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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.
In civil engineering, the corrosion of steel reinforcements in structural elements of concrete bares a risk of
stability-reduction, mainly caused by the exposure to chlorides. 3D computed tomography (CT) reveals the inner
structure of concrete and allows one to investigate the corrosion with non-destructive testing methods. To carry
out such investigations, specimens with a large artificial crack and an embedded steel rebar have been
manufactured. 3D CT images of those specimens were acquired in the original state. Subsequently three cycles
of electrochemical pre-damaging together with CT imaging were applied. These time series have been evaluated
by means of image processing algorithms to segment and quantify the corrosion products. Visualization of the
results supports the understanding of how corrosion propagates into cracks and pores. Furthermore, pitting of
structural elements can be seen without dismantling. In this work, several image processing and visualization
techniques are presented that have turned out to be particularly effective for the visualization and segmentation
of corrosion products. Their combination to a workflow for corrosion analysis is the main contribution of this
work.
The cartilaginous endoskeletons of sharks and rays are covered by tiles of mineralized cartilage called tesserae that enclose areas of unmineralized cartilage. These tesselated layers are vital to the growth as well as the material properties of the skeleton, providing both flexibility and strength. An understanding of the principles behind the tiling of the mineralized layer requires a quantitative analysis of shark and ray skeletal tessellation. However, since a single skeletal element comprises several thousand tesserae, manual segmentation is infeasible. We developed an automated segmentation pipeline that, working from micro-CT data, allows quantification of all tesserae in a skeletal element in less than an hour. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. In micro-CT scans, tesserae usually appear as round or star-shaped plate-like tiles, wider than deep and connected by mineralized intertesseral joints. Based on these observations, we exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Utilizing a two-dimensional distance map that measures the distance in the plane of the mineralized layer only greatly improves the segmentation. We developed post-processing techniques to quickly correct segmentation errors in regions where tesseral shape differs from the assumed shape. Evaluation of our results is done qualitatively by visual comparison with raw datasets, and quantitatively by comparison to manual segmentations. Furthermore, we generate two-dimensional abstractions of the tiling network based on the neighborhood, allowing representation of complex, biological forms as simpler geometries. We apply our newly developed techniques to the analysis of the left and right hyomandibulae of four ages of stingray enabling the first quantitative analyses of the tesseral tiling structure, while clarifying how these patterns develop across ontogeny.
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.
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 report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.
Two new species of cheilostome Bryozoa are described from continental-slope habitats off Mauritania, including canyon and coldwater-coral (mound) habitats. Internal structures of both species were visualised and quantified using micro-computed tomographic (micro-CT) methods. Cellaria bafouri n. sp. is characterised by the arrangement of zooids in alternating longitudinal rows, a smooth cryptocyst, and the presence of an ooecial plate with denticles. Smittina imragueni n. sp. exhibits many similarities with Smittina cervicornis (Pallas, 1766), but differs especially in the shape and orientation of the suboral avicularium. Observations on Smittina imragueni and material labelled as Smittina cervicornis suggest that the latter represents a species group, members of which have not yet been discriminated, possibly because of high intracolony variation and marked astogenetic changes in surface morphology. Both new species are known only from the habitats where they were collected, probably reflecting the paucity of bryozoan sampling from this geographic area and depth range. Both species are able to tolerate low oxygen concentration, which is assumed to be compensated by the high nutrient supply off Mauritania. The application of micro-CT for the semiautomatic quantification of zooidal skeletal characters was successfully tested. We were able to automatically distinguish individual zooidal cavities and acquire corresponding morphological datasets. Comparing the obtained results with conventional SEM measurements allowed ascertaining the reliability of this new method. The employment of micro-CT allows the observation and quantification of previously un- seen characters that can be used in describing and differentiating species that were previously indistinguishable. Further- more, this method might help elucidate processes of colony growth and the function of individual zooids during this process.
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.