TY - GEN A1 - Kähler, Ralf A1 - Simon, Mark A1 - Hege, Hans-Christian T1 - Fast Volume Rendering of Sparse High-Resolution Datasets Using Adaptive Mesh Refinement Hierarchies N2 - In this paper we present an algorithm that accelerates 3D texture-based volume rendering of large and sparse data sets. A hierarchical data structure (known as AMR tree) consisting of nested uniform grids is employed in order to efficiently encode regions of interest. The hierarchies resulting from this kind of space partitioning yield a good balance between the amount of volume to render and the number of texture bricks -- a prerequisite for fast rendering. Comparing our approach to an octree based algorithm we show that our algorithm increases rendering performance significantly for sparse data. A further advantage is that less parameter tuning is necessary. T3 - ZIB-Report - 01-25 KW - scalar field visualization KW - volume visualization KW - volume rendering KW - 3D texture mapping KW - hierarchical space partitioning KW - AMR tree KW - octree KW - spar Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6516 ER - TY - GEN A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Interactive Volume Rendering of Adaptive Mesh Refinement Data N2 - Many phenomena in nature and engineering happen simultaneously on rather diverse spatial and temporal scales, i.e.\ exhibit a multi-scale character. Therefore various hierarchical data structures and numerical schemes have been devised to represent quantitatively such phenomena. A special numerical multilevel technique, associated with a particular hierarchical data structure, is so-called Adaptive Mesh Refinement (AMR). This scheme achieves locally very high spatial and temporal resolutions. Due to its popularity, many scientists are in need of interactive visualization tools for AMR data. In this article we present a 3D texture-based volume rendering algorithm for AMR data, that directly utilizes the hierarchical structure. Thereby interactive rendering even for large data sets is achieved. In particular the problems of interpolation artifacts, opacity corrections, and texture memory limitations are addressed. The algorithm's value in practice is demonstrated with simulation and image data. T3 - ZIB-Report - 01-30 KW - Scalar field visualization KW - multiresolution volume rendering KW - AMR hierarchies KW - 3D texture mapping Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6561 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin T1 - Progress Towards a Combined MRI/Hyperthermia System N2 - 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. T3 - ZIB-Report - 00-07 KW - hyperthermia KW - medical therapy planning KW - applicator design KW - interventional MRI Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5755 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Polthier, Konrad T1 - Visualization and Mathematics '97 N2 - 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} T3 - ZIB-Report - TR-97-06 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5480 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Merzky, Andre A1 - Zachow, Stefan T1 - Distributed Visualization with OpenGL Vizserver: Practical Experiences N2 - The increasing demand for distributed solutions in computing technology does not stop when it comes to visualization techniques. However, the capabilities of todays applications to perform remote rendering are limited by historical design legacys. Especially the popular X11 protokoll, which has been proven to be extremely flexible and usefull for remote 2D graphics applications, breaks down for the case of remote 3D rendering. In this white paper, we give a short overview of generic remote rendering technologies available today, and compare their performance to the recently released vizserver by SGI: a network extension to the SGI OpenGL rendering engines. T3 - ZIB-Report - 00-31 KW - remote visualization KW - high performance computing Y1 - 2000 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5992 ER - TY - GEN A1 - Schmidt-Ehrenberg, Johannes A1 - Hege, Hans-Christian T1 - Visual Analysis of Molecular Conformations by Means of a Dynamic Density Mixture Model N2 - 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. T3 - ZIB-Report - 05-02 KW - multimodal circular distribution KW - mixture estimation KW - molecular conformations Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8361 ER - TY - GEN A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian T1 - Dual Streamline Seeding - Method and Implementation N2 - This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces. N2 - In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist. T3 - ZIB-Report - 08-49 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11032 SN - 1438-0064 ER - TY - GEN A1 - Best, Christoph A1 - Hege, Hans-Christian T1 - Visualizing conformations in molecular dynamics N2 - 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. T3 - ZIB-Report - SC-98-42 KW - Molecular Dynamics KW - Conformations KW - Visualization KW - Cluster Analysis Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3859 ER - TY - GEN A1 - Hege, Hans-Christian T1 - Datenabhängigkeitsanalyse und Programmtransformationen auf CRAY-Rechnern mit dem Fortran-Präprozessor fpp N2 - 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. T3 - ZIB-Report - TR-90-04 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4685 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Stüben, Hinnerk T1 - Vectorization and Parallelization of Irregular Problems via Graph coloring. N2 - Efficient implementations of irregular problems on vector and parallel architectures are generally hard to realize. An important class of problems are Gauß-Seidel iteration schemes applied to irregular data sets. The unstructured data dependences arising there prevent restructuring compilers from generating efficient code for vector or parallel machines. It is shown, how to structure the data dependences by decomposing the underlying data set using graph coloring techniques and by specifying a particular execution order already on the algorithm level. Methods to master the irregularities originating from different types of tasks are proposed. An application is given and some open issues and future developments are discussed. T3 - ZIB-Report - SC-90-16 Y1 - 1990 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-443 ER - TY - GEN A1 - Baumann, Wolfgang A1 - Hege, Hans-Christian A1 - Schwarz, Uwe A1 - Stüben, Hinnerk T1 - Netzverteilte Visualisierung und Simulation N2 - Dieser Bericht beschreibt die Ergebnisse eines Anwendungsprojektes, das parallel zum Aufbau des Berliner Hochgeschwindigkeitsdatennetzes (Berlin Regional Testbed) am ZIB durchgeführt wurde. Es werden allgemeine Werkzeuge und anwendungsspezifische Arbeitsumgebungen zur netzverteilten Visualisierung und Simulation vorgestellt. Die allgemeinen Werkzeuge unterstützen folgende Aufgaben: Kopplung von Simulationen auf (Hochleistungs-)Rechnern an lokale Grafikarbeitsplätze, objektorientierte und verteilte Visualisierung, Remote-Videoaufzeichnung, Bilddatenkompression und digitaler Filmschnitt. Die spezifischen Arbeitsumgebungen wurden für Aufgaben aus den Bereichen Numerische Mathematik, Astrophysik, Strukturforschung, Chemie, Polymerphysik und Strömungsmechanik entwickelt. T3 - ZIB-Report - TR–96–08 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5379 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Sedlmayr(ed.), E. T1 - Scientific Computing in der Theoretischen Physik. Collected Abstracts. N2 - 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. März 1994 am Fachbereich Mathematik und Informatik der Freien Universität 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 für partielle Differentialgleichungen sowie Monte-Carlo-Methoden und molekulardynamische Verfahren für Probleme der Statistischen Physik und Quantenfeldtheorie. Der Workshop fand ein äusserst positives Echo und führte über 70 Teilnehmer der verschiedenen Teilgebiete der Theoretischen Physik und ca. 50 Teilnehmer aus dem Bereich der Numerischen Mathematik zusammen. \originalTeX T3 - ZIB-Report - TR-94-01 Y1 - 1994 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5068 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Höllerer, Tobias A1 - Stalling, Detlev T1 - Volume Rendering - Mathematicals Models and Algorithmic Aspects. N2 - 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. T3 - ZIB-Report - TR-93-07 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-4994 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Polthier, Konrad T1 - Visualization and Mathematics. International Workshop N2 - International Workshop with support of the Deutsche Forschungsgemeinschaft (DFG) and Max-Planck-Gesellschaft (MPG) Berlin (Dahlem), Germany, May 30 - June 2, 1995 T3 - ZIB-Report - TR-95-02 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5179 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Zöckler, Malte T1 - A Generalized Marching Cubes Algorithm Based on Non-Binary Classifications N2 - We present a new technique for generating surface meshes from a uniform set of discrete samples. Our method extends the well-known marching cubes algorithm used for computing polygonal isosurfaces. While in marching cubes each vertex of a cubic grid cell is binary classified as lying above or below an isosurface, in our approach an arbitrary number of vertex classes can be specified. Consequently the resulting surfaces consist of patches separating volumes of two different classes each. Similar to the marching cubes algorithm all grid cells are traversed and classified according to the number of different vertex classes involved and their arrangement. The solution for each configuration is computed based on a model that assigns probabilities to the vertices and interpolates them. We introduce an automatic method to find a triangulation which approximates the boundary surfaces - implicitly given by our model - in a topological correct way. Look-up tables guarantee a high performance of the algorithm. In medical applications our method can be used to extract surfaces from a 3D segmentation of tomographic images into multiple tissue types. The resulting surfaces are well suited for subsequent volumetric mesh generation, which is needed for simulation as well as visualization tasks. The proposed algorithm provides a robust and unique solution, avoiding ambiguities occuring in other methods. The method is of great significance in modeling and animation too, where it can be used for polygonalization of non-manifold implicit surfaces. T3 - ZIB-Report - SC-97-05 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2741 ER - TY - GEN A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast and Resolution Independent Line Integral Convolution N2 - Line Integral Convolution (LIC) is a powerful technique for generating striking images and animations from vector data. Introduced in 1993, the method has rapidly found many application areas, ranging from computer arts to scientific visualization. Based upon locally filtering an input texture along a curved stream line segment in a vector field, it is able to depict directional information at high spatial resolutions. We present a new method for computing LIC images, which minimizes the total number of stream lines to be computed and thereby reduces computational costs by an order of magnitude compared to the original algorithm. Our methods utilizes fast, error-controlled numerical integrators. Decoupling the characteristic lengths in vector field grid, input texture and output image, it allows to compute filtered images at arbitrary resolution. This feature is of great significance in computer animation as well as in scientific visualization, where it can be used to explore vector data by smoothly enlarging structure of details. We also present methods for improved texture animation, employing constant filter kernels only. To obtain an optimal motion effect, spatial decay of correlation between intensities of distant pixels in the output image has to be controlled. This is achieved by blending different phase shifted box filter animations and by adaptively rescaling the contrast of the output frames. T3 - ZIB-Report - SC-94-37 Y1 - 1995 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1653 ER - TY - GEN A1 - Grammel, Martin A1 - Hege, Hans-Christian A1 - Wunderling, Roland T1 - On the Impact of Communication Latencies on Distributed Sparse LU Factorization. N2 - Sparse LU factorization offers some potential for parallelism, but at a level of very fine granularity. However, most current distributed memory MIMD architectures have too high communication latencies for exploiting all parallelism available. To cope with this, latencies must be avoided by coarsening the granularity and by message fusion. However, both techniques limit the concurrency, thereby reducing the scalability. In this paper, an implementation of a parallel LU decomposition algorithm for linear programming bases is presented for distributed memory parallel computers with noticable communication latencies. Several design decisions due to latencies, including data distribution and load balancing techniques, are discussed. An approximate performance model is set up for the algorithm, which allows to quantify the impact of latencies on its performance. Finally, experimental results for an Intel iPSC/860 parallel computer are reported and discussed. T3 - ZIB-Report - SC-93-28 Y1 - 1993 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-1245 ER - TY - GEN A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev T1 - Numerical Algorithms and Visualization in Medical Treament Planning N2 - After a short summary on therapy planning and the underlying technologies we discuss quantitative medicine by giving a short overview on medical image data, summarizing some applications of computer based treatment planning, and outlining requirements on medical planning systems. Then we continue with a description of our medical planning system {\sf HyperPlan}. It supports typical working steps in therapy planning, like data aquisition, segmentation, grid generation, numerical simulation and optimization, accompanying these with powerful visualization and interaction techniques. T3 - ZIB-Report - SC-96-54 Y1 - 1996 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2643 ER - TY - GEN A1 - Stalling, Detlev A1 - Zöckler, Malte A1 - Hege, Hans-Christian T1 - Fast Display of Illuminated Field Lines N2 - A new technique for interactive vector field visualization using large numbers of properly illuminated field lines is presented. Taking into account ambient, diffuse, and specular reflection terms as well as transparency and depth cueing, we employ a realistic shading model which significantly increases quality and realism of the resulting images. While many graphics workstations offer hardware support for illuminating surface primitives, usually no means for an accurate shading of line primitives are provided. However, we show that proper illumination of lines can be implemented by exploiting the texture mapping capabilities of modern graphics hardware. In this way high rendering performance with interactive frame rates can be achieved. We apply the technique to render large numbers of integral curves of a vector field. The impression of the resulting images can be further improved by a number of visual enhancements, like transparency and depth-cueing. We also describe methods for controlling the distribution of field lines in space. These methods enable us to use illuminated field lines for interactive exploration of vector fields. T3 - ZIB-Report - SC-96-58 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2686 ER - TY - GEN A1 - Battke, Henrik A1 - Stalling, Detlev A1 - Hege, Hans-Christian T1 - Fast Line Integral Convolution for Arbitrary Surfaces in 3D N2 - We describe an extension of the line integral convolution method (LIC) for imaging of vector fields on arbitrary surfaces in 3D space. Previous approaches were limited to curvilinear surfaces, i.e.~surfaces which can be parametrized globally using 2D-coordinates. By contrast our method also handles the case of general, possibly multiply connected surfaces. The method works by tesselating a given surface with triangles. For each triangle local euclidean coordinates are defined and a local LIC texture is computed. No scaling or distortion is involved when mapping the texture onto the surface. The characteristic length of the texture remains constant. In order to exploit the texture hardware of modern graphics computers we have developed a tiling strategy for arranging a large number of triangular texture pieces within a single rectangular texture image. In this way texture memory is utilized optimally and even large textured surfaces can be explored interactively. T3 - ZIB-Report - SC-96-59 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2690 ER - TY - GEN A1 - Deuflhard, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Beck, Rudolf A1 - Hege, Hans-Christian T1 - Hyperthermia Treatment Planning in Clinical Cancer Therapy: Modelling, Simulation and Visualization N2 - \noindent The speaker and his co-workers in Scientific Computing and Visualization have established a close cooperation with medical doctors at the Rudolf--Virchow--Klinikum of the Humboldt University in Berlin on the topic of regional hyperthermia. In order to permit a patient--specific treatment planning, a special software system ({\sf\small HyperPlan}) has been developed. \noindent A mathematical model of the clinical system ({\it radio frequency applicator with 8 antennas, water bolus, individual patient body}) involves Maxwell's equations in inhomogeneous media and a so--called bio--heat transfer PDE describing the temperature distribution in the human body. The electromagnetic field and the thermal phenomena need to be computed at a speed suitable for the clinical environment. An individual geometric patient model is generated as a quite complicated tetrahedral ``coarse'' grid (several thousands of nodes). Both Maxwell's equations and the bio--heat transfer equation are solved on that 3D--grid by means of {\em adaptive} multilevel finite element methods, which automatically refine the grid where necessary in view of the required accuracy. Finally optimal antenna parameters for the applicator are determined . \noindent All steps of the planning process are supported by powerful visualization methods. Medical images, contours, grids, simulated electromagnetic fields and temperature distributions can be displayed in combination. A number of new algorithms and techniques had to be developed and implemented. Special emphasis has been put on advanced 3D interaction methods and user interface issues. T3 - ZIB-Report - SC-97-26 Y1 - 1997 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-2958 ER - TY - GEN A1 - Hege, Hans-Christian A1 - Stalling, Detlev T1 - Fast LIC with Higher Order Filter Kernels N2 - 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. T3 - ZIB-Report - SC-97-74 Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-3439 ER - TY - GEN A1 - Zachow, Stefan A1 - Zilske, Michael A1 - Hege, Hans-Christian T1 - 3D reconstruction of individual anatomy from medical image data: Segmentation and geometry processing N2 - For medical diagnosis, visualization, and model-based therapy planning three-dimensional geometric reconstructions of individual anatomical structures are often indispensable. Computer-assisted, model-based planning procedures typically cover specific modifications of “virtual anatomy” as well as numeric simulations of associated phenomena, like e.g. mechanical loads, fluid dynamics, or diffusion processes, in order to evaluate a potential therapeutic outcome. Since internal anatomical structures cannot be measured optically or mechanically in vivo, three-dimensional reconstruction of tomographic image data remains the method of choice. In this work the process chain of individual anatomy reconstruction is described which consists of segmentation of medical image data, geometrical reconstruction of all relevant tissue interfaces, up to the generation of geometric approximations (boundary surfaces and volumetric meshes) of three-dimensional anatomy being suited for finite element analysis. All results presented herein are generated with amira ® – a highly interactive software system for 3D data analysis, visualization and geometry reconstruction. T3 - ZIB-Report - 07-41 KW - Medical image segmentation KW - computational geometry KW - virtual anatomy KW - finite element meshes Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10440 SN - 1438-0064 ER - TY - CHAP A1 - Beck, Rudolf A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Stalling, Detlev ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Numerical Algorithms and Visualization in Medical Treament Planning T2 - Visualization and Mathematics Y1 - 1997 SP - 303 EP - 328 PB - Springer-Verlag ER - TY - CHAP A1 - Beck, Rudolf A1 - Hege, Hans-Christian A1 - Seebass, Martin A1 - Wust, Peter A1 - Deuflhard, Peter A1 - Felix, Roland ED - Franconi, Cafiero T1 - Adaptive finite element codes for numerical calculations in hyperthermia treatment planning T2 - Proc. of the 7th Int. Congress on Hyperthermic Oncology, Rome, Italy, April 1996 Y1 - 1996 VL - 2 SP - 515 EP - 517 ER - TY - CHAP A1 - Nadobny, Johanna A1 - Wust, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - A Quantitative Comparison between the VSIE and the FDTD method using Electrically Equivalent Patient and Antenna Models T2 - Proc. 16th Ann. Meeting Europ. Soc. Hyperthermic Oncology (ESHO-97), Berlin, Germany, April 1997 Y1 - 1997 SP - 145 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Hege, Hans-Christian A1 - Seebass, Martin ED - Grönemeyer, W. T1 - Progress Towards a Combined MRI Hyperthermia System T2 - Proc. Second Int. Congress HIGH CARE 2000, Bochum Y1 - 2000 ER - TY - JOUR A1 - Gellermann, Johanna A1 - Wust, Peter A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Nadobny, Johanna A1 - Beck, Rudolf A1 - Hege, Hans-Christian A1 - Deuflhard, Peter A1 - Felix, Roland T1 - Clinical evaluation and verification of the hyperthermia treatment planning system hyperplan JF - Int J Radiat Oncol Biol Phys Y1 - 2000 VL - 47 IS - 4 SP - 1145 EP - 1156 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Seebass, Martin A1 - Stalling, Detlev A1 - Beck, Rudolf A1 - Hege, Hans-Christian ED - Sydow, Achim T1 - Hyperthermia Treatment Planning in Clinical Cancer Therapy:Modelling, Simulation, and Visualization T2 - Computational Physics, Chemistry and Biology Y1 - 1997 VL - 3 PB - Wissenschaft und Technik Verlag CY - Plenary keynote talk, 15th IMACS World Congress 1997 on Scientific Computation, Modelling and Applied Mathematics ER - TY - JOUR A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - A nonlinear elastic soft tissue model for craniofacial surgery simulations JF - ESAIM, Proc. Y1 - 2002 U6 - https://doi.org/10.1051/proc:2002011 VL - 12 SP - 61 EP - 66 ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - A nonlinear soft tissue model for craniofacial surgery simulations T2 - Proc. of Modeling and Simulation for Computer-aided Medicine and Surgery (MS4CMS Y1 - 2002 PB - INRIA CY - Paris, France ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - Biomechanical modeling of individual facial emotion expressions T2 - Proc. of Visualization, Imaging, and Image Processing (VIIP) Y1 - 2002 SP - 7 EP - 11 CY - Malaga, Spain ER - TY - CHAP A1 - Lamecker, Hans A1 - Seebaß, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Fitzpatrick, J. ED - Sonka, Milan T1 - A 3d statistical shape model of the pelvic bone for segmentation T2 - Proc. SPIE Medical Imaging 2004 Y1 - 2004 VL - 5370 SP - 1341 EP - 1351 ER - TY - CHAP A1 - Lamecker, Hans A1 - Seebass, Martin A1 - Lange, Thomas A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Westwood, J. T1 - Visualization of the variability of 3D statistical shape models by animation T2 - Proc. Medicine Meets Virtual Reality Y1 - 2004 VL - 98 SP - 190 EP - 196 PB - IOS Press ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Meiler, M. ED - Saupe, D. ED - Krugel, F. ED - Handels, H. ED - Lehmann, T. T1 - Biomechanisches Modell zur Abschätzung der individuellen Gesichtsmimik T2 - Proc.of Workshop Bildverarbeitung für die Medizin (BVM) Y1 - 2002 SP - 25 EP - 28 CY - Leipzig, Germany ER - TY - CHAP A1 - Zachow, Stefan A1 - Weiser, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Payan, Y. T1 - Soft Tissue Prediction in Computer Assisted Maxillofacial Surgery Planning T2 - Biomechanics Applied to Computer Assisted Surgery Y1 - 2005 SP - 277 EP - 298 PB - Research Signpost ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface JF - IEEE Transactions on Visualization and Computer Graphics N2 - 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. Y1 - 2014 U6 - https://doi.org/10.1109/TVCG.2014.2346404 VL - 20 IS - 12 SP - 2486 EP - 2495 ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Ligand Excluded Surface: A New Type of Molecular Surface N2 - 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. T3 - ZIB-Report - 14-27 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-51194 SN - 1438-0064 ER - TY - JOUR A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Udvary, Daniel A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - Generation of dense statistical connectomes from sparse morphological data JF - Frontiers in Neuroanatomy Y1 - 2014 U6 - https://doi.org/10.3389/fnana.2014.00129 VL - 8 IS - 129 ER - TY - CHAP A1 - Klindt, Marco A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian ED - Arnold, David ED - Kaminski, Jaime ED - Niccolucci, Franco ED - Stork, Andre T1 - Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition T2 - VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers Y1 - 2012 UR - http://diglib.eg.org/EG/DL/PE/VAST/VAST12S/025-028.pdf U6 - https://doi.org/10.2312/PE/VAST/VAST12S/025-028 SP - 25 EP - 28 PB - Eurographics Association CY - Brighton, UK ER - TY - CHAP A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions T2 - EVA 2012 Berlin Y1 - 2012 SP - 150 EP - 155 PB - Gesellschaft zur Förderung angewandter Informatik e.V. CY - Volmerstraße 3, 12489 Berlin ER - TY - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Bondar, Ana-Nicoleta A1 - Hege, Hans-Christian T1 - Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization T2 - Proceedings of IEEE Symposium on Biological Data Visualization (biovis’12) Y1 - 2012 U6 - https://doi.org/10.1109/BioVis.2012.6378599 SP - 99 EP - 106 ER - TY - CHAP A1 - Pöthkow, Kai A1 - Hege, Hans-Christian ED - Laidlaw, David ED - Vilanova, Anna T1 - Uncertainty Propagation in DT-MRI Anisotropy Isosurface Extraction T2 - New Developments in the Visualization and Processing of Tensor Fields Y1 - 2012 SP - 209 EP - 225 PB - Springer CY - Berlin ER - TY - GEN A1 - Stalling, Detlev A1 - Westerhoff, Malte A1 - Hege, Hans-Christian ED - Hansen, Charles ED - Johnson, Christopher T1 - Amira: A highly interactive system for visual data analysis T2 - The Visualization Handbook Y1 - 2005 U6 - https://doi.org/10.1016/B978-012387582-2/50040-X SP - 749 EP - 767 PB - Elsevier ER - TY - CHAP A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Hannes A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Statistical shape modeling for craniosynostosis planning T2 - 2nd International Conference Advanced Digital Technology in Head and Neck Reconstruction 2005, Abstract Volume Y1 - 2005 SP - 64 CY - Banff, Alberta ER - TY - JOUR A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Topological methods for 2D time-dependent vector fields based on stream lines and path lines JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2005 U6 - https://doi.org/10.1109/TVCG.2005.68 VL - 11 IS - 4 ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Maxillofacial surgery planning with 3D soft tissue prediction - modeling, planning, simulation JF - 2. Int. Conf. on Advanced Digital Technology in Head and Neck Reconstruction, Abstract 33 Y1 - 2005 SP - 64 CY - Banff, Alberta, CA ER - TY - JOUR A1 - Saparin, Peter A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Zaikin, Alexei A1 - Kurths, Jürgen A1 - Hege, Hans-Christian A1 - Gowin, Wolfgang T1 - Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity JF - Acta Astronautica Y1 - 2005 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 56 IS - 9-12 SP - 820 EP - 830 ER - TY - CHAP A1 - Ullmer, Brygg A1 - Hutanu, Andrei A1 - Benger, Werner A1 - Hege, Hans-Christian ED - Staadt, Oliver T1 - Emerging Tangible Interfaces for Facilitating Collaborative Immersive Visualizations T2 - Proc. of NSF Lake Tahoe Workshop on Collaborative Virtual Reality and Visualization (extended abstract) Y1 - 2003 ER - TY - CHAP A1 - Theisel, Holger A1 - Weinkauf, Tino A1 - Hege, Hans-Christian A1 - Seidel, Hans-Peter T1 - Saddle Connectors - An Approach to Visualizing the Topological Skeleton of Complex 3D Vector Fields T2 - Proc. IEEE Visualization 2003 Y1 - 2003 U6 - https://doi.org/10.1109/VISUAL.2003.1250376 SP - 225 EP - 232 CY - Seattle ER -