@misc{StallingZoecklerSanderetal., author = {Stalling, Detlev and Z{\"o}ckler, Malte and Sander, Oliver and Hege, Hans-Christian}, title = {Weighted Labels for 3D Image Segmentation}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-3828}, number = {SC-98-39}, abstract = {Segmentation tools in medical imaging are either based on editing geometric curves or on the assignment of region labels to image voxels. While the first approach is well suited to describe smooth contours at subvoxel accuracy, the second approach is conceptually more simple and guarantees a unique classification of image areas. However, contours extracted from labeled images typically exhibit strong staircase artifacts and are not well suited to represent smooth tissue boundaries. In this paper we describe how this drawback can be circumvented by supplementing region labels with additional weights. We integrated our approach into an interactive segmentation system providing a well-defined set of manual and semi-automatic editing tools. All tools update both region labels as well as the corresponding weights simultaneously, thus allowing one to define segmentation results at high resolution. We applied our techniques to generate 3D polygonal models of anatomical structures.}, language = {en} } @misc{MahnkeArltBaumetal., author = {Mahnke, Heinz-Eberhard and Arlt, Tobias and Baum, Daniel and Hege, Hans-Christian and Herter, Felix and Lindow, Norbert and Manke, Ingo and Siopi, Tzulia and Menei, Eve and Etienne, Marc and Lepper, Verena}, title = {Virtual unfolding of folded papyri}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74338}, abstract = {The historical importance of ancient manuscripts is unique since they provide information about the heritage of ancient cultures. Often texts are hidden in rolled or folded documents. Due to recent impro- vements in sensitivity and resolution, spectacular disclosures of rolled hidden texts were possible by X-ray tomography. However, revealing text on folded manuscripts is even more challenging. Manual unfolding is often too risky in view of the fragile condition of fragments, as it can lead to the total loss of the document. X-ray tomography allows for virtual unfolding and enables non-destructive access to hid- den texts. We have recently demonstrated the procedure and tested unfolding algorithms on a mockup sample. Here, we present results on unfolding ancient papyrus packages from the papyrus collection of the Mus{\´e}e du Louvre, among them objects folded along approximately orthogonal folding lines. In one of the packages, the first identification of a word was achieved, the Coptic word for "Lord".}, language = {en} } @misc{ZoecklerStallingHege, 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}, 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{BengerHegeMerzkyetal., 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}, 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{BengerHegeHeusler, 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}, 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{SchmidtEhrenbergHege, 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}, 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{HegeHutanuKaehleretal., 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}, 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{KaehlerHege, 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}, 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{BengerHege, author = {Benger, Werner and Hege, Hans-Christian}, title = {Tensor Splats}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-7393}, number = {03-17}, 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{ZoecklerReinBrandtetal., author = {Z{\"o}ckler, Malte and Rein, Karlheinz and Brandt, Robert and Stalling, Detlev and Hege, Hans-Christian}, title = {Creating Virtual Insect Brains with Amira}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6589}, number = {01-32}, abstract = {By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants.}, language = {en} } @misc{StallingSeebassZoeckleretal., author = {Stalling, Detlev and Seebass, Martin and Z{\"o}ckler, Malte and Hege, Hans-Christian}, title = {Hyperthermia Treatment Planning with HyperPlan - User's Manual}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5957}, number = {00-27}, abstract = {HyperPlan is a software system for performing 3D-simulations and treatment planning in regional hyperthermia. It allows the user to understand the complex effects of electromagnetic wave propagation and heat transport inside a patient's body. Optimized power amplitudes and phase settings can be calculated for the BSD radiowave applicators Sigma 60 and Sigma 2000 (eye-applicator). HyperPlan is built on top of the modular, object-oriented visualization system Amira. This system already contains powerful algorithms for image processing, geometric modelling and 3D graphics display. HyperPlan provides a number of hyperthermia-specific modules, allowing the user to create 3D tetrahedral patient models suitable for treatment planning. In addition, all numerical simulation modules required for hyperthermia simulation are part of HyperPlan. This guide provides a step-by-step introduction to hyperthermia planning using HyperPlan. It also describes the usage of the underlying visualization system Amira.}, language = {en} } @misc{DeuflhardHege, author = {Deuflhard, Peter and Hege, Hans-Christian}, title = {Die Vision einer individuellen quantitativen Medizin}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-8805}, number = {05-47}, abstract = {Die Autoren schreiben dieses Papier aus der eingeschr{\"a}nkten Sicht der Mathematik und der Informationstechnik. Um den speziellen Beitrag dieser Disziplinen {\"u}berhaupt diskutieren zu k{\"o}nnen, sehen wir uns jedoch gezwungen, einen Rahmen abzustecken, den wir f{\"u}r das Jahr 2020 vorhersehen -- nach Wahrscheinlichkeit und aus unserem engeren fachlichen Blickwinkel. Vorab bitten wir schon einmal bei den medizinischen Fachleuten um Nachsicht, wenn wir uns in ihrem Revier allzu dillettantisch bewegen. Vielleicht f{\"o}rdert aber auch unser eingeschr{\"a}nkter Blickwinkel ansonsten unbedachte Aspekte zutage -- das hoffen wir zumindest.}, language = {de} } @misc{HoerthBaumKnoeteletal., author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, abstract = {Purpose/Aims of the Study: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro computed tomography (μCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. Materials and Methods: We investigated bone during healing by means of μCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. Results: We present an approach for the registration of 2D data in a 3D μCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into μCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. Conclusions: By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.}, language = {en} } @misc{VohraHarthIsoeetal., author = {Vohra, Sumit Kumar and Harth, Philipp and Isoe, Yasuko and Bahl, Armin and Fotowat, Haleh and Engert, Florian and Hege, Hans-Christian and Baum, Daniel}, title = {A Visual Interface for Exploring Hypotheses about Neural Circuits}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89932}, abstract = {One of the fundamental problems in neurobiological research is to understand how neural circuits generate behaviors in response to sensory stimuli. Elucidating such neural circuits requires anatomical and functional information about the neurons that are active during the processing of the sensory information and generation of the respective response, as well as an identification of the connections between these neurons. With modern imaging techniques, both morphological properties of individual neurons as well as functional information related to sensory processing, information integration and behavior can be obtained. Given the resulting information, neurobiologists are faced with the task of identifying the anatomical structures down to individual neurons that are linked to the studied behavior and the processing of the respective sensory stimuli. Here, we present a novel interactive tool that assists neurobiologists in the aforementioned task by allowing them to extract hypothetical neural circuits constrained by anatomical and functional data. Our approach is based on two types of structural data: brain regions that are anatomically or functionally defined, and morphologies of individual neurons. Both types of structural data are interlinked and augmented with additional information. The presented tool allows the expert user to identify neurons using Boolean queries. The interactive formulation of these queries is supported by linked views, using, among other things, two novel 2D abstractions of neural circuits. The approach was validated in two case studies investigating the neural basis of vision-based behavioral responses in zebrafish larvae. Despite this particular application, we believe that the presented tool will be of general interest for exploring hypotheses about neural circuits in other species, genera and taxa.}, language = {en} } @misc{NavaYazdaniHegevonTycowicz, author = {Nava-Yazdani, Esfandiar and Hege, Hans-Christian and von Tycowicz, Christoph}, title = {A Hierarchical Geodesic Model for Longitudinal Analysis on Manifolds}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85187}, abstract = {In many applications, geodesic hierarchical models are adequate for the study of temporal observations. We employ such a model derived for manifold-valued data to Kendall's shape space. In particular, instead of the Sasaki metric, we adapt a functional-based metric, which increases the computational efficiency and does not require the implementation of the curvature tensor. We propose the corresponding variational time discretization of geodesics and employ the approach for longitudinal analysis of 2D rat skulls shapes as well as 3D shapes derived from an imaging study on osteoarthritis. Particularly, we perform hypothesis test and estimate the mean trends.}, language = {en} }