@article{WeinkaufGuenther2009, author = {Weinkauf, Tino and G{\"u}nther, David}, title = {Separatrix Persistence: Extraction of Salient Edges on Surfaces Using Topological Methods}, volume = {28}, journal = {Computer Graphics Forum (Proc. SGP'09)}, number = {5}, doi = {10.1111/j.1467-8659.2009.01528.x}, pages = {1519 -- 1528}, year = {2009}, language = {en} } @inproceedings{KussProhaskaMeyeretal.2008, author = {Kuß, Anja and Prohaska, Steffen and Meyer, Bj{\"o}rn and Rybak, J{\"u}rgen and Hege, Hans-Christian}, title = {Ontology-Based Visualization of Hierarchical Neuroanatomical Structures}, booktitle = {Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008}, pages = {177 -- 184}, year = {2008}, language = {en} } @inproceedings{GoubergritsPoethkePetzetal.2008, author = {Goubergrits, Leonid and P{\"o}thke, Jens and Petz, Christoph and Hege, Hans-Christian and Spuler, Andreas and Kertzscher, Ulrich}, title = {3D Bildgebung von zerebralen Aneurysmen}, booktitle = {Bildverarbeitung f{\"u}r die Medizin}, doi = {10.1007/978-3-540-78640-5_31}, pages = {153 -- 157}, year = {2008}, language = {en} } @article{GoubergritsKertzscherSchoenebergetal.2008, author = {Goubergrits, Leonid and Kertzscher, Ulrich and Sch{\"o}neberg, Bastian and Wellnhofer, Ernst and Petz, Christoph}, title = {CFD analysis in an anatomically realistic coronary artery model based on non-invasive 3D imaging}, volume = {24(4)}, journal = {Int. J. Cardiovasc. Imaging}, doi = {10.1007/s10554-007-9275-z}, pages = {411 -- 421}, year = {2008}, language = {en} } @inproceedings{PetzProhaskaGoubergritsetal.2008, author = {Petz, Christoph and Prohaska, Steffen and Goubergrits, Leonid and Kertzscher, Ulrich and Hege, Hans-Christian}, title = {Near-Wall Flow Visualization in Flattened Surface Neighborhoods}, booktitle = {Proc. Simulation and Visualization 2008}, address = {Magdeburg, Germany}, pages = {93 -- 105}, year = {2008}, language = {en} } @article{SahnerWeberLameckeretal.2008, author = {Sahner, Jan and Weber, Britta and Lamecker, Hans and Prohaska, Steffen}, title = {Extraction of feature Lines on surface meshes based on discrete Morse theory}, volume = {27}, journal = {Computer Graphics Forum}, number = {3}, address = {Eindhoven, Netherlands}, doi = {10.1111/j.1467-8659.2008.01202.x}, pages = {735 -- 742}, year = {2008}, language = {en} } @inproceedings{KastenPetzHotzetal.2009, author = {Kasten, Jens and Petz, Christoph and Hotz, Ingrid and Noack, Bernd R. and Hege, Hans-Christian}, title = {Localized Finite-time Lyapunov Exponent for Unsteady Flow Analysis}, volume = {1}, booktitle = {Vision Modeling and Visualization}, editor = {Magnor, Marcus and Rosenhahn, Bodo and Theisel, Holger}, publisher = {Universit{\"a}t Magdeburg, Inst. f. Simulation u. Graph.}, isbn = {978-3-9804874-8-1}, pages = {265 -- 274}, year = {2009}, language = {en} } @misc{BoddenClasenKneis2007, author = {Bodden, Eric and Clasen, Malte and Kneis, Joachim}, title = {Arithmetic coding revealed - a guided tour from theory to praxis}, publisher = {Technical Report SABLE-TR-2007-5, Sable Research Group, School of Computer Science, McGill University}, year = {2007}, language = {en} } @article{PaarClasen2007, author = {Paar, Philip and Clasen, Malte}, title = {Earth, Landscape, Biotope, Plant. Interactive visualisation with Biosphere3D}, journal = {Proceedings of CORP - 12th International Conference on Urban Planning and Spatial Development in the Information Society, May 20th - 23rd}, pages = {207 -- 214}, year = {2007}, language = {en} } @inproceedings{ClasenHege2007, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Clipmap-based Terrain Data Synthesis}, booktitle = {Proc. SimVis 2007}, editor = {Schulze, Thomas and Preim, Bernhard and Schumann, Heidrun}, publisher = {SCS Publishing House e.V.}, pages = {385 -- 398}, year = {2007}, language = {en} } @article{SaparinThomsenProhaskaetal.2005, author = {Saparin, Peter and Thomsen, Jesper and Prohaska, Steffen and Zaikin, Alexei and Kurths, J{\"u}rgen and Hege, Hans-Christian and Gowin, Wolfgang}, title = {Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity}, volume = {56}, journal = {Acta Astronautica}, number = {9-12}, doi = {10.1016/j.actaastro.2005.01.007}, pages = {820 -- 830}, year = {2005}, language = {en} } @article{ProhaskaDreherDewhirstetal.2004, author = {Prohaska, Steffen and Dreher, Matthew and Dewhirst, Mark and Chilkoti, Ashutosh and Pries, Axel}, title = {3-D reconstruction of tumor vascular networks}, volume = {41}, journal = {J. Vas. Res.}, pages = {463}, year = {2004}, language = {en} } @inproceedings{ProhaskaHutanuKaehleretal.2004, author = {Prohaska, Steffen and Hutanu, Andrei and K{\"a}hler, Ralf and Hege, Hans-Christian}, title = {Interactive exploration of large remote micro-CT scans}, booktitle = {Proc. IEEE Visualization 2004}, address = {Austin, Texas}, doi = {10.1109/VIS.2004.51}, pages = {345 -- 352}, year = {2004}, language = {en} } @inproceedings{FouardMalandainProhaskaetal.2004, author = {Fouard, C{\´e}line and Malandain, Gr{\´e}goire and Prohaska, Steffen and Westerhoff, Malte and Cassot, Francis and Mazel, Christophe and Asselot, Didier and Marc-Vergnes, Jean-Pierre}, title = {Skeletonization by blocks for large 3D datasets: Application to brain microcirculation}, booktitle = {IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'04)}, address = {Arlington, Virginia}, doi = {10.1109/ISBI.2004.1398481}, pages = {89 -- 92}, year = {2004}, language = {en} } @inproceedings{FouardMalandainProhaskaetal.2004, author = {Fouard, C{\´e}line and Malandain, Gr{\´e}goire and Prohaska, Steffen and Westerhoff, Malte and Cassot, Francis and Mazel, Christophe and Asselot, Didier and Marc-Vergnes, Jean-Pierre}, title = {Squelettisation par blocs pour des grands volumes de donn{\´e}es 3D}, booktitle = {Reconnaissance des Formes et Intelligence Artificielle (RFIA 2004)}, address = {Toulouse, France}, year = {2004}, language = {en} } @article{HutanuAllenBecketal.2006, author = {Hutanu, Andrei and Allen, Gabrielle and Beck, Stephen and Holub, Petr and Kaiser, Hartmut and Kulshrestha, Archit and Liska, Milos and MacLaren, Jon and Matyska, Ludek and Paruchuri, Ravi and Prohaska, Steffen and Seidel, Edward and Ullmer, Brygg and Venkataraman, Shalini}, title = {Distributed and collaborative visualization of large data sets using high-speed networks}, volume = {22(8)}, journal = {Future Generation Comp. Syst}, doi = {10.1016/j.future.2006.03.026}, pages = {1004 -- 1010}, year = {2006}, language = {en} } @article{HegeWeinkaufProhaskaetal.2005, author = {Hege, Hans-Christian and Weinkauf, Tino and Prohaska, Steffen and Hutanu, Andrei}, title = {Towards distributed visualization and analysis of large flow data}, volume = {48 (2)}, journal = {JSME International Journal, Series B}, pages = {241 -- 246}, year = {2005}, language = {en} } @inproceedings{DercksenProhaskaHege2005, author = {Dercksen, Vincent J. and Prohaska, Steffen and Hege, Hans-Christian}, title = {Fast cross-sectional display of large data sets}, booktitle = {IAPR Conference on Machine Vision Applications}, address = {Tsukuba, Japan}, pages = {336 -- 339}, year = {2005}, language = {en} } @inproceedings{Prohaska2006, author = {Prohaska, Steffen}, title = {Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen}, volume = {10}, booktitle = {Kartographische Schriften}, pages = {103 -- 110}, year = {2006}, language = {en} } @misc{HorenkoSchmidtEhrenbergSchuette2006, author = {Horenko, Illia and Schmidt-Ehrenberg, Johannes and Sch{\"u}tte, Christof}, title = {Set-oriented dimension reduction: Localizing principal component analysis via hidden Markov models}, volume = {4216}, journal = {Computational Life Sciences II}, publisher = {Springer}, pages = {98 -- 115}, year = {2006}, language = {en} } @inproceedings{ClasenHege2006, author = {Clasen, Malte and Hege, Hans-Christian}, title = {Terrain rendering using spherical clipmaps}, booktitle = {EuroVis 2006 - Eurographics / IEEE VGTC Symposium on Visualization}, pages = {91 -- 98}, year = {2006}, language = {en} } @inproceedings{SchmidtEhrenbergHege2005, author = {Schmidt-Ehrenberg, Johannes and Hege, Hans-Christian}, title = {Visual analysis of molecular conformations by means of a dynamic density mixture model}, volume = {3695}, booktitle = {Computational Life Sciences: First International Symposium, CompLife 2005}, publisher = {Springer}, address = {Konstanz, Germany}, pages = {229 -- 240}, year = {2005}, language = {en} } @inproceedings{KaehlerProhaskaHutanuetal.2005, author = {K{\"a}hler, Ralf and Prohaska, Steffen and Hutanu, Andrei and Hege, Hans-Christian}, title = {Visualization of time-dependent remote adaptive mesh refinement data}, booktitle = {Proc. IEEE Visualization 2005}, address = {Minneapolis, USA}, doi = {10.1109/VISUAL.2005.1532793}, pages = {175 -- 182}, year = {2005}, language = {en} } @article{ThomsenLaibKolleretal.2005, author = {Thomsen, Jesper and Laib, Andreas and Koller, Bruno and Prohaska, Steffen and Mosekilde, L. and Gowin, Wolfgang}, title = {Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies}, volume = {218}, journal = {Journal of Microscopy}, pages = {171 -- 179}, year = {2005}, language = {en} } @inproceedings{ProhaskaHutanu2005, author = {Prohaska, Steffen and Hutanu, Andrei}, title = {Remote data access for interactive visualization}, booktitle = {13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies}, pages = {17 -- 22}, year = {2005}, language = {en} } @article{FouardMalandainProhaskaetal.2006, author = {Fouard, C{\´e}line and Malandain, Gr{\´e}goire and Prohaska, Steffen and Westerhoff, Malte}, title = {Blockwise processing applied to brain micro-vascular network study}, volume = {25}, journal = {IEEE Transactions on Medical Imaging}, number = {10}, doi = {10.1109/TMI.2006.880670}, pages = {1319 -- 1328}, year = {2006}, language = {en} } @article{ZaikinSaparinKurthsetal.2005, author = {Zaikin, Alexei and Saparin, Peter and Kurths, J{\"u}rgen and Prohaska, Steffen and Gowin, Wolfgang}, title = {Modeling resorption in 2D-CT and 3D μ-CT bone images}, volume = {15(9)}, journal = {Int. J. of Bif. and Chaos}, pages = {2995 -- 3009}, year = {2005}, language = {en} } @inproceedings{RoehrichtClasen2005, author = {R{\"o}hricht, W. and Clasen, Malte}, title = {Multum, non multi - Hierarchische Bit Trees bei der Pflanzenverteilung mit oik}, booktitle = {Simulation in Umwelt- und Geowissenschaften. Workshop Dresden 2005}, publisher = {Shaker}, address = {Aachen}, year = {2005}, language = {en} } @article{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}, journal = {PLoS ONE}, doi = {10.1371/journal.pone.0113222}, pages = {e113222}, year = {2014}, language = {en} } @misc{RedemannWeberMoelleretal.2014, author = {Redemann, Stefanie and Weber, Britta and M{\"o}ller, Marit and Verbavatz, Jean-Marc and Hyman, Anthony and Baum, Daniel and Prohaska, Steffen and M{\"u}ller-Reichert, Thomas}, title = {The Segmentation of Microtubules in Electron Tomograms Using Amira}, journal = {Mitosis: Methods and Protocols}, publisher = {Springer}, doi = {10.1007/978-1-4939-0329-0_12}, pages = {261 -- 278}, year = {2014}, language = {en} } @misc{CostaOstrovskyMantonetal.2015, author = {Costa, Marta and Ostrovsky, Aaron D. and Manton, James D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, journal = {bioRxiv preprint}, doi = {10.1101/006346}, year = {2015}, language = {en} } @misc{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}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53426}, year = {2015}, abstract = {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.}, 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} } @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} } @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{SeidelBlumerZaslanskyetal.2017, author = {Seidel, Ronald and Blumer, Michael and Zaslansky, Paul and Kn{\"o}tel, David and Huber, Daniel R. and Weaver, James C. and Fratzl, Peter and Omelon, Sidney and Bertinetti, Luca and Dean, Mason N.}, title = {Ultrastructural, material and crystallographic description of endophytic masses - a possible damage response in shark and ray tessellated calcified cartilage}, journal = {Journal of Structural Biology}, doi = {10.1016/j.jsb.2017.03.004}, year = {2017}, abstract = {The cartilaginous endoskeletons of Elasmobranchs (sharks and rays) are reinforced superficially by minute, mineralized tiles, called tesserae. Unlike the bony skeletons of other vertebrates, elasmobranch skeletons have limited healing capability and their tissues' mechanisms for avoiding damage or managing it when it does occur are largely unknown. Here we describe an aberrant type of mineralized elasmobranch skeletal tissue called endophytic masses (EPMs), which grow into the uncalcified cartilage of the skeleton, but exhibit a strikingly different morphology compared to tesserae and other elasmobranch calcified tissues. We use biological and materials characterization techniques, including computed tomography, electron and light microscopy, x-ray and Raman spectroscopy and histology to characterize the morphology, ultrastructure and chemical composition of tesserae-associated EPMs in different elasmobranch species. EPMs appear to develop between and in intimate association with tesserae, but lack the lines of periodic growth and varying mineral density characteristic of tesserae. EPMs are mineral-dominated (high mineral and low organic content), comprised of birefringent bundles of large monetite or brushite crystals aligned end to end in long strings. Both Unusual skeletal mineralization in elasmobranchs tesserae and EPMs appear to develop in a type-2 collagen-based matrix, but in contrast to tesserae, all chondrocytes embedded or in contact with EPMs are dead and mineralized. The differences outlined between EPMs and tesserae demonstrate them to be distinct tissues. We discuss several possible reasons for EPM development, including tissue reinforcement, repair, and disruptions of mineralization processes, within the context of elasmobranch skeletal biology as well as descriptions of damage responses of other vertebrate mineralized tissues.}, 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} } @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{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} } @article{KnoetelSeidelProhaskaetal.2017, author = {Kn{\"o}tel, David and Seidel, Ronald and Prohaska, Steffen and Dean, Mason N. and Baum, Daniel}, title = {Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage}, journal = {PLOS ONE}, doi = {10.1371/journal.pone.0188018}, year = {2017}, abstract = {Introduction - Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays. Methods - Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size. Results - Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.}, language = {en} }