailed closed loop monitoring of the actual treatment is to be developed. For this purpose the hyperthermia applicator is combined with an MRI system, which will allow to check the positioning of the patients and to measure individual blood perfusion as well as the 3D temperature distribution. The measurements will then be employed for an on-line control of the whole treatment. In this intended setting, new fast feedback control algorithms will come into play.}, language = {en} } @misc{HegeHoellererStalling1993, author = {Hege, Hans-Christian and H{\"o}llerer, Tobias and Stalling, Detlev}, title = {Volume Rendering - Mathematicals Models and Algorithmic Aspects.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4994}, number = {TR-93-07}, year = {1993}, abstract = {In this paper various algorithms for rendering gaseous phenomena are reviewed. In computer graphics such algorithms are used to model natural scenes containing clouds, fog, flames and so on. On the other hand it has become an important technique in scientific visualization to display three dimensional scalar datasets as cloudy objects. Our emphasis is on this latter subject of so-called {\em direct volume rendering}. All algorithms will be discussed within the framework of linear transport theory. The equation of transfer is derived. This equation is suitable to describe the radiation field in a participating medium where absorption, emission, and scattering of light can occur. Almost all volume rendering algorithms can be shown to solve special cases of the equation of transfer. Related problems like the mapping from data values to model parameters or possible parallelization strategies will be discussed as well.}, language = {en} } @misc{HegePolthier1997, author = {Hege, Hans-Christian and Polthier, Konrad}, title = {Visualization and Mathematics '97}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5480}, number = {TR-97-06}, year = {1997}, abstract = {This report contains paper abstracts of the workshop "Visualization and Mathematics" held in Berlin-Dahlem in September 1997. The meeting serves as a forum for an international community of researchers and practitioners on the application of visualization techniques in mathematics and on mathematical concepts in visualization. It is the second symposium in a series of workshops bringing together mathematicians and experts from scientific visualization. The themes of the workshop include: \begin{itemize} \item - applications in differential geometry and partial differential equations \item - algorithmic aspects of adaptive and hierarchical techniques in space and time \item - time control of animated objects and corresponding algorithms \item - algorithmic representation of objects for display, storage and exchange \item - new visualization techniques for mathematical structures \item - integration of visualization with symbolic and numerical computation. \end{itemize}}, language = {en} } @misc{HegePolthier1995, author = {Hege, Hans-Christian and Polthier, Konrad}, title = {Visualization and Mathematics. International Workshop}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5179}, number = {TR-95-02}, year = {1995}, abstract = {International Workshop with support of the Deutsche Forschungsgemeinschaft (DFG) and Max-Planck-Gesellschaft (MPG) Berlin (Dahlem), Germany, May 30 - June 2, 1995}, language = {en} } @misc{Hege1990, author = {Hege, Hans-Christian}, title = {Datenabh{\"a}ngigkeitsanalyse und Programmtransformationen auf CRAY-Rechnern mit dem Fortran-Pr{\"a}prozessor fpp}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4685}, number = {TR-90-04}, year = {1990}, abstract = {The FORTRAN preprocessor fpp in the newly introduced Autotasking System of CRAY Research allows automatic vectorization and parallelization on basis of a data dependence analysis. An introduction into data dependence analysis is given, showing how data dependence graphs unveil opportunities for program transformations like vectorization and concurrentization. The report contains a complete description of the preprocessors functionality, its options and directives for increasing the effectiveness of the dependence analyzer and steering the code transformations. Finally, some advice is given for the practical use of fpp on CRAY computers.}, language = {de} } @misc{BengerHegeHeusler2000, author = {Benger, Werner and Hege, Hans-Christian and Heusler, Stefan}, title = {Visions of Numerical Relativity 1999}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4429}, number = {SC-99-53}, year = {2000}, abstract = {We present visualizations of recent supercomputer simulations from numerical relativity, exploiting the progress in visualization techniques and numerical methods also from an artistic point of view. The sequences have been compiled into a video tape, showing colliding black holes, orbiting and merging neutron stars as well as collapsing gravitational waves. In this paper we give some background information and provide a glance at the presented sequences.}, language = {en} } @misc{ZoecklerStallingHege1999, author = {Z{\"o}ckler, Malte and Stalling, Detlev and Hege, Hans-Christian}, title = {Fast and Intuitive Generation of Geometric Shape Transitions}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4219}, number = {SC-99-33}, year = {1999}, abstract = {We describe a novel method for continuously transforming two triangulated models of arbitrary topology into each other. Equal global topology for both objects is assumed, extensions for genus changes during metamorphosis are provided. The proposed method addresses the major challenge in 3D metamorphosis, namely specifying the morphing process intuitively, with minimal user interaction and sufficient detail. Corresponding regions and point features are interactively identified. These regions are parametrized automatically and consistently, providing a basis for smooth interpolation. Utilizing suitable 3D interaction techniques a simple and intuitive control over the whole morphing process is offered.}, language = {en} } @misc{SchmidtEhrenbergHege1999, author = {Schmidt-Ehrenberg, Johannes and Hege, Hans-Christian}, title = {Visualizing Quantum Mechanical Phenomena}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4287}, number = {SC-99-39}, year = {1999}, abstract = {In this paper we discuss several ways to visualize stationary and non-stationary quantum mechanical systems. We demonstrate an approach for the quantitative interpretation of probability density isovalues which yields a reasonable correlation between isosurfaces for different timesteps. As an intuitive quantity for visualizing the momentum of a quantum system we propose the probability flow density which can be treated by vector field visualization techniques. Finally, we discuss the visualization of non-stationary systems by a sequence of single timestep images.}, language = {en} } @misc{BengerHegeMerzkyetal.1999, author = {Benger, Werner and Hege, Hans-Christian and Merzky, Andre and Radke, Thomas and Seidel, Edward}, title = {Efficient Distributed File I/O for Visualization in Grid Environments}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4326}, number = {SC-99-43}, year = {1999}, abstract = {Large scale simulations running in metacomputing environments face the problem of efficient file I/O. For efficiency it is desirable to write data locally, distributed across the computing environment, and then to minimize data transfer, i.e.\ reduce remote file access. Both aspects require I/O approaches which differ from existing paradigms. For the data output of distributed simulations, one wants to use fast local parallel I/O for all participating nodes, producing a single distributed logical file, while keeping changes to the simulation code as small as possible. For reading the data file as in postprocessing and file based visualization, one wants to have efficient partial access to remote and distributed files, using a global naming scheme and efficient data caching, and again keeping the changes to the postprocessing code small. However, all available software solutions require the entire data to be staged locally (involving possible data recombination and conversion), or suffer from the performance problems of remote or distributed file systems. In this paper we show how to interface the HDF5 I/O library via its flexible Virtual File Driver layer to the Globus Data Grid. We show, that combining these two toolkits in a suitable way provides us with a new I/O framework, which allows efficient, secure, distributed and parallel file I/O in a metacomputing environment.}, language = {en} } @misc{HegeStalling1998, author = {Hege, Hans-Christian and Stalling, Detlev}, title = {Fast LIC with Higher Order Filter Kernels}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-3439}, number = {SC-97-74}, year = {1998}, abstract = {Line integral convolution (LIC) has become a well-known and popular method for visualizing vector fields. The method works by convolving a random input texture along the integral curves of the vector field. In order to accelerate image synthesis significantly, an efficient algorithm has been proposed that utilizes pixel coherence in field line direction. This algorithm, called ``fast LIC'', originally was restricted to simple box-type filter kernels. Here we describe a generalization of fast LIC for piecewise polynomial filter kernels. Expanding the filter kernels in terms of truncated power functions allows us to exploit a certain convolution theorem. The convolution integral is expressed as a linear combination of repeated integrals (or repeated sums in the discrete case). Compared to the original algorithm the additional expense for using higher order filter kernels, e.g.\ of B-spline type, is very low. Such filter kernels produce smoother, less noisier results than a box filter. This is evident from visual investigation, as well as from analysis of pixel correlations. Thus, our method represents a useful extension of the fast LIC algorithm for the creation of high-quality LIC images.}, language = {en} } @misc{SchmidtEhrenbergHege2004, author = {Schmidt-Ehrenberg, Johannes and Hege, Hans-Christian}, title = {Visual Analysis of Molecular Conformations by Means of a Dynamic Density Mixture Model}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-8361}, number = {05-02}, year = {2004}, abstract = {We propose an approach for transforming the sampling of a molecular conformation distribution into an analytical model based on Hidden Markov Models. The model describes the sampled shape density as a mixture of multivariate unimodal densities. Thus, it delivers an interpretation of the sampled density as a set of typical shapes that appear with different probabilities and are characterized by their geometry, their variability and transition probabilities between the shapes. The gained model is used to identify atom groups of constant shape that are connected by metastable torsion angles. Based on this description an alignment for the original sampling is computed. As it takes into account the different shapes contained in the sampled set, this alignment allows to compute reasonable average shapes and meaningful shape density plots. Furthermore, it enables us to visualize typical conformations.}, 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} } @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} }