TY - GEN A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ebell, Gino A1 - Ehrig, Karsten A1 - Heyn, Andreas A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben N2 - Kurzfassung. Durch die Alkalität des Betons wird Betonstahl dauerhaft vor Korrosion geschützt. Infolge von Chlorideintrag kann dieser Schutz nicht länger aufrechterhalten werden und führt zu Lochkorrosion. Die zerstörungsfreie Prüfung von Stahlbetonproben mit 3D-CT bietet die Möglichkeit, eine Probe mehrfach gezielt vorzuschädigen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung des Schädigungsgrades müssen die bei dieser Untersuchung anfallenden großen Bilddaten mit Bildverarbeitungsmethoden ausgewertet werden. Ein wesentlicher Schritt dabei ist die Segmentierung der Bilddaten, bei der zwischen Korrosionsprodukt (Rost), Betonstahl (BSt), Beton, Rissen, Poren und Umgebung unterschieden werden muss. Diese Segmentierung bildet die Grundlage für statistische Untersuchungen des Schädigungsfortschritts. Hierbei sind die Änderung der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Veränderung über die Zeit sowie ihrer räumlichen Verteilung in der Probe von Interesse. Aufgrund der Größe der CT-Bilddaten ist eine manuelle Segmentierung nicht durchführbar, so dass automatische Verfahren unabdingbar sind. Dabei ist insbesondere die Segmentierung der Korrosionsprodukte in den Bilddaten ein schwieriges Problem. Allein aufgrund der Grauwerte ist eine Zuordnung nahezu unmöglich, denn die Grauwerte von Beton und Korrosionsprodukt unterscheiden sich kaum. Eine formbasierte Suche ist nicht offensichtlich, da die Korrosionsprodukte in Beton diffuse Formen haben. Allerdings lässt sich Vorwissen über die Ausbreitung der Korrosionsprodukte nutzen. Sie bilden sich in räumlicher Nähe des BSt (in Bereichen vorheriger Volumenabnahme des BSt), entlang von Rissen sowie in Porenräumen, die direkt am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der Korrosionsprodukterkennung zunächst eine BSt-Volumen-, Riss- und Porenerkennung durchgeführt. Dieser in der Arbeit näher beschriebene Schritt erlaubt es, halbautomatisch Startpunkte (Seed Points) für die Korrosionsprodukterkennung zu finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte Algorithmen auf ihre Eignung untersucht werden. T3 - ZIB-Report - 14-24 KW - Beton KW - Korrosionserkennung KW - Bildverarbeitung KW - Computertomografie KW - concrete KW - corrosiondetection KW - image processing KW - computed tomography Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50912 SN - 1438-0064 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 - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage N2 - Introduction – Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods – Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results – Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours. T3 - ZIB-Report - 17-62 KW - micro-CT KW - image segmentation KW - 2D distance map KW - hierarchical watershed KW - stingray KW - tesserae KW - biological tilings KW - Amira Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65785 SN - 1438-0064 ER - TY - GEN A1 - Kozlikova, Barbora A1 - Krone, Michael A1 - Falk, Martin A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Viola, Ivan A1 - Parulek, Julius A1 - Hege, Hans-Christian T1 - Visualization of Biomolecular Structures: State of the Art N2 - Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets. T3 - ZIB-Report - 15-63 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57217 SN - 1438-0064 ER - TY - GEN A1 - Krone, Michael A1 - Kozlikova, Barbora A1 - Lindow, Norbert A1 - Baaden, Marc A1 - Baum, Daniel A1 - Parulek, Julius A1 - Hege, Hans-Christian A1 - Viola, Ivan T1 - Visual Analysis of Biomolecular Cavities: State of the Art N2 - In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field. T3 - ZIB-Report - 16-42 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60193 SN - 1438-0064 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials N2 - An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation. T3 - ZIB-Report - 13-56 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42510 SN - 1438-0064 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data N2 - Materials with a trabecular structure notably combine advantages such as lightweight, reasonable strength, and permeability for fluids. This combination of advantages is especially interesting for tissue engineering in trauma surgery and orthopedics. Bone-substituting scaffolds for instance are designed with a trabecular structure in order to allow cell migration for bone ingrowth and vascularization. An emerging and recently very popular technology to produce such complex, porous structures is 3D printing. However, several technological aspects regarding the scaffold architecture, the printable resolution, and the feature size have to be considered when fabricating scaffolds for bone tissue replacement and regeneration. Here, we present a strategy to assess and prepare realistic trabecular structures for 3D printing using image analysis with the aim of preserving the structural elements. We discuss critical conditions of the printing system and present a 3-stage approach to adapt a trabecular structure from $\mu$CT data while incorporating knowledge about the printing system. In the first stage, an image-based extraction of solid and void structures is performed, which results in voxel- and graph-based representations of the extracted structures. These representations not only allow us to quantify geometrical properties such as pore size or strut geometry and length. But, since the graph represents the geometry and the topology of the initial structure, it can be used in the second stage to modify and adjust feature size, volume and sample size in an easy and consistent way. In the final reconstruction stage, the graph is then converted into a voxel representation preserving the topology of the initial structure. This stage generates a model with respect to the printing conditions to ensure a stable and controlled voxel placement during the printing process. T3 - ZIB-Report - 17-26 KW - trabecular structures KW - image-based analysis KW - additive manufacturing KW - printability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64004 SN - 1438-0064 ER - TY - GEN A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. T3 - ZIB-Report - 17-78 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66338 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel A1 - Titschack, Jürgen T1 - Cavity and Pore Segmentation in 3D Images with Ambient Occlusion N2 - Many natural objects contain pores and cavities that are filled with the same material that also surrounds the object. When such objects are imaged using, for example, computed tomography, the pores and cavities cannot be distinguished from the surrounding material by considering gray values and texture properties of the image. In this case, morphological operations are often used to fill the inner region. This is efficient, if the pore and cavity structures are small compared to the overall size of the object and if the object’s shape is mainly convex. If this is not the case, the segmentation might be very difficult and may result in a lot of noise. We propose the usage of ambient occlusion for the segmentation of pores and cavities. One nice property of ambient occlusion is that it generates smooth scalar fields. Due to this smoothness property, a segmentation based on those fields will result in smooth boundaries at the pore and cavity openings. This is often desired, particularly when dealing with natural objects. T3 - ZIB-Report - 16-17 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59151 SN - 1438-0064 ER - TY - GEN A1 - Baum, Daniel T1 - An Evaluation of Color Maps for Visual Data Exploration T3 - ZIB-Report - 19-42 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74259 SN - 1438-0064 ER -