TY - JOUR A1 - Eigen, Lennart A1 - Baum, Daniel A1 - Dean, Mason N. A1 - Werner, Daniel A1 - Wölfer, Jan A1 - Nyakatura, John A. T1 - Ontogeny of a tessellated surface: carapace growth of the longhorn cowfish Lactoria cornuta JF - Journal of Anatomy N2 - Biological armors derive their mechanical integrity in part from their geometric architectures, often involving tessellations: individual structural elements tiled together to form surface shells. The carapace of boxfish, for example, is comprised of mineralized polygonal plates, called scutes, arranged in a complex geometric pattern and nearly completely encasing the body. In contrast to artificial armors, the boxfish exoskeleton grows with the fish; the relationship between the tessellation and the gross structure of the armor is therefore critical to sustained protection throughout growth. To clarify whether or how the boxfish tessellation is maintained or altered with age, we quantify architectural aspects of the tessellated carapace of the longhorn cowfish Lactoria cornuta through ontogeny (across nearly an order of magnitude in standard length) and in a high-throughput fashion, using high-resolution microCT data and segmentation algorithms to characterize the hundreds of scutes that cover each individual. We show that carapace growth is canalized with little variability across individuals: rather than continually adding scutes to enlarge the carapace surface, the number of scutes is surprisingly constant, with scutes increasing in volume, thickness, and especially width with age. As cowfish and their scutes grow, scutes become comparatively thinner, with the scutes at the edges (weak points in a boxy architecture) being some of the thickest and most reinforced in younger animals and thinning most slowly across ontogeny. In contrast, smaller scutes with more variable curvature were found in the limited areas of more complex topology (e.g. around fin insertions, mouth, and anus). Measurements of Gaussian and mean curvature illustrate that cowfish are essentially tessellated boxes throughout life: predominantly zero curvature surfaces comprised of mostly flat scutes, and with scutes with sharp bends used sparingly to form box edges. Since growth of a curved, tiled surface with a fixed number of tiles would require tile restructuring to accommodate the surface’s changing radius of curvature, our results therefore illustrate a previously unappreciated advantage of the odd boxfish morphology: by having predominantly flat surfaces, it is the box-like body form that in fact permits a relatively straightforward growth system of this tessellated architecture (i.e. where material is added to scute edges). Our characterization of the ontogeny and maintenance of the carapace tessellation provides insights into the potentially conflicting mechanical, geometric and developmental constraints of this species, but also perspectives into natural strategies for constructing mutable tiled architectures. Y1 - 2022 U6 - https://doi.org/10.1111/joa.13692 VL - 241 IS - 3 SP - 565 EP - 580 PB - Wiley ER - TY - GEN A1 - Paskin, Martha A1 - Baum, Daniel A1 - Dean, Mason N. A1 - von Tycowicz, Christoph T1 - A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks -- Source Code and Data N2 - Source code and novel dataset of basking shark head skeletons facilitating the reproduction of the results presented in 'A Kendall Shape Space Approach to 3D Shape Estimation from 2D Landmarks' - ECCV 2022. Y1 - 2022 U6 - https://doi.org/10.12752/8730 ER - TY - JOUR A1 - Schotte, Merlind A1 - Chaumel, Júlia A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Image analysis pipeline for segmentation of a biological porosity network, the lacuno-canalicular system in stingray tesserae JF - MethodsX N2 - A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools will be required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for the subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semi-automatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. * The first step of this processing pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required modern, recently developed tools. * For proofreading, we developed a graph-based interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. * Finally, the tesserae and their corresponding lacunae were subdivided into anatomical regions of interest (structural wedges) using a semi- manual approach. Y1 - 2020 U6 - https://doi.org/10.1016/j.mex.2020.100905 VL - 7 SP - 100905 ER - TY - JOUR A1 - Chaumel, Júlia A1 - Schotte, Merlind A1 - Bizzarro, Joseph J. A1 - Zaslansky, Paul A1 - Fratzl, Peter A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Co-aligned chondrocytes: Zonal morphological variation and structured arrangement of cell lacunae in tessellated cartilage JF - Bone N2 - In most vertebrates the embryonic cartilaginous skeleton is replaced by bone during development. During this process, cartilage cells (chondrocytes) mineralize the extracellular matrix and undergo apoptosis, giving way to bone cells (osteocytes). In contrast, sharks and rays (elasmobranchs) have cartilaginous skeletons throughout life, where only the surface mineralizes, forming a layer of tiles (tesserae). Elasmobranch chondrocytes, unlike those of other vertebrates, survive cartilage mineralization and are maintained alive in spaces (lacunae) within tesserae. However, the function(s) of the chondrocytes in the mineralized tissue remain unknown. Applying a custom analysis workflow to high-resolution synchrotron microCT scans of tesserae, we characterize the morphologies and arrangements of stingray chondrocyte lacunae, using lacunar morphology as a proxy for chondrocyte morphology. We show that the cell density is comparable in unmineralized and mineralized tissue from our study species and that cells maintain the similar volume even when they have been incorporated into tesserae. This discovery supports previous hypotheses that elasmobranch chondrocytes, unlike those of other taxa, do not proliferate, hypertrophy or undergo apoptosis during mineralization. Tessera lacunae show zonal variation in their shapes—being flatter further from and more spherical closer to the unmineralized cartilage matrix and larger in the center of tesserae— and show pronounced organization into parallel layers and strong orientation toward neighboring tesserae. Tesserae also exhibit local variation in lacunar density, with the density considerably higher near pores passing through the tesseral layer, suggesting pores and cells interact (e.g. that pores contain a nutrient source). We hypothesize that the different lacunar types reflect the stages of the tesserae formation process, while also representing local variation in tissue architecture and cell function. Lacunae are linked by small passages (canaliculi) in the matrix to form elongate series at the tesseral periphery and tight clusters in the center of tesserae, creating a rich connectivity among cells. The network arrangement and the shape variation of chondrocytes in tesserae indicate that cells may interact within and between tesserae and manage mineralization differently from chondrocytes in other vertebrates, perhaps performing analogous roles to osteocytes in bone. Y1 - 2020 U6 - https://doi.org/10.1016/j.bone.2020.115264 VL - 134 SP - 115264 ER - TY - JOUR A1 - Baum, Daniel A1 - Weaver, James C. A1 - Zlotnikov, Igor A1 - Knötel, David A1 - Tomholt, Lara A1 - Dean, Mason N. T1 - High-Throughput Segmentation of Tiled Biological Structures using Random-Walk Distance Transforms JF - Integrative And Comparative Biology N2 - Various 3D imaging techniques are routinely used to examine biological materials, the results of which are usually a stack of grayscale images. In order to quantify structural aspects of the biological materials, however, they must first be extracted from the dataset in a process called segmentation. If the individual structures to be extracted are in contact or very close to each other, distance-based segmentation methods utilizing the Euclidean distance transform are commonly employed. Major disadvantages of the Euclidean distance transform, however, are its susceptibility to noise (very common in biological data), which often leads to incorrect segmentations (i.e. poor separation of objects of interest), and its limitation of being only effective for roundish objects. In the present work, we propose an alternative distance transform method, the random-walk distance transform, and demonstrate its effectiveness in high-throughput segmentation of three microCT datasets of biological tilings (i.e. structures composed of a large number of similar repeating units). In contrast to the Euclidean distance transform, this random-walk approach represents the global, rather than the local, geometric character of the objects to be segmented and, thus, is less susceptible to noise. In addition, it is directly applicable to structures with anisotropic shape characteristics. Using three case studies—stingray tessellated cartilage, starfish dermal endoskeleton, and the prismatic layer of bivalve mollusc shell—we provide a typical workflow for the segmentation of tiled structures, describe core image processing concepts that are underused in biological research, and show that for each study system, large amounts of biologically-relevant data can be rapidly segmented, visualized and analyzed. Y1 - 2019 U6 - https://doi.org/10.1093/icb/icz117 ER - TY - JOUR A1 - Knötel, David A1 - Seidel, Ronald A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage JF - PLOS ONE N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0188018 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Zaslansky, Paul A1 - Prohaska, Steffen A1 - Dean, Mason N. A1 - Baum, Daniel T1 - Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material) N2 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens. Y1 - 2017 U6 - https://doi.org/10.12752/4.DKN.1.0 N1 - Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. ER - TY - JOUR A1 - Seidel, Ronald A1 - Blumer, Michael A1 - Zaslansky, Paul A1 - Knötel, David A1 - Huber, Daniel R. A1 - Weaver, James C. A1 - Fratzl, Peter A1 - Omelon, Sidney A1 - Bertinetti, Luca A1 - Dean, Mason N. T1 - Ultrastructural, material and crystallographic description of endophytic masses – a possible damage response in shark and ray tessellated calcified cartilage JF - Journal of Structural Biology N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1016/j.jsb.2017.03.004 ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Hosny, Ahmed A1 - Zaslansky, Paul A1 - Weaver, James C. A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Understanding the Tiling Rules of the Tessellated Mineralized Endoskeleton of Sharks and Rays T2 - Poster, Euro Bio-inspired Materials 2016, Potsdam, Germany, February 22 - 25, 2016 N2 - 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. Y1 - 2016 ER - TY - GEN A1 - Dean, Mason N. A1 - Hosny, Ahmed A1 - Seidel, Ronald A1 - Baum, Daniel T1 - Biological strategies for fatique and wear avoidance: lessons from stingray skeletons and teeth T2 - Poster, Tomography for Scientific Advancement symposium (ToScA) Y1 - 2016 ER - TY - CHAP A1 - Dean, Mason N. A1 - Seidel, R. A1 - Knötel, David A1 - Lyons, K. A1 - Baum, Daniel A1 - Weaver, James C. A1 - Fratzl, Peter T1 - To build a shark: 3D tiling laws of tessellated cartilage T2 - Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA N2 - 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. Y1 - 2016 UR - https://academic.oup.com/icb/article-pdf/56/suppl_1/e1/9102603/icw002.pdf VL - 56 (suppl 1) ER - TY - GEN A1 - Knötel, David A1 - Seidel, Ronald A1 - Weaver, James C. A1 - Baum, Daniel A1 - Dean, Mason N. T1 - Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays T2 - Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015 N2 - 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. Y1 - 2015 ER - TY - GEN A1 - Seidel, Ronald A1 - Knötel, David A1 - Baum, Daniel A1 - Weaver, James C. A1 - Dean, Mason N. T1 - Material and structural characterization of mineralized elasmobranch cartilage – lessons in repeated tiling patterns in mechanically loaded 3D objects T2 - Poster, Tomography for Scientific Advancement symposium (ToScA), London, UK, September 1 - 3, 2014 N2 - 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. Y1 - 2014 ER -