TY - JOUR A1 - Saparin, Peter A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Zaikin, Alexei A1 - Kurths, Jürgen A1 - Hege, Hans-Christian A1 - Gowin, Wolfgang T1 - Quantification of spatial structure of human proximal tibial bone biopsies using 3D measures of complexity JF - Acta Astronautica Y1 - 2005 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 56 IS - 9-12 SP - 820 EP - 830 ER - TY - JOUR A1 - Prohaska, Steffen A1 - Dreher, Matthew A1 - Dewhirst, Mark A1 - Chilkoti, Ashutosh A1 - Pries, Axel T1 - 3-D reconstruction of tumor vascular networks JF - J. Vas. Res. Y1 - 2004 VL - 41 SP - 463 ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hutanu, Andrei A1 - Kähler, Ralf A1 - Hege, Hans-Christian T1 - Interactive exploration of large remote micro-CT scans T2 - Proc. IEEE Visualization 2004 Y1 - 2004 U6 - https://doi.org/10.1109/VIS.2004.51 SP - 345 EP - 352 CY - Austin, Texas ER - TY - CHAP A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte A1 - Cassot, Francis A1 - Mazel, Christophe A1 - Asselot, Didier A1 - Marc-Vergnes, Jean-Pierre T1 - Skeletonization by blocks for large 3D datasets: Application to brain microcirculation T2 - IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'04) Y1 - 2004 U6 - https://doi.org/10.1109/ISBI.2004.1398481 SP - 89 EP - 92 CY - Arlington, Virginia ER - TY - CHAP A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte A1 - Cassot, Francis A1 - Mazel, Christophe A1 - Asselot, Didier A1 - Marc-Vergnes, Jean-Pierre T1 - Squelettisation par blocs pour des grands volumes de données 3D T2 - Reconnaissance des Formes et Intelligence Artificielle (RFIA 2004) Y1 - 2004 CY - Toulouse, France ER - TY - JOUR A1 - Hutanu, Andrei A1 - Allen, Gabrielle A1 - Beck, Stephen A1 - Holub, Petr A1 - Kaiser, Hartmut A1 - Kulshrestha, Archit A1 - Liska, Milos A1 - MacLaren, Jon A1 - Matyska, Ludek A1 - Paruchuri, Ravi A1 - Prohaska, Steffen A1 - Seidel, Edward A1 - Ullmer, Brygg A1 - Venkataraman, Shalini T1 - Distributed and collaborative visualization of large data sets using high-speed networks JF - Future Generation Comp. Syst Y1 - 2006 U6 - https://doi.org/10.1016/j.future.2006.03.026 VL - 22(8) SP - 1004 EP - 1010 ER - TY - JOUR A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Towards distributed visualization and analysis of large flow data JF - JSME International Journal, Series B Y1 - 2005 VL - 48 (2) SP - 241 EP - 246 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Fast cross-sectional display of large data sets T2 - IAPR Conference on Machine Vision Applications Y1 - 2005 SP - 336 EP - 339 CY - Tsukuba, Japan ER - TY - CHAP A1 - Prohaska, Steffen T1 - Interaktive Visualisierung und Datenanalyse: Herausforderungen durch wachsende Datenmengen T2 - Kartographische Schriften Y1 - 2006 VL - 10 SP - 103 EP - 110 ER - TY - CHAP A1 - Kähler, Ralf A1 - Prohaska, Steffen A1 - Hutanu, Andrei A1 - Hege, Hans-Christian T1 - Visualization of time-dependent remote adaptive mesh refinement data T2 - Proc. IEEE Visualization 2005 Y1 - 2005 U6 - https://doi.org/10.1109/VISUAL.2005.1532793 SP - 175 EP - 182 CY - Minneapolis, USA ER - TY - JOUR A1 - Thomsen, Jesper A1 - Laib, Andreas A1 - Koller, Bruno A1 - Prohaska, Steffen A1 - Mosekilde, L. A1 - Gowin, Wolfgang T1 - Stereological measures of trabecular bone structure: Comparison of 3D micro computed tomography with 2D histological sections in human proximal tibial bone biopsies JF - Journal of Microscopy Y1 - 2005 VL - 218 SP - 171 EP - 179 ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Remote data access for interactive visualization T2 - 13th Annual Mardi Gras Conference: Frontiers of Grid Applications and Technologies Y1 - 2005 SP - 17 EP - 22 ER - TY - JOUR A1 - Fouard, Céline A1 - Malandain, Grégoire A1 - Prohaska, Steffen A1 - Westerhoff, Malte T1 - Blockwise processing applied to brain micro-vascular network study JF - IEEE Transactions on Medical Imaging Y1 - 2006 U6 - https://doi.org/10.1109/TMI.2006.880670 VL - 25 IS - 10 SP - 1319 EP - 1328 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Kurths, Jürgen A1 - Prohaska, Steffen A1 - Gowin, Wolfgang T1 - Modeling resorption in 2D-CT and 3D μ-CT bone images JF - Int. J. of Bif. and Chaos Y1 - 2005 VL - 15(9) SP - 2995 EP - 3009 ER - TY - JOUR A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms JF - PLoS ONE Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0113222 SP - e113222 ER - TY - GEN A1 - Redemann, Stefanie A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Hyman, Anthony A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Müller-Reichert, Thomas T1 - The Segmentation of Microtubules in Electron Tomograms Using Amira T2 - Mitosis: Methods and Protocols Y1 - 2014 U6 - https://doi.org/10.1007/978-1-4939-0329-0_12 SP - 261 EP - 278 PB - Springer ER - TY - GEN A1 - Costa, Marta A1 - Ostrovsky, Aaron D. A1 - Manton, James D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases T2 - bioRxiv preprint Y1 - 2015 U6 - https://doi.org/10.1101/006346 ER - TY - GEN A1 - Hoerth, Rebecca M. A1 - Baum, Daniel A1 - Knötel, David A1 - Prohaska, Steffen A1 - Willie, Bettina M. A1 - Duda, Georg A1 - Hege, Hans-Christian A1 - Fratzl, Peter A1 - Wagermaier, Wolfgang T1 - Registering 2D and 3D Imaging Data of Bone during Healing N2 - 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. T3 - ZIB-Report - 15-01 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53426 SN - 1438-0064 ER - TY - GEN A1 - Weber, Britta A1 - Tranfield, Erin M. A1 - Höög, Johanna L. A1 - Baum, Daniel A1 - Antony, Claude A1 - Hyman, Tony A1 - Verbavatz, Jean-Marc A1 - Prohaska, Steffen T1 - Automated stitching of microtubule centerlines across serial electron tomograms N2 - 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. T3 - ZIB-Report - 14-41 KW - electron tomography KW - microtubules KW - serial sectioning KW - image analysis KW - geometry reconstruction KW - image and geometry alignment KW - point correspondence Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52958 SN - 1438-0064 ER - TY - JOUR A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Günster, Jens A1 - Krauß-Schüler, Stefanie T1 - Adapting trabecular structures for 3D printing: an image processing approach based on µCT data JF - Biomedical Physics & Engineering Express N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1088/2057-1976/aa7611 VL - 3 IS - 3 PB - IOP Publishing 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 -