@article{HoerthBaumKnoeteletal.2015, author = {Hoerth, Rebecca M. and Baum, Daniel and Kn{\"o}tel, David and Prohaska, Steffen and Willie, Bettina M. and Duda, Georg and Hege, Hans-Christian and Fratzl, Peter and Wagermaier, Wolfgang}, title = {Registering 2D and 3D Imaging Data of Bone during Healing}, volume = {56}, journal = {Connective Tissue Research}, number = {2}, publisher = {Taylor \& Francis}, doi = {10.3109/03008207.2015.1005210}, pages = {133 -- 143}, year = {2015}, language = {en} } @article{CourniaAllenAndricioaeietal.2015, author = {Cournia, Zoe and Allen, Toby W. and Andricioaei, Ioan and Antonny, Bruno and Baum, Daniel and Brannigan, Grace and Buchete, Nicolae-Viorel and Deckman, Jason T. and Delemotte, Lucie and del Val, Coral and Friedman, Ran and Gkeka, Paraskevi and Hege, Hans-Christian and H{\´e}nin, J{\´e}r{\^o}me and Kasimova, Marina A. and Kolocouris, Antonios and Klein, Michael L. and Khalid, Syma and Lemieux, Joanne and Lindow, Norbert and Roy, Mahua and Selent, Jana and Tarek, Mounir and Tofoleanu, Florentina and Vanni, Stefano and Urban, Sinisa and Wales, David J. and Smith, Jeremy C. and Bondar, Ana-Nicoleta}, title = {Membrane Protein Structure, Function and Dynamics: A Perspective from Experiments and Theory}, volume = {248}, journal = {Journal of Membrane Biology}, number = {4}, doi = {10.1007/s00232-015-9802-0}, pages = {611 -- 640}, year = {2015}, language = {en} } @misc{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54353}, year = {2015}, abstract = {Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time.}, language = {en} } @misc{WeberTranfieldHoeoegetal.2014, author = {Weber, Britta and Tranfield, Erin M. and H{\"o}{\"o}g, Johanna L. and Baum, Daniel and Antony, Claude and Hyman, Tony and Verbavatz, Jean-Marc and Prohaska, Steffen}, title = {Automated stitching of microtubule centerlines across serial electron tomograms}, issn = {1438-0064}, doi = {10.1371/journal.pone.0113222}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52958}, year = {2014}, abstract = {Tracing microtubule centerlines in serial section electron tomography requires microtubules to be stitched across sections, that is lines from different sections need to be aligned, endpoints need to be matched at section boundaries to establish a correspondence between neighboring sections, and corresponding lines need to be connected across multiple sections. We present computational methods for these tasks: 1) An initial alignment is computed using a distance compatibility graph. 2) A fine alignment is then computed with a probabilistic variant of the iterative closest points algorithm, which we extended to handle the orientation of lines by introducing a periodic random variable to the probabilistic formulation. 3) Endpoint correspondence is established by formulating a matching problem in terms of a Markov random field and computing the best matching with belief propagation. Belief propagation is not generally guaranteed to converge to a minimum. We show how convergence can be achieved, nonetheless, with minimal manual input. In addition to stitching microtubule centerlines, the correspondence is also applied to transform and merge the electron tomograms. We applied the proposed methods to samples from the mitotic spindle in C. elegans, the meiotic spindle in X. laevis, and sub-pellicular microtubule arrays in T. brucei. The methods were able to stitch microtubules across section boundaries in good agreement with experts' opinions for the spindle samples. Results, however, were not satisfactory for the microtubule arrays. For certain experiments, such as an analysis of the spindle, the proposed methods can replace manual expert tracing and thus enable the analysis of microtubules over long distances with reasonable manual effort.}, language = {en} } @inproceedings{DeanSeidelKnoeteletal.2016, 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}, 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}, year = {2016}, 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} } @misc{AboulhassanSicatBaumetal.2017, author = {Aboulhassan, Amal and Sicat, Ronell and Baum, Daniel and Wodo, Olga and Hadwiger, Markus}, title = {Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63239}, year = {2017}, abstract = {The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.}, language = {en} } @article{KozlikovaKroneFalketal.2016, 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}, volume = {36}, journal = {Computer Graphics Forum}, number = {8}, doi = {10.1111/cgf.13072}, pages = {178 -- 204}, year = {2016}, 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} } @inproceedings{ArltLindowBaumetal.2016, 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}, booktitle = {Eighth Joint BER II and BESSY II User Meeting, Dec 7-9, 2016, Berlin, Germany}, year = {2016}, 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} } @article{AboulhassanSicatBaumetal.2017, author = {Aboulhassan, Amal and Sicat, Ronell and Baum, Daniel and Wodo, Olga and Hadwiger, Markus}, title = {Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies}, volume = {36}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley}, doi = {10.1111/cgf.13191}, pages = {329 -- 339}, year = {2017}, abstract = {The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.}, language = {en} } @article{HombergBaumProhaskaetal.2017, author = {Homberg, Ulrike and Baum, Daniel and Prohaska, Steffen and G{\"u}nster, Jens and Krauß-Sch{\"u}ler, Stefanie}, title = {Adapting trabecular structures for 3D printing: an image processing approach based on µCT data}, volume = {3}, journal = {Biomedical Physics \& Engineering Express}, number = {3}, publisher = {IOP Publishing}, doi = {10.1088/2057-1976/aa7611}, year = {2017}, abstract = {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.}, language = {en} } @misc{HombergBaumProhaskaetal.2017, author = {Homberg, Ulrike and Baum, Daniel and Prohaska, Steffen and G{\"u}nster, Jens and Krauß-Sch{\"u}ler, Stefanie}, title = {Adapting trabecular structures for 3D printing: an image processing approach based on µCT data}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64004}, year = {2017}, abstract = {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.}, language = {en} } @inproceedings{BaumMahlowLameckeretal.2014, author = {Baum, Daniel and Mahlow, Kristin and Lamecker, Hans and Zachow, Stefan and M{\"u}ller, Johannes and Hege, Hans-Christian}, title = {The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis)}, booktitle = {Abstract in DigitalSpecimen 2014}, year = {2014}, abstract = {Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term 'surface-based morphometrics'. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called 'surface paths', might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique.}, language = {en} } @article{PaetschBaumProhaskaetal.2014, author = {Paetsch, Olaf and Baum, Daniel and Prohaska, Steffen and Ehrig, Karsten and Ebell, Gino and Meinel, Dietmar and Heyn, Andreas}, title = {Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben}, journal = {DGZfP-Jahrestagung 2014 Konferenzband}, year = {2014}, language = {de} } @misc{PaetschBaumEbelletal.2014, author = {Paetsch, Olaf and Baum, Daniel and Ebell, Gino and Ehrig, Karsten and Heyn, Andreas and Meinel, Dietmar and Prohaska, Steffen}, title = {Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50912}, year = {2014}, abstract = {Kurzfassung. Durch die Alkalit{\"a}t des Betons wird Betonstahl dauerhaft vor Korrosion gesch{\"u}tzt. Infolge von Chlorideintrag kann dieser Schutz nicht l{\"a}nger aufrechterhalten werden und f{\"u}hrt zu Lochkorrosion. Die zerst{\"o}rungsfreie Pr{\"u}fung von Stahlbetonproben mit 3D-CT bietet die M{\"o}glichkeit, eine Probe mehrfach gezielt vorzusch{\"a}digen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung des Sch{\"a}digungsgrades m{\"u}ssen 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 f{\"u}r statistische Untersuchungen des Sch{\"a}digungsfortschritts. Hierbei sind die {\"A}nderung der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Ver{\"a}nderung {\"u}ber die Zeit sowie ihrer r{\"a}umlichen Verteilung in der Probe von Interesse. Aufgrund der Gr{\"o}ße der CT-Bilddaten ist eine manuelle Segmentierung nicht durchf{\"u}hrbar, 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 unm{\"o}glich, 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 l{\"a}sst sich Vorwissen {\"u}ber die Ausbreitung der Korrosionsprodukte nutzen. Sie bilden sich in r{\"a}umlicher N{\"a}he des BSt (in Bereichen vorheriger Volumenabnahme des BSt), entlang von Rissen sowie in Porenr{\"a}umen, die direkt am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der Korrosionsprodukterkennung zun{\"a}chst eine BSt-Volumen-, Riss- und Porenerkennung durchgef{\"u}hrt. Dieser in der Arbeit n{\"a}her beschriebene Schritt erlaubt es, halbautomatisch Startpunkte (Seed Points) f{\"u}r die Korrosionsprodukterkennung zu finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte Algorithmen auf ihre Eignung untersucht werden.}, language = {de} } @article{FaerberTitschackSchoenbergetal.2016, 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}, volume = {13}, journal = {Biogeosciences}, number = {11}, address = {http://www.biogeosciences.net/13/3461/2016/}, doi = {10.5194/bg-13-3461-2016}, pages = {3461 -- 3474}, year = {2016}, 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{KozlikovaKroneFalketal.2015, author = {Kozlikova, 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}, issn = {1438-0064}, doi = {10.2312/eurovisstar.20151112}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-57217}, year = {2015}, 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} } @inproceedings{KozlikovaKroneLindowetal.2015, author = {Kozlikova, Barbora and Krone, Michael and Lindow, Norbert and Falk, Martin 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}, booktitle = {EuroVis 2015 STARS Proceedings}, doi = {10.2312/eurovisstar.20151112}, pages = {61 -- 81}, year = {2015}, 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 report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.}, language = {en} } @misc{TitschackBaum2014, author = {Titschack, J{\"u}rgen and Baum, Daniel}, title = {Advanced computed tomography analyses of cold-water coral mound cores: new insights into mound formation processes}, journal = {Poster, 19th International Sedimentological Congress, Geneva, Switzerland, 2014, August 18 - 22}, year = {2014}, language = {en} } @misc{TitschackBaum2015, author = {Titschack, J{\"u}rgen and Baum, Daniel}, title = {Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals}, journal = {Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Krak{\´o}w, Poland}, year = {2015}, language = {en} } @misc{KnoetelSeidelWeaveretal.2015, author = {Kn{\"o}tel, David and Seidel, Ronald and Weaver, James C. and Baum, Daniel and Dean, Mason N.}, title = {Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015}, year = {2015}, abstract = {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.}, language = {en} } @misc{KnoetelSeidelHosnyetal.2016, 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}, journal = {Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016}, year = {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{SeidelKnoetelBaumetal.2014, author = {Seidel, Ronald and Kn{\"o}tel, David and Baum, Daniel and Weaver, James C. and Dean, Mason N.}, title = {Material and structural characterization of mineralized elasmobranch cartilage - lessons in repeated tiling patterns in mechanically loaded 3D objects}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA), London, UK, September 1 - 3, 2014}, year = {2014}, abstract = {Biological tissues achieve a wide range of properties and function, however with limited components. The organization of these constituent parts is a decisive factor in the impressive properties of biological materials, with tissues often exhibiting complex arrangements of hard and soft materials. The "tessellated" cartilage of the endoskeleton of sharks and rays, for example, is a natural composite of mineralized polygonal tiles (tesserae), collagen fiber bundles, and unmineralized cartilage, resulting in a material that is both flexible and strong, with optimal stiffness. The properties of the materials and the tiling geometry are vital to the growth and mechanics of the system, but had not been investigated due to the technical challenges involved. We use high-resolution materials characterization techniques (qBEI, µCT) to show that tesserae exhibit great variability in mineral density, supporting theories of accretive growth mechanisms. We present a developmental series of tesserae and outline the development of unique structural features that appear to function in load bearing and energy dissipation, with some structural features far exceeding cortical bone's mineral content and tissue stiffness. To examine interactions among tesserae, we developed an advanced tiling-recognition-algorithm to semi-automatically detect and isolate individual tiles in microCT scans of tesseral mats. The method allows quantification of shape variation across a wide area, allowing localization of regions of high/low reinforcement or flexibility in the skeleton. The combination of our material characterization and visualization techniques allows the first quantitative 3d description of anatomy and material properties of tesserae and the organization of tesseral networks in elasmobranch mineralized cartilage, providing insight into form-function relationships of the repeating tiled pattern. We aim to combine detailed knowledge of intra-tesseral morphology and mineralization to model the relationships of tesseral shapes and skeletal surface curvature, to understand fundamental tiling laws important for complex, mechanically loaded 3d objects.}, language = {en} } @inproceedings{PaetschBaumProhaskaetal.2015, author = {Paetsch, Olaf and Baum, Daniel and Prohaska, Steffen and Ehrig, Karsten and Meinel, Dietmar and Ebell, Gino}, title = {3D Corrosion Detection in Time-dependent CT Images of Concrete}, booktitle = {DIR-2015 Proceedings}, year = {2015}, abstract = {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.}, language = {en} }