TY - GEN A1 - Baum, Daniel A1 - Lindow, Norbert A1 - Hege, Hans-Christian A1 - Lepper, Verena A1 - Siopi, Tzulia A1 - Kutz, Frank A1 - Mahlow, Kristin A1 - Mahnke, Heinz-Eberhard T1 - Revealing hidden text in rolled and folded papyri N2 - Ancient Egyptian papyri are often folded, rolled up or kept as small packages, sometimes even sealed. Physically unrolling or unfolding these packages might severely damage them. We demonstrate a way to get access to the hidden script without physical unfolding by employing computed tomography and mathematical algorithms for virtual unrolling and unfolding. Our algorithmic approaches are combined with manual interaction. This provides the necessary flexibility to enable the unfolding of even complicated and partly damaged papyrus packages. In addition, it allows us to cope with challenges posed by the structure of ancient papyrus, which is rather irregular, compared to other writing substrates like metallic foils or parchment. Unfolding of packages is done in two stages. In the first stage, we virtually invert the physical folding process step by step until the partially unfolded package is topologically equivalent to a scroll or a papyrus sheet folded only along one fold line. To minimize distortions at this stage, we apply the method of moving least squares. In the second stage, the papyrus is simply flattened, which requires the definition of a medial surface. We have applied our software framework to several papyri. In this work, we present the results of applying our approaches to mockup papyri that were either rolled or folded along perpendicular fold lines. In the case of the folded papyrus, our approach represents the first attempt to address the unfolding of such complicated folds. T3 - ZIB-Report - 17-02 KW - unfolding, papyri, computed tomography Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61826 SN - 1438-0064 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie T2 - Tagungsband der DACH Jahrestagung 2012 Y1 - 2012 ER - 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 - 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 - 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 - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko N2 - We compute trajectories of dust grains starting from a homogeneous surface activity-profile on a irregularly shaped cometary nucleus. Despite the initially homogeneous dust distribution a collimation in jet-like structures becomes visible. The fine structure is caused by concave topographical features with similar bundles of normal vectors. The model incorporates accurately determined gravitational forces, rotation of the nucleus, and gas-dust interaction. Jet-like dust structures are obtained for a wide range of gas-dust interactions. For the comet 67P/Churyumov-Gerasimenko, we derive the global dust distribution around the nucleus and find several areas of agreement between the homogeneous dust emission model and the Rosetta observation of dust jets, including velocity-dependent bending of trajectories. Y1 - 2015 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 - CHAP A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Hege, Hans-Christian T1 - Atomic Accessibility Radii for Molecular Dynamics Analysis T2 - Workshop on Molecular Graphics and Visual Analysis of Molecular Data 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. Y1 - 2018 SN - 978-3-03868-061-1 U6 - https://doi.org/10.2312/molva.20181101 PB - The Eurographics Association ER - TY - JOUR A1 - Nyakatura, John A1 - Baumgarten, Roxane A1 - Baum, Daniel A1 - Stark, Heiko A1 - Youlatos, Dionisios T1 - Muscle internal structure revealed by contrast-enhanced μCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel JF - Mammalian Biology N2 - In individuals of similar body mass representing closely related species with different lifestyles, muscle architectural properties can be assumed to reflect adaptation to differing, lifestyle-related functional demands. We here employ a fiber recognition algorithm on contrast-enhanced micro-computed tomography (μCT) scans of one specimen each of an arboreal (Sciurus vulgaris) and a fossorial (Spermophilus citellus) sciuromorph rodent. The automated approach accounts for potential heterogeneity of architectural properties within a muscle by analyzing all fascicles that compose a muscle. Muscle architectural properties (volume, fascicle length, and orientation, and force-generating capacity) were quantified in 14 hindlimb (hip, knee, and ankle) extensor muscles and compared between specimens. We expected the arboreal squirrel to exhibit greater force-generating capacity and a greater capacity for length change allowing more powerful hindlimb extension. Generally and mostly matching our expectations, the S. vulgaris specimen had absolutely and relatively larger extensor muscles than the S. citellus specimen which were thus metabolically more expensive and demonstrate the relatively larger investment into powerful hindlimb extension necessary in the arboreal context. We conclude that detailed quantitative data on hindlimb muscle internal structure as was gathered here for a very limited sample further lends support to the notion that muscle architecture reflects adaptation to differential functional demands in closely related species with different locomotor behaviors and lifestyles. Y1 - 2019 U6 - https://doi.org/10.1016/j.mambio.2019.10.007 VL - 99 SP - 71 EP - 80 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 - TY - JOUR A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage JF - Bone N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. Y1 - 2020 U6 - https://doi.org/10.1016/j.bone.2020.115264 VL - 134 SP - 115264 ER - TY - GEN A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. T3 - ZIB-Report - 20-04 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-77087 SN - 1438-0064 ER - TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - GEN A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. T3 - ZIB-Report - 20-12 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78237 SN - 1438-0064 ER -