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  <doc>
    <id>5295</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2014-10-28</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated stitching of microtubule centerlines across serial electron tomograms</title>
    <abstract language="eng">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.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-52958</identifier>
    <identifier type="doi">10.1371/journal.pone.0113222</identifier>
    <enrichment key="SourceTitle">published in PLoS ONE</enrichment>
    <author>Britta Weber</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Erin M. Tranfield</author>
    <author>Johanna L. Höög</author>
    <author>Daniel Baum</author>
    <author>Claude Antony</author>
    <author>Tony Hyman</author>
    <author>Jean-Marc Verbavatz</author>
    <author>Steffen Prohaska</author>
    <series>
      <title>ZIB-Report</title>
      <number>14-41</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electron tomography</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>microtubules</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>serial sectioning</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>geometry reconstruction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image and geometry alignment</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>point correspondence</value>
    </subject>
    <collection role="ccs" number="I.4.9">Applications</collection>
    <collection role="ccs" number="">Biology and genetics (REVISED)</collection>
    <collection role="pacs" number="87.17.-d">Cell processes</collection>
    <collection role="msc" number="60-XX">PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5295/zibreport-14-41_v1.pdf</file>
  </doc>
  <doc>
    <id>6313</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>56 (suppl 1)</volume>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">To build a shark: 3D tiling laws of tessellated cartilage</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA</parentTitle>
    <identifier type="url">https://academic.oup.com/icb/article-pdf/56/suppl_1/e1/9102603/icw002.pdf</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Mason N. Dean</author>
    <submitter>David Knötel</submitter>
    <author>R. Seidel</author>
    <author>David Knötel</author>
    <author>K. Lyons</author>
    <author>Daniel Baum</author>
    <author>James C. Weaver</author>
    <author>Peter Fratzl</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="knoetel">Knötel, David</collection>
    <collection role="projects" number="TESSERAE">TESSERAE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6298</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>178</pageFirst>
    <pageLast>204</pageLast>
    <pageNumber/>
    <edition/>
    <issue>8</issue>
    <volume>36</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-11-18</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Visualization of Biomolecular Structures: State of the Art Revisited</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Computer Graphics Forum</parentTitle>
    <identifier type="doi">10.1111/cgf.13072</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Barbora Kozlíková</author>
    <submitter>Daniel Baum</submitter>
    <author>Michael Krone</author>
    <author>Martin Falk</author>
    <author>Norbert Lindow</author>
    <author>Marc Baaden</author>
    <author>Daniel Baum</author>
    <author>Ivan Viola</author>
    <author>Julius Parulek</author>
    <author>Hans-Christian Hege</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="projects" number="MOL-ANALYSIS">MOL-ANALYSIS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6308</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>329</pageFirst>
    <pageLast>339</pageLast>
    <pageNumber>11</pageNumber>
    <edition/>
    <issue>3</issue>
    <volume>36</volume>
    <type>article</type>
    <publisherName>Wiley</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2017-06-30</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Computer Graphics Forum</parentTitle>
    <identifier type="doi">10.1111/cgf.13191</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-63239</enrichment>
    <author>Amal Aboulhassan</author>
    <submitter>Daniel Baum</submitter>
    <author>Ronell Sicat</author>
    <author>Daniel Baum</author>
    <author>Olga Wodo</author>
    <author>Markus Hadwiger</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6277</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Ultrastructural, material and crystallographic description of endophytic masses – a possible damage response in shark and ray tessellated calcified cartilage</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Journal of Structural Biology</parentTitle>
    <identifier type="doi">10.1016/j.jsb.2017.03.004</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Ronald Seidel</author>
    <submitter>David Knötel</submitter>
    <author>Michael Blumer</author>
    <author>Paul Zaslansky</author>
    <author>David Knötel</author>
    <author>Daniel R. Huber</author>
    <author>James C. Weaver</author>
    <author>Peter Fratzl</author>
    <author>Sidney Omelon</author>
    <author>Luca Bertinetti</author>
    <author>Mason N. Dean</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="knoetel">Knötel, David</collection>
    <collection role="projects" number="TESSERAE">TESSERAE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6422</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>3</issue>
    <volume>3</volume>
    <type>article</type>
    <publisherName>IOP Publishing</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Adapting trabecular structures for 3D printing: an image processing approach based on µCT data</title>
    <abstract language="eng">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.&#13;
&#13;
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.</abstract>
    <parentTitle language="eng">Biomedical Physics &amp; Engineering Express</parentTitle>
    <identifier type="doi">10.1088/2057-1976/aa7611</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-64004</enrichment>
    <author>Ulrike Homberg</author>
    <submitter>Ulrike Homberg</submitter>
    <author>Daniel Baum</author>
    <author>Steffen Prohaska</author>
    <author>Jens Günster</author>
    <author>Stefanie Krauß-Schüler</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="BAM-3D-PRINTING">BAM-3D-PRINTING</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5718</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>3461</pageFirst>
    <pageLast>3474</pageLast>
    <pageNumber>14</pageNumber>
    <edition/>
    <issue>11</issue>
    <volume>13</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace>http://www.biogeosciences.net/13/3461/2016/</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Long-term macrobioerosion in the Mediterranean Sea assessed by micro-computed tomography</title>
    <abstract language="eng">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&#13;
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.</abstract>
    <parentTitle language="eng">Biogeosciences</parentTitle>
    <identifier type="doi">10.5194/bg-13-3461-2016</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <submitter>Daniel Baum</submitter>
    <author>Claudia Färber</author>
    <author>Jürgen Titschack</author>
    <author>Christine H. L. Schönberg</author>
    <author>Karsten Ehrig</author>
    <author>Karin Boos</author>
    <author>Daniel Baum</author>
    <author>Bernd Illerhaus</author>
    <author>Ulla Asgaard</author>
    <author>Richard G. Bromley</author>
    <author>André Freiwald</author>
    <author>Max Wisshak</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="CORALS">CORALS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5823</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>poster</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays</title>
    <abstract language="eng">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.</abstract>
    <parentTitle language="eng">Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016</parentTitle>
    <author>David Knötel</author>
    <submitter>David Knötel</submitter>
    <author>Ronald Seidel</author>
    <author>Ahmed Hosny</author>
    <author>Paul Zaslansky</author>
    <author>James C. Weaver</author>
    <author>Daniel Baum</author>
    <author>Mason N. Dean</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="knoetel">Knötel, David</collection>
    <collection role="projects" number="TESSERAE">TESSERAE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6631</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
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    <title language="eng">Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage</title>
    <abstract language="eng">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.&#13;
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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.&#13;
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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.</abstract>
    <parentTitle language="eng">PLOS ONE</parentTitle>
    <identifier type="doi">10.1371/journal.pone.0188018</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-65785</enrichment>
    <enrichment key="zib_relatedIdentifier">https://doi.org/10.12752/4.DKN.1.0</enrichment>
    <author>David Knötel</author>
    <submitter>David Knötel</submitter>
    <author>Ronald Seidel</author>
    <author>Steffen Prohaska</author>
    <author>Mason N. Dean</author>
    <author>Daniel Baum</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="knoetel">Knötel, David</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="TESSERAE">TESSERAE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
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