TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Breßler, David A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben T2 - Tagungsband der DGZfP Jahrestagung 2013 Y1 - 2013 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2012 SP - 321 EP - 330 ER - TY - JOUR A1 - Krone, Michael A1 - Kozlíková, 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 JF - Computer Graphics Forum 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. Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12928 SN - 1467-8659 VL - 35 IS - 3 SP - 527 EP - 551 ER - TY - GEN A1 - Dean, Mason N. A1 - Hosny, Ahmed A1 - Seidel, Ronald A1 - Baum, Daniel T1 - Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth T2 - Poster, Tomography for Scientific Advancement symposium (ToScA) Y1 - 2016 ER - TY - JOUR A1 - Titschack, Jürgen A1 - Fink, Hiske G. A1 - Baum, Daniel A1 - Wienberg, Claudia A1 - Hebbeln, Dierk A1 - Freiwald, André T1 - Mediterranean cold-water corals - an important regional carbonate factory? JF - The Depositional Record Y1 - 2016 U6 - https://doi.org/10.1002/dep2.14 VL - 2 IS - 1 SP - 74 EP - 96 ER - TY - CHAP A1 - Baum, Daniel A1 - Titschack, Jürgen T1 - Cavity and Pore Segmentation in 3D Images with Ambient Occlusion T2 - EuroVis 2016 - Short Papers Y1 - 2016 U6 - https://doi.org/10.2312/eurovisshort.20161171 PB - The Eurographics Association 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 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis N2 - In molecular structure analysis and visualization, the molecule’s atoms are often modeled as hard spheres parametrized by their positions and radii. While the atom positions result from experiments or molecular simulations, for the radii typically values are taken from literature. Most often, van der Waals (vdW) radii are used, for which diverse values exist. As a consequence, different visualization and analysis tools use different atomic radii, and the analyses are less objective than often believed. Furthermore, for the geometric accessibility analysis of molecular structures, vdW radii are not well suited. The reason is that during the molecular dynamics simulation, depending on the force field and the kinetic energy in the system, non-bonded atoms can come so close to each other that their vdW spheres intersect. In this paper, we introduce a new kind of atomic radius, called atomic accessibility radius’, that better characterizes the accessibility of an atom in a given molecular trajectory. The new radii reflect the movement possibilities of atoms in the simulated physical system. They are computed by solving a linear program that maximizes the radii of the atoms under the constraint that non-bonded spheres do not intersect in the considered molecular trajectory. Using this data-driven approach, the actual accessibility of atoms can be visualized more precisely. T3 - ZIB-Report - 18-18 KW - molecular dynamics KW - atomic radii KW - cavity analysis Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68468 SN - 1438-0064 ER - TY - JOUR A1 - Mohr, Gunther A1 - Altenburg, Simon J. A1 - Ulbricht, Alexander A1 - Heinrich, Philipp A1 - Baum, Daniel A1 - Maierhofer, Christiane A1 - Hilgenberg, Kai T1 - In-situ defect detection in laser powder bed fusion by using thermography and optical tomography – comparison to computed tomography JF - Metals Y1 - 2020 U6 - https://doi.org/10.3390/met10010103 VL - 10 IS - 1 SP - 103 ER - TY - JOUR A1 - Ziesche, Ralf F. A1 - Arlt, Tobias A1 - Finegan, Donal P. A1 - Heenan, Thomas M.M. A1 - Tengattini, Alessandro A1 - Baum, Daniel A1 - Kardjilov, Nikolay A1 - Markötter, Henning A1 - Manke, Ingo A1 - Kockelmann, Winfried A1 - Brett, Dan J.L. A1 - Shearing, Paul R. T1 - 4D imaging of lithium-batteries using correlative neutron and X-ray tomography with a virtual unrolling technique JF - Nature Communications N2 - The temporally and spatially resolved tracking of lithium intercalation and electrode degradation processes are crucial for detecting and understanding performance losses during the operation of lithium-batteries. Here, high-throughput X-ray computed tomography has enabled the identification of mechanical degradation processes in a commercial Li/MnO2 primary battery and the indirect tracking of lithium diffusion; furthermore, complementary neutron computed tomography has identified the direct lithium diffusion process and the electrode wetting by the electrolyte. Virtual electrode unrolling techniques provide a deeper view inside the electrode layers and are used to detect minor fluctuations which are difficult to observe using conventional three dimensional rendering tools. Moreover, the ‘unrolling’ provides a platform for correlating multi-modal image data which is expected to find wider application in battery science and engineering to study diverse effects e.g. electrode degradation or lithium diffusion blocking during battery cycling. Y1 - 2020 U6 - https://doi.org/10.1038/s41467-019-13943-3 VL - 11 SP - 777 ER -