@article{FaerberTitschackSchoenbergetal., author = {F{\"a}rber, Claudia and Titschack, J{\"u}rgen and Sch{\"o}nberg, Christine H. L. and Ehrig, Karsten and Boos, Karin and Baum, Daniel and Illerhaus, Bernd and Asgaard, Ulla and Bromley, Richard G. and Freiwald, Andr{\´e} and Wisshak, Max}, title = {Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography}, series = {Biogeosciences}, volume = {13}, journal = {Biogeosciences}, number = {11}, address = {http://www.biogeosciences.net/13/3461/2016/}, doi = {10.5194/bg-13-3461-2016}, pages = {3461 -- 3474}, abstract = {Biological erosion is a key process for the recycling of carbonate and the formation of calcareous sediments in the oceans. Experimental studies showed that bioerosion is subject to distinct temporal variability, but previous long-term studies were restricted to tropical waters. Here, we present results from a 14-year bioerosion experiment that was carried out along the rocky limestone coast of the island of Rhodes, Greece, in the Eastern Mediterranean Sea, in order to monitor the pace at which bioerosion affects carbonate substrate and the sequence of colonisation by bioeroding organisms. Internal macrobioerosion was visualised and quantified by micro-computed tomography and computer-algorithm-based segmentation procedures. Analysis of internal macrobioerosion traces revealed a dominance of bioeroding sponges producing eight types of characteristic Entobia cavity networks, which were matched to five different clionaid sponges by spicule identification in extracted tissue. The morphology of the entobians strongly varied depending on the species of the producing sponge, its ontogenetic stage, available space, and competition by other bioeroders. An early community developed during the first 5 years of exposure with initially very low macrobioerosion rates and was followed by an intermediate stage when sponges formed large and more diverse entobians and bioerosion rates increased. After 14 years, 30 \% of the block volumes were occupied by boring sponges, yielding maximum bioerosion rates of 900 g m^-2 yr^-1. A high spatial variability in macrobioerosion prohibited clear conclusions about the onset of macrobioerosion equilibrium conditions. This highlights the necessity of even longer experimental exposures and higher replication at various factor levels in order to better understand and quantify temporal patterns of macrobioerosion in marine carbonate environments.}, language = {en} } @misc{KnoetelSeidelHosnyetal., author = {Kn{\"o}tel, David and Seidel, Ronald and Hosny, Ahmed and Zaslansky, Paul and Weaver, James C. and Baum, Daniel and Dean, Mason N.}, title = {Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays}, series = {Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016}, journal = {Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016}, abstract = {The endoskeletons of sharks and rays are composed of an unmineralized cartilaginous core, covered in an outer layer of mineralized tiles called tesserae. The tessellated layer is vital to the growth as well as the material properties of the skeletal element, providing both flexibility and strength. However, characterizing the relationship between tesseral size and shape, and skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. Using a custom-made semi-automatic segmentation algorithm, we present the first quantitative and three-dimensional description of tesserae in micro-CT scans of whole skeletal elements. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. We exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Additionally, we have developed post-processing techniques to quickly correct segmentation errors. Our data reveals that the tessellation is not regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick-or disc-shaped tesserae are found in planar areas. We apply our newly developed techniques on the left and right hyomandibula (skeletal elements supporting the jaws) from four different ages of a stingray species, to clarify how tiling patterns develop across ontogeny and differ within and between individuals. We evaluate the functional consequences of tesseral morphologies using finite element analysis and 3d-printing, for a better understanding of shark skeletal mechanics, but also to extract fundamental engineering design principles of tiling arrangements on load-bearing three-dimensional objects.}, language = {en} } @misc{DeanHosnySeideletal., author = {Dean, Mason N. and Hosny, Ahmed and Seidel, Ronald and Baum, Daniel}, title = {Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth}, series = {Poster, Tomography for Scientific Advancement symposium (ToScA)}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA)}, language = {en} } @misc{KroneKozlikovaLindowetal., author = {Krone, Michael and Kozlikova, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan}, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60193}, abstract = {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.}, language = {en} } @inproceedings{ArltLindowBaumetal., author = {Arlt, Tobias and Lindow, Norbert and Baum, Daniel and Hilger, Andre and Mahnke, Ingo and Hege, Hans-Christian and Lepper, Verena and Siopi, Tzulia and Mahnke, Heinz.Eberhard}, title = {Virtual Access to Hidden Texts - Study of Ancient Papyri}, series = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, abstract = {When physical unfolding/unrolling of papyri is not possible or too dangerous for preserving the precious object, tomographic approaches may be the ap- propriate alternative. Requirements are the resolution and the contrast to distinguish writing and substrate. The steps to be performed are the following: (1) Select the object of interest (archaeological arguments, cultural back- ground of the object, etc.). (2) Find the proper physical procedure, especially with respect to contrast, take the tomographic data, e.g. by absorption x-ray tomography. (3) Apply mathematical unfolding transformations to the tomographic data, in order to obtain a 2d-planar reconstruction of text.}, language = {en} } @inproceedings{DeanSeidelKnoeteletal., author = {Dean, Mason N. and Seidel, R. and Kn{\"o}tel, David and Lyons, K. and Baum, Daniel and Weaver, James C. and Fratzl, Peter}, title = {To build a shark: 3D tiling laws of tessellated cartilage}, series = {Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA}, volume = {56 (suppl 1)}, booktitle = {Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA}, abstract = {The endoskeleton of sharks and rays (elasmobranchs) is comprised of a cartilaginous core, covered by thousands of mineralized tiles, called tesserae. Characterizing the relationship between tesseral morphometrics, skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. We integrate material property, histology, electron microscopy and synchrotron and laboratory µCT scans of skeletal elements from an ontogenetic series of round stingray Urobatis halleri, to gain insights into the generation and maintenance of a natural tessellated system. Using a custom-made semiautomatic segmentation algorithm, we present the first quantitative and 3d description of tesserae across whole skeletal elements. The tessellation is not interlocking or regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick- or disc-shaped tesserae are found in planar/flatter areas. Comparison of the tessellation across ontogeny, shows that in younger animals, the forming tesseral network is less densely packed, appearing as a covering of separate, poorly mineralized islands that grow together with age to form a complete surface. Some gaps in the tessellation are localized to specific regions in all samples, indicating they are real features, perhaps either regions of delayed mineralization or of tendon insertion. We will use the structure of elasmobranch skeletons as a road map for understanding shark and ray skeletal mechanics, but also to extract fundamental engineering principles for tiled composite materials.}, language = {en} } @article{KozlikovaKroneFalketal., author = {Kozl{\´i}kov{\´a}, Barbora and Krone, Michael and Falk, Martin and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Viola, Ivan and Parulek, Julius and Hege, Hans-Christian}, title = {Visualization of Biomolecular Structures: State of the Art Revisited}, series = {Computer Graphics Forum}, volume = {36}, journal = {Computer Graphics Forum}, number = {8}, doi = {10.1111/cgf.13072}, pages = {178 -- 204}, abstract = {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.}, language = {en} } @misc{BaumTitschack, author = {Baum, Daniel and Titschack, J{\"u}rgen}, title = {Cavity and Pore Segmentation in 3D Images with Ambient Occlusion}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-59151}, abstract = {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.}, language = {en} } @article{TitschackFinkBaumetal., author = {Titschack, J{\"u}rgen and Fink, Hiske G. and Baum, Daniel and Wienberg, Claudia and Hebbeln, Dierk and Freiwald, Andr{\´e}}, title = {Mediterranean cold-water corals - an important regional carbonate factory?}, series = {The Depositional Record}, volume = {2}, journal = {The Depositional Record}, number = {1}, doi = {10.1002/dep2.14}, pages = {74 -- 96}, language = {en} } @inproceedings{BaumTitschack, author = {Baum, Daniel and Titschack, J{\"u}rgen}, title = {Cavity and Pore Segmentation in 3D Images with Ambient Occlusion}, series = {EuroVis 2016 - Short Papers}, booktitle = {EuroVis 2016 - Short Papers}, publisher = {The Eurographics Association}, doi = {10.2312/eurovisshort.20161171}, language = {en} } @article{KroneKozlikovaLindowetal.2016, author = {Krone, Michael and Kozl{\´i}kov{\´a}, Barbora and Lindow, Norbert and Baaden, Marc and Baum, Daniel and Parulek, Julius and Hege, Hans-Christian and Viola, Ivan}, title = {Visual Analysis of Biomolecular Cavities: State of the Art}, series = {Computer Graphics Forum}, volume = {35}, journal = {Computer Graphics Forum}, number = {3}, issn = {1467-8659}, doi = {10.1111/cgf.12928}, pages = {527 -- 551}, year = {2016}, abstract = {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.}, language = {en} }