TY - GEN A1 - Kober, Cornelia A1 - Sader, Robert A1 - Zeilhofer, Hans-Florian A1 - Prohaska, Steffen A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Anisotrope Materialmodellierung für den menschlichen Unterkiefer N2 - Im Rahmen der biomechanischen Simulation knöcherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungelöst. Computertomographische Datensätze liefern eine räumliche Verteilung der (Röntgen-)Dichte und ermöglichen damit eine gute Darstellung der individuellen Geometrie. Weiter können die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsabängige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz für eine anisotrope Materialbeschreibung vorgestellt, die es ermöglicht, den Einfluss der individuellen knöchernen Struktur auf das makroskopische Materialverhalten abzuschätzen. T3 - ZIB-Report - 01-31 KW - menschlicher Unterkiefer KW - Simulation mit der Methode der finiten Elemente KW - innerer Aufbau des Knochens KW - anisotrope Elastizität Y1 - 2001 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-6574 ER - TY - GEN A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian T1 - Dual Streamline Seeding - Method and Implementation N2 - This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces. N2 - In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist. T3 - ZIB-Report - 08-49 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-11032 SN - 1438-0064 ER - TY - GEN A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ebell, Gino A1 - Ehrig, Karsten A1 - Heyn, Andreas A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben N2 - Kurzfassung. Durch die Alkalität des Betons wird Betonstahl dauerhaft vor Korrosion geschützt. Infolge von Chlorideintrag kann dieser Schutz nicht länger aufrechterhalten werden und führt zu Lochkorrosion. Die zerstörungsfreie Prüfung von Stahlbetonproben mit 3D-CT bietet die Möglichkeit, eine Probe mehrfach gezielt vorzuschädigen und den Korrosionsfortschritt zu untersuchen. Zur Quantifizierung des Schädigungsgrades müssen die bei dieser Untersuchung anfallenden großen Bilddaten mit Bildverarbeitungsmethoden ausgewertet werden. Ein wesentlicher Schritt dabei ist die Segmentierung der Bilddaten, bei der zwischen Korrosionsprodukt (Rost), Betonstahl (BSt), Beton, Rissen, Poren und Umgebung unterschieden werden muss. Diese Segmentierung bildet die Grundlage für statistische Untersuchungen des Schädigungsfortschritts. Hierbei sind die Änderung der BSt-Geometrie, die Zunahme von Korrosionsprodukten und deren Veränderung über die Zeit sowie ihrer räumlichen Verteilung in der Probe von Interesse. Aufgrund der Größe der CT-Bilddaten ist eine manuelle Segmentierung nicht durchführbar, so dass automatische Verfahren unabdingbar sind. Dabei ist insbesondere die Segmentierung der Korrosionsprodukte in den Bilddaten ein schwieriges Problem. Allein aufgrund der Grauwerte ist eine Zuordnung nahezu unmöglich, denn die Grauwerte von Beton und Korrosionsprodukt unterscheiden sich kaum. Eine formbasierte Suche ist nicht offensichtlich, da die Korrosionsprodukte in Beton diffuse Formen haben. Allerdings lässt sich Vorwissen über die Ausbreitung der Korrosionsprodukte nutzen. Sie bilden sich in räumlicher Nähe des BSt (in Bereichen vorheriger Volumenabnahme des BSt), entlang von Rissen sowie in Porenräumen, die direkt am BSt und in dessen Nahbereich liegen. Davon ausgehend wird vor der Korrosionsprodukterkennung zunächst eine BSt-Volumen-, Riss- und Porenerkennung durchgeführt. Dieser in der Arbeit näher beschriebene Schritt erlaubt es, halbautomatisch Startpunkte (Seed Points) für die Korrosionsprodukterkennung zu finden. Weiterhin werden verschiedene in der Bildverarbeitung bekannte Algorithmen auf ihre Eignung untersucht werden. T3 - ZIB-Report - 14-24 KW - Beton KW - Korrosionserkennung KW - Bildverarbeitung KW - Computertomografie KW - concrete KW - corrosiondetection KW - image processing KW - computed tomography Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50912 SN - 1438-0064 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 - 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 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. T3 - ZIB-Report - 17-62 KW - micro-CT KW - image segmentation KW - 2D distance map KW - hierarchical watershed KW - stingray KW - tesserae KW - biological tilings KW - Amira Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65785 SN - 1438-0064 ER - TY - CHAP A1 - Klindt, Marco A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian ED - Arnold, David ED - Kaminski, Jaime ED - Niccolucci, Franco ED - Stork, Andre T1 - Conveying Archaeological Contexts to Museum Visitors: Case Study Pergamon Exhibition T2 - VAST12: The 13th International Symposium on Virtual Reality, Archaeology and Intelligent Cultural Heritage - Short Papers Y1 - 2012 UR - http://diglib.eg.org/EG/DL/PE/VAST/VAST12S/025-028.pdf U6 - https://doi.org/10.2312/PE/VAST/VAST12S/025-028 SP - 25 EP - 28 PB - Eurographics Association CY - Brighton, UK ER - TY - CHAP A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions T2 - EVA 2012 Berlin Y1 - 2012 SP - 150 EP - 155 PB - Gesellschaft zur Förderung angewandter Informatik e.V. CY - Volmerstraße 3, 12489 Berlin ER - 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 - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - A Virtual Laboratory for Assessment of Bone Biopsies T2 - 14th IAA Humans in Space Symposium Y1 - 2003 SP - 7 CY - Banff, Alberta, Canada 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 - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - J. Moorhead, Robert ED - Gross, Markus ED - I. Joy, Kenneth T1 - Fast Visualization of Plane-Like Structures in Voxel Data T2 - Proceedings of IEEE Visualization 2002 Y1 - 2002 U6 - https://doi.org/10.1109/VISUAL.2002.1183753 SP - 29 EP - 36 PB - IEEE Computer Society Press CY - Boston MA, USA ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Schirmacher, Hartmut A1 - Westerhoff, Malte A1 - Lamecker, Hans A1 - Prohaska, Steffen A1 - Zachow, Stefan T1 - From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models T2 - Proceedings of the Japan Korea Computer Graphics Conference 2002 Y1 - 2002 PB - Kanazawa University CY - Kanazawa City, Ishikawa, Japan ER - TY - JOUR A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Visual Analysis of Trabecular Bone Structure JF - Journal of Gravitational Physiology Y1 - 2002 VL - 9 (1) SP - 171 EP - 172 ER - TY - GEN A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Felsenberg, Dieter A1 - Kurths, Jürgen A1 - Zaikin, Alexei A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Regional Structural Skeletal Discordance Assessed by Measures of Complexity Y1 - 2002 ER - TY - JOUR A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Kurths, Jürgen A1 - Gowin, Wolfgang T1 - Bone Modeling and Structural Measures of Complexity JF - Journal of Gravitational Physiology Y1 - 2002 U6 - https://doi.org/10.1016/j.actaastro.2005.01.007 VL - 9 SP - 175 EP - 176 ER - TY - JOUR A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Felsenberg, Dieter T1 - Femoral Neck Fractures: Reasons for the Most Common Location of Fractures JF - Acta Orthop. Scand. (Suppl. 304) Y1 - 2002 VL - 73 SP - 26 ER - TY - CHAP A1 - Saparin, Peter A1 - Gowin, Wolfgang A1 - Zaikin, Alexei A1 - Thomsen, Jesper A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Kurths, Jürgen T1 - Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity T2 - 14th IAA Humans in Space Symposium Y1 - 2003 CY - Banff, Alberta, Canada ER - TY - CHAP A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Interactive Visualization to Support Quantification of Bone Biopsies T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Saparin, Peter A1 - Gowin, Wolfgang A1 - Zaikin, Alexei A1 - Prohaska, Steffen T1 - Quantification of changes in human bone structure at different skeletal locations using measures of complexity T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Gowin, Wolfgang A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Hege, Hans-Christian A1 - Belle, Stefan A1 - Felsenberg, Dieter T1 - Architectural Reasons for the Femoral Neck Fracture Location T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Zaikin, Alexei A1 - Saparin, Peter A1 - Prohaska, Steffen A1 - Kurths, Jürgen A1 - Gowin, Wolfgang T1 - 2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures. T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Thomsen, Jesper A1 - Koller, Bruno A1 - Laib, Andreas A1 - Prohaska, Steffen A1 - Giehl, Michael A1 - Gowin, Wolfgang T1 - Comparison between Static Histomorphometric Measures Conducted by Traditionally 2D Histomorphometry and 3D μ-CT in Human Tibial Biopsies T2 - 2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’ Y1 - 2003 CY - Berlin-Adlershof ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Weinkauf, Tino A1 - Prohaska, Steffen A1 - Hutanu, Andrei T1 - Distributed visualization and analysis of fluid dynamics data T2 - Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration Y1 - 2004 SP - 145 EP - 150 CY - Sendai, Japan ER - TY - JOUR A1 - Rigort, Alexander A1 - Günther, David A1 - Hegerl, Reiner A1 - Baum, Daniel A1 - Weber, Britta A1 - Prohaska, Steffen A1 - Medalia, Ohad A1 - Baumeister, Wolfgang A1 - Hege, Hans-Christian T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks JF - Journal of Structural Biology Y1 - 2012 U6 - https://doi.org/10.1016/j.jsb.2011.08.012 VL - 177 SP - 135 EP - 144 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Automatic Extraction and Analysis of Realistic Pore Structures from µCT Data for Pore Space Characterization of Graded Soil T2 - Proceedings of the 6th International Conference on Scour and Erosion (ICSE-6) Y1 - 2012 SP - 345 EP - 352 ER - TY - JOUR A1 - Weber, Britta A1 - Greenan, Garrett A1 - Prohaska, Steffen A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Müller-Reichert, Thomas A1 - Hyman, Anthony A1 - Verbavatz, Jean-Marc T1 - Automated tracing of microtubules in electron tomograms of plastic embedded samples of Caenorhabditis elegans embryos JF - Journal of Structural Biology Y1 - 2012 UR - http://www.sciencedirect.com/science/article/pii/S1047847711003509 U6 - https://doi.org/10.1016/j.jsb.2011.12.004 VL - 178 IS - 2 SP - 129 EP - 138 ER - TY - JOUR A1 - Kleinfeld, David A1 - Bharioke, Arjun A1 - Blinder, Pablo A1 - Bock, David A1 - Briggman, Kevin A1 - Chklovskii, Dmitri A1 - Denk, Winfried A1 - Helmstaedter, Moritz A1 - Kaufhold, John A1 - Lee, Wei-Chung A1 - Meyer, Hanno A1 - Micheva, Kristina A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Reid, R. A1 - Smith, Stephen A1 - Takemura, Shinya A1 - Tsai, Philbert A1 - Sakmann, Bert T1 - Large-scale automated histology in the pursuit of connectomes JF - Journal of Neuroscience Y1 - 2011 UR - http://www.zib.de/prohaska/docs/Kleinfeld_JNS_Connectomes_2011.pdf U6 - https://doi.org/10.1523/JNEUROSCI.4077-11.2011 VL - 31 IS - 45 SP - 16125 EP - 16138 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Accelerated Visualization of Dynamic Molecular Surfaces JF - Comput. Graph. Forum Y1 - 2010 U6 - https://doi.org/10.1111/j.1467-8659.2009.01693.x VL - 29 SP - 943 EP - 952 ER - TY - CHAP A1 - Reininghaus, Jan A1 - Günther, David A1 - Hotz, Ingrid A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - TADD: A Computational Framework for Data Analysis Using Discrete Morse Theory T2 - Mathematical Software - ICMS 2010 Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15582-6_35 VL - 6327 SP - 198 EP - 208 PB - Springer ER - TY - JOUR A1 - Kuß, Anja A1 - Gensel, Maria A1 - Meyer, Björn A1 - Dercksen, Vincent J. A1 - Prohaska, Steffen T1 - Effective Techniques to Visualize Filament-Surface Relationships JF - Comput. Graph. Forum Y1 - 2010 VL - 29 SP - 1003 EP - 1012 ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian ED - Bremer, Peer-Timo ED - Hotz, Ingrid ED - Pascucci, Valerio ED - Peikert, Ronald T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials BT - Theory, Algorithms, and Applications T2 - Topological Methods in Data Analysis and Visualization III Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-04099-8_15 SP - 235 EP - 248 PB - Springer ER - TY - CHAP A1 - Rosanwo, Olufemi A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Hotz, Ingrid A1 - Hege, Hans-Christian ED - Eades, Peter ED - Ertl, Thomas ED - Shen, Han-Wei T1 - Dual Streamline Seeding T2 - Proceedings of the IEEE Pacific Visualization Symposium Y1 - 2009 SP - 9 EP - 16 CY - Beijing, China ER - TY - CHAP A1 - Homberg, Ulrike A1 - Binner, Richard A1 - Prohaska, Steffen A1 - Dercksen, Vincent J. A1 - Kuß, Anja A1 - Kalbe, Ute T1 - Determining Geometric Grain Structure from X-Ray Micro-Tomograms of Gradated Soil T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 37 EP - 52 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Ebell, Gino T1 - 3D Corrosion Detection in Time-dependent CT Images of Concrete T2 - DIR-2015 Proceedings N2 - In civil engineering, the corrosion of steel reinforcements in structural elements of concrete bares a risk of stability-reduction, mainly caused by the exposure to chlorides. 3D computed tomography (CT) reveals the inner structure of concrete and allows one to investigate the corrosion with non-destructive testing methods. To carry out such investigations, specimens with a large artificial crack and an embedded steel rebar have been manufactured. 3D CT images of those specimens were acquired in the original state. Subsequently three cycles of electrochemical pre-damaging together with CT imaging were applied. These time series have been evaluated by means of image processing algorithms to segment and quantify the corrosion products. Visualization of the results supports the understanding of how corrosion propagates into cracks and pores. Furthermore, pitting of structural elements can be seen without dismantling. In this work, several image processing and visualization techniques are presented that have turned out to be particularly effective for the visualization and segmentation of corrosion products. Their combination to a workflow for corrosion analysis is the main contribution of this work. Y1 - 2015 UR - http://www.ndt.net/events/DIR2015/app/content/Paper/36_Paetsch.pdf ER - TY - GEN A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Wiebel, Alexander A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Definition, Extraction, and Validation of Pore Structures in Porous Materials N2 - An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation. T3 - ZIB-Report - 13-56 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42510 SN - 1438-0064 ER - TY - GEN 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 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. T3 - ZIB-Report - 17-26 KW - trabecular structures KW - image-based analysis KW - additive manufacturing KW - printability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64004 SN - 1438-0064 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Baumgart, Johannes A1 - Lindow, Norbert A1 - Shelley, Michael A1 - Nazockdast, Ehssan A1 - Kratz, Andrea A1 - Prohaska, Steffen A1 - Brugués, Jan A1 - Fürthauer, Sebastian A1 - Müller-Reichert, Thomas T1 - C. elegans chromosomes connect to centrosomes by anchoring into the spindle network JF - Nature Communications N2 - The mitotic spindle ensures the faithful segregation of chromosomes. Here we combine the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging to reconstruct all microtubules in 3D and identify their plus- and minus-ends. We classify them as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions, and quantify distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms15288 VL - 8 IS - 15288 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 - GEN A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. T3 - ZIB-Report - 17-06 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63053 SN - 1438-0064 ER - TY - JOUR A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Ehrig, Karsten A1 - Ebell, Gino A1 - Meinel, Dietmar A1 - Heyn, Andreas T1 - Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben JF - DGZfP-Jahrestagung 2014 Konferenzband Y1 - 2014 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 - GEN A1 - Lindow, Norbert A1 - Redemann, Stefanie A1 - Fabig, Gunar A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Quantification of Three-Dimensional Spindle Architecture N2 - Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. Three-dimensional reconstruction of microtubules, however, is only the first step towards biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms. T3 - ZIB-Report - 18-07 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66562 SN - 1438-0064 ER - TY - JOUR A1 - Zhukova, Yulia A1 - Hiepen, Christian A1 - Knaus, Petra A1 - Osterland, Marc A1 - Prohaska, Steffen A1 - Dunlop, John W. C. A1 - Fratzl, Peter A1 - Skorb, Ekaterina V. T1 - The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration JF - Advanced Healthcare Materials N2 - Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants. Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood. The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively. The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair. Y1 - 2017 U6 - https://doi.org/10.1002/adhm.201601244 ER - TY - CHAP A1 - Kaplan, Bernhard A1 - Buchmann, Jens A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017 N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. Y1 - 2017 U6 - https://doi.org/10.1117/12.2251945 VL - 10064 SP - 100645J EP - 100645J-13 ER - TY - CHAP A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Experimental validation of a Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing N2 - Quantitative photoacoustic tomography (qPAT) aims to extract physiological parameters, such as blood oxygen saturation (sO2), from measured multi-wavelength image data sets. The challenge of this approach lies in the inherently nonlinear fluence distribution in the tissue, which has to be accounted for by using an appropriate model, and the large scale of the inverse problem. In addition, the accuracy of experimental and scanner-specific parameters, such as the wavelength dependence of the incident fluence, the acoustic detector response, the beam profile and divergence, needs to be considered. This study aims at quantitative imaging of blood sO2, as it has been shown to be a more robust parameter compared to absolute concentrations. We propose a Monte-Carlo–based inversion scheme in conjunction with a reduction in the number of variables achieved using image segmentation. The inversion scheme is experimentally validated in tissue-mimicking phantoms consisting of polymer tubes suspended in a scattering liquid. The tubes were filled with chromophore solutions at different concentration ratios. 3-D multi-spectral image data sets were acquired using a Fabry-Perot based PA scanner. A quantitative comparison of the measured data with the output of the forward model is presented. Parameter estimates of chromophore concentration ratios were found to be within 5 % of the true values. Y1 - 2017 U6 - https://doi.org/10.1117/12.2252359 VL - 10064 SP - 1006416 EP - 1006416-8 ER - TY - JOUR A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases JF - Neuron N2 - Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. Y1 - 2016 U6 - https://doi.org/10.1016/j.neuron.2016.06.012 VL - 91 IS - 2 SP - 293 EP - 311 ER - TY - GEN A1 - Osterland, Marc A1 - Benn, Andreas A1 - Prohaska, Steffen A1 - Schütte, Christof T1 - Single Cell Tracking in Phase-Contrast Microscopy T2 - EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life N2 - In this work, we developed an automatic algorithm to analyze cell migration in chemotaxis assays, based on phase-contrast time-lapse microscopy. While manual approaches are still widely used in recent publications, our algorithm is able to track hundreds of single cells per frame. The extracted paths are analysed with traditional geometrical approaches as well as diffusion-driven Markov state models (MSM). Based on these models, a detailed view on spatial and temporal effects is possible. Using our new approach on experimental data, we are able to distinguish between directed migration (e.g. towards a VEGF gradient) and random migration without favored direction. A calculation of the committor probabilities reveals that cells of the whole image area are more likely to migrate directly towards the VEGF than away from it during the first four hours. However, in absence of a chemoattractant, cells migrate more likely to their nearest image border. These conclusions are supported by the spatial mean directions. In a next step, the cell-cell interaction during migration and the migration of cell clusters will be analyzed. Furthermore, we want to observe phenotypical changes during migration based on fluorescence microscopy and machine learning. The algorithm is part of a collaborative platform which brings the experimental expertise of scientists from life sciences and the analytical knowledge of computer scientists together. This platform is built using web-based technologies with a responsive real-time user interface. All data, including raw and metadata as well as the accompanying results, will be stored in a secure and scalable compute cluster. The compute cluster provides sufficient space and computational power for modern image-based experiments and their analyses. Specific versions of data and results can be tagged to keep immutable records for archival. Y1 - 2015 ER - TY - CHAP A1 - Ritter, Zully A1 - Prohaska, Steffen A1 - Brand, R. A1 - Friedmann, A. A1 - Hege, Hans-Christian A1 - Goebbels, Jürgen A1 - Felsenberg, Dieter T1 - Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study T2 - Proc. ISB 2011 Y1 - 2011 ER - TY - CHAP A1 - Streicher, Doreen A1 - Paetsch, Olaf A1 - Seiler, Robert A1 - Prohaska, Steffen A1 - Krause, Martin A1 - Boller, Christian T1 - 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira T2 - Proc. DGZfP-Jahrestagung 2011 Y1 - 2011 ER - TY - GEN A1 - Günther, David A1 - Reininghaus, Jan A1 - Prohaska, Steffen A1 - Weinkauf, Tino A1 - Hege, Hans-Christian ED - Peikert, Ronny ED - Hauser, Helwig ED - Carr, Hamish T1 - Efficient Computation of a Hierarchy of Discrete 3D Gradient Vector Fields T2 - Topological Methods in Data Analysis and Visualization II Y1 - 2012 U6 - https://doi.org/10.1007/978-3-642-23175-9_2 SP - 15 EP - 29 PB - Springer ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Meyer, Björn A1 - Rybak, Jürgen A1 - Hege, Hans-Christian T1 - Ontology-Based Visualization of Hierarchical Neuroanatomical Structures T2 - Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine VCBM 2008 Y1 - 2008 SP - 177 EP - 184 ER - TY - CHAP A1 - Petz, Christoph A1 - Prohaska, Steffen A1 - Goubergrits, Leonid A1 - Kertzscher, Ulrich A1 - Hege, Hans-Christian T1 - Near-Wall Flow Visualization in Flattened Surface Neighborhoods T2 - Proc. Simulation and Visualization 2008 Y1 - 2008 UR - http://www.simvis.org/Tagung2008/sv-proceedings.html SP - 93 EP - 105 CY - Magdeburg, Germany ER - TY - JOUR A1 - Sahner, Jan A1 - Weber, Britta A1 - Lamecker, Hans A1 - Prohaska, Steffen T1 - Extraction of feature Lines on surface meshes based on discrete Morse theory JF - Computer Graphics Forum Y1 - 2008 U6 - https://doi.org/10.1111/j.1467-8659.2008.01202.x VL - 27 IS - 3 SP - 735 EP - 742 CY - Eindhoven, Netherlands ER - TY - CHAP A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Homberg, Ulrike A1 - Slowik, Volker T1 - Modelling and Analysis of Particle and Pore Structures in Soils T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 53 EP - 60 ER - TY - CHAP A1 - Semar, Olivier A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Kalbe, Ute A1 - Mehlhorn, Tobias A1 - Prohaska, Steffen A1 - Slowik, Volker A1 - Witt, Karl Josef T1 - Conditions for Suffosive Erosion Phemomena in Soils – Concept and Approach T2 - Workshop Internal Erosion Y1 - 2009 VL - 21 SP - 29 EP - 35 ER - TY - CHAP A1 - Clasen, Malte A1 - Prohaska, Steffen T1 - Image-Error-Based Level of Detail for Landscape Visualization T2 - Proc. VMV 2010 Y1 - 2010 SP - 267 EP - 274 ER - TY - CHAP A1 - Homberg, Ulrike A1 - Baum, Daniel A1 - Prohaska, Steffen ED - Mücklich, Frank ED - Slussallek, Philipp ED - Schladitz, Katja T1 - Describing and Analyzing the Dual Structures of Porous Media T2 - Proc. 3D-Microstructure Meeting Y1 - 2011 SP - 24 EP - 25 ER - TY - CHAP A1 - Weber, Britta A1 - Möller, Marit A1 - Verbavatz, Jean-Marc A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Prohaska, Steffen T1 - Fast Tracing of Microtubule Centerlines in Electron Tomograms T2 - BioVis 2011 Abstracts, 1st IEEE Symposium on Biological Data Visualization Y1 - 2011 ER - TY - CHAP A1 - Ehrig, Karsten A1 - Goebbels, Jürgen A1 - Meinel, Dietmar A1 - Paetsch, Olaf A1 - Prohaska, Steffen A1 - Zobel, Valentin T1 - Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography T2 - International Symposium on Digital Industrial Radiology and Computed Tomography Y1 - 2011 ER - TY - JOUR A1 - Petz, Christoph A1 - Kasten, Jens A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Hierarchical Vortex Regions in Swirling Flow JF - Computer Graphics Forum Y1 - 2009 VL - 28 IS - 3 SP - 863 EP - 870 ER - TY - CHAP A1 - Dercksen, Vincent J. A1 - Weber, Britta A1 - Günther, David A1 - Oberlaender, Marcel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - Automatic alignment of stacks of filament data T2 - Proc. IEEE International Symposium on Biomedical Imaging Y1 - 2009 SP - 971 EP - 974 PB - IEEE press CY - Boston, USA ER - TY - CHAP A1 - Kuß, Anja A1 - Prohaska, Steffen A1 - Rybak, Jürgen T1 - Using Ontologies for the Visualization of Hierarchical Neuroanatomical Structures T2 - Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics Y1 - 2009 U6 - https://doi.org/10.3389/conf.neuro.11.2009.08.017 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie T2 - Tagungsband der DACH Jahrestagung 2012 Y1 - 2012 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Breßler, David A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben T2 - Tagungsband der DGZfP Jahrestagung 2013 Y1 - 2013 ER - TY - CHAP A1 - Paetsch, Olaf A1 - Baum, Daniel A1 - Ehrig, Karsten A1 - Meinel, Dietmar A1 - Prohaska, Steffen T1 - Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography T2 - Proceedings of Conference on Industrial Computed Tomography Y1 - 2012 SP - 321 EP - 330 ER - TY - JOUR A1 - Ziegler, Alexander A1 - Ogurreck, Malte A1 - Steinke, Thomas A1 - Beckmann, Felix A1 - Prohaska, Steffen A1 - Ziegler, Andreas T1 - Opportunities and challenges for digital morphology JF - Biology Direct Y1 - 2010 U6 - https://doi.org/10.1186/1745-6150-5-45 VL - 5 IS - 1 SP - 45 ER - TY - CHAP A1 - Binner, Richard A1 - Homberg, Ulrike A1 - Prohaska, Steffen A1 - Kalbe, Ute A1 - Witt, Karl Josef T1 - Identification of Descriptive Parameters of the Soil Pore Structure using Experiments and CT Data T2 - Proceedings of the 5th International Conference on Scour and Erosion (ICSE-5) Y1 - 2010 SP - 397 EP - 407 PB - American Society of Civil Engineers (ASCE) 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 - 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 - 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 - 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 - JOUR A1 - Cassot, Francis A1 - Lauwers, Frederic A1 - Fouard, Céline A1 - Prohaska, Steffen A1 - Lauwer-Cances, Valerie T1 - A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex JF - Microcirculation Y1 - 2006 VL - 13 SP - 15 EP - 32 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 - 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 - 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 - JOUR A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Lindow, Norbert A1 - Powers, James A. A1 - Cota, Vanessa A1 - Quintanilla, Luis J. A1 - Brugués, Jan A1 - Prohaska, Steffen A1 - Chu, Diana S. A1 - Müller-Reichert, Thomas T1 - Sperm-specific meiotic chromosome segregation in C. elegans JF - eLife Y1 - 2020 U6 - https://doi.org/10.7554/eLife.50988 VL - 9 SP - e50988 ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms JF - Photoacoustics N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. Y1 - 2020 U6 - https://doi.org/10.1016/j.pacs.2019.100157 VL - 17 SP - 100157 ER - TY - JOUR A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen A1 - Baum, Daniel T1 - Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography JF - bioRxiv N2 - We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets. Y1 - 2020 U6 - https://doi.org/10.1101/2020.05.28.120899 ER - TY - JOUR A1 - Jin, Eugene Jennifer A1 - Kiral, Ferdi Ridvan A1 - Ozel, Mehmet Neset A1 - Burchardt, Lara Sophie A1 - Osterland, Marc A1 - Epstein, Daniel A1 - Wolfenberg, Heike A1 - Prohaska, Steffen A1 - Hiesinger, Peter Robin T1 - Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals JF - Current Biology N2 - Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains. We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ‘‘hub’’ compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent, whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.02.032 VL - 28 IS - 7 SP - 1027 EP - 1038.e4 ER - TY - GEN A1 - Lindow, Norbert A1 - Brünig, Florian A1 - Dercksen, Vincent J. A1 - Fabig, Gunar A1 - Kiewisz, Robert A1 - Redemann, Stefanie A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures N2 - In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor. The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection. Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures. T3 - ZIB-Report - 19-30 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73739 SN - 1438-0064 ER - TY - JOUR A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - 3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent JF - Journal of Biomedical Optics N2 - Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori. Y1 - 2019 U6 - https://doi.org/10.1117/1.JBO.24.6.066001 VL - 24 IS - 6 SP - 066001 ER - TY - CHAP A1 - Lindow, Norbert A1 - Redemann, Stefanie A1 - Brünig, Florian A1 - Fabig, Gunar A1 - Müller-Reichert, Thomas A1 - Prohaska, Steffen T1 - Quantification of three-dimensional spindle architecture T2 - Methods in Cell Biology Part B N2 - Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms. Y1 - 2018 U6 - https://doi.org/10.1016/bs.mcb.2018.03.012 SN - 0091-679X VL - 145 SP - 45 EP - 64 PB - Academic Press ER - TY - GEN A1 - Redemann, Stefanie A1 - Lantzsch, Ina A1 - Lindow, Norbert A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Müller-Reichert, Thomas T1 - A switch in microtubule orientation during C. elegans meiosis N2 - In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes. T3 - ZIB-Report - 18-34 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69855 SN - 1438-0064 ER - TY - JOUR A1 - Redemann, Stefanie A1 - Lantzsch, Ina A1 - Lindow, Norbert A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Müller-Reichert, Thomas T1 - A switch in microtubule orientation during C. elegans meiosis JF - Current Biology N2 - In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes. Y1 - 2018 U6 - https://doi.org/10.1016/j.cub.2018.07.012 SN - 0960-9822 ER - TY - JOUR A1 - Lantzsch, Ina A1 - Yu, Che-Hang A1 - Chen, Yu-Zen A1 - Zimyanin, Vitaly A1 - Yazdkhasti, Hossein A1 - Lindow, Norbert A1 - Szentgyoergyi, Erik A1 - Pani, Ariel M A1 - Prohaska, Steffen A1 - Srayko, Martin A1 - Fürthauer, Sebastian A1 - Redemann, Stefanie T1 - Microtubule reorganization during female meiosis in C. elegans JF - eLife N2 - Most female meiotic spindles undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of meiotic spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic \textit{Caenorhabditis elegans} spindles. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over within seconds. The results show that the metaphase to anaphase transition correlates with an increase in microtubule numbers and a decrease in their average length. Detailed analysis of the tomographic data revealed that the microtubule length changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the spindle reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe. This suggests that the most prominent drivers of spindle rearrangements are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on katanin. Y1 - 2021 U6 - https://doi.org/10.7554/eLife.58903 VL - 10 SP - e58903 ER - TY - GEN A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - 3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent N2 - Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori. T3 - ZIB-Report - 19-16 KW - quantitative photoacoustic imaging KW - blood oxygen saturation KW - inverse problem KW - model-based inversion KW - Monte Carlo KW - spectral unmixing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72995 SN - 1438-0064 ER - TY - GEN A1 - Buchmann, Jens A1 - Kaplan, Bernhard A1 - Powell, Samuel A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms N2 - Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies. T3 - ZIB-Report - 19-60 KW - quantitative photoacoustic imaging KW - blood oxygen saturation KW - inverse problem KW - model-based inversion KW - Monte Carlo KW - spectral unmixing Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-75416 SN - 1438-0064 ER - TY - THES A1 - Prohaska, Steffen T1 - Skeleton-based visualization of massive voxel objects with network-like architecture T1 - Skelettbasierte Visualisierung großer Voxel-Objekte mit netzwerkartiger Architektur N2 - This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation. N2 - Die vorliegende Arbeit führt I/O-effiziente Algorithmen und Standard-Algorithmen zur Berechnung von Voxel-Skeletten aus großen Voxel-Objekten mit komplexer, netzwerkartiger Struktur und zur Umwandlung solcher Voxel-Skelette in stückweise-lineare Geometrie ein. Die vorgestellten Techniken werden zur Visualisierung und Analyse komplexer drei-dimensionaler Bilddaten, beispielsweise aus Biologie und Medizin, eingesetzt. Abschnitt 2.3.1 leistet mit der Diskussion von topologischem Thinning im Grid-Cell-Modell einen Beitrag zu den theoretischen Grundlagen von Thinning-Algorithmen. Im Grid-Cell-Modell wird ein Voxel-Objekt als Zellkomplex dargestellt, der aus den Ecken, Kanten, Flächen und den eingeschlossenen Volumina der Voxel gebildet wird. Topologisch unklare Situationen an Verzweigungen und blockierte Voxel-Kombinationen werden aufgelöst. Die Charakterisierung von Zellpaaren, die im Thinning-Prozess entfernt werden dürfen, ist einfacher als bekannte Charakterisierungen von so genannten "Simple Voxels". Eine wesentliche Schlussfolgerung ist, dass das Grid-Cell-Modell atomaren Voxeln überlegen ist, wenn Algorithmen detaillierte Kontrolle über Topologie benötigen. Abschnitt 2.3.2 präsentiert ein rauschunempfindliches Maß, das den geodätischen Abstand entlang der Oberfläche verwendet, um zweidimensionale Skelette zu berechnen, welche dünne, aber geometrisch bedeutsame, Strukturen des Objekts rauschunempfindlich abbilden. Das Maß wird im weiteren mit Thinning kombiniert, um die Erosion von Voxeln auf Linien zuzusteuern, die zentriert in plattenförmigen Strukturen liegen. Maße, die auf dem geodätischen Abstand aufbauen, scheinen sehr geeignet zu sein, um ein- und zwei-dimensionale Skelette bei vorhandenem Rauschen zu identifizieren. Eine theoretische Begründung für diese Beobachtung steht noch aus. In Abschnitt 6 werden die diskutierten Methoden zur Visualisierung von Knochenfeinstruktur eingesetzt. Abschnitt 3 beschreibt eine Methode, um Voxel-Skelette durch kontrollierte Retraktion in eine stückweise-lineare geometrische Darstellung umzuwandeln, die als Eingabe für Geometrieverarbeitung und effizientes Rendering von Voxel-Skeletten dient. Es zeigt sich, dass eine detaillierte Betrachtung der topologischen Eigenschaften eines Voxel-Skeletts einer Betrachtung von allgemeinen Voxel-Konfigurationen für die Umwandlung zu einer geometrischen Darstellung überlegen ist. Die diskutierte Methode bildet die Grundlage für die Anwendungen, die in Abschnitt 6 diskutiert werden. Abschnitt 5 führt einen I/O-effizienten Algorithmus für Thinning ein. Die vorgestellte Methode erweitert bekannte Algorithmen zur Berechung von Chamfer-Distanztransformationen und Thinning so, dass diese effizient ausführbar sind, wenn die Eingabedaten den verfügbaren Hauptspeicher übersteigen. Der Einfluss der Blockgrenzen auf die Algorithmen wurde analysiert, um global korrekte Ergebnisse sicherzustellen. Eine detaillierte Analyse ist einer naiven Zerlegung, die die Einflüsse von Blockgrenzen vernachlässigt, überlegen. In Abschnitt 6 wird, aufbauend auf den I/O-effizienten Algorithmen, ein Verfahren zur quantitativen Analyse von Mikrogefäßnetzwerken diskutiert. KW - Visualisierung KW - Bilddatenanalyse KW - Skelettberechnung KW - Geometrieerzeugung KW - I/O-effiziente Algorithmen KW - visualization KW - image data analysis KW - skeletonization KW - geometry generation KW - external memory algorithms Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-14888 UR - http://opus.kobv.de/ubp/volltexte/2007/1488/ ER - TY - GEN A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases N2 - Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish. T3 - ZIB-Report - 16-34 KW - neuroinformatics KW - NBLAST KW - neuron similarity KW - cell type KW - clustering Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59672 SN - 1438-0064 ER - TY - GEN A1 - Clasen, Malte A1 - Paar, Philip A1 - Prohaska, Steffen T1 - Level of Detail for Trees Using Clustered Ellipsoids N2 - We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts. T3 - ZIB-Report - 11-41 KW - level of detail KW - rendering KW - natural scene KW - Gaussian mixture model Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14251 SN - 1438-0064 ER - TY - GEN A1 - Kaplan, Bernhard A1 - Laufer, Jan A1 - Prohaska, Steffen A1 - Buchmann, Jens T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. T3 - ZIB-Report - 17-04 KW - quantitative photoacoustic tomography KW - model-based inversion KW - oxygen saturation KW - chromophore concentration KW - photoacoustic imaging KW - Monte Carlo methods for light transport KW - boundary conditions KW - coordinate search Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62318 SN - 1438-0064 ER - TY - GEN A1 - Klindt, Marco A1 - Baum, Daniel A1 - Prohaska, Steffen A1 - Hege, Hans-Christian T1 - iCon.text – a customizable iPad app for kiosk applications in museum exhibitions N2 - We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar. The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage. The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer. The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network". T3 - ZIB-Report - 13-07 KW - HCI KW - Cultural Heritage KW - Kiosk application KW - iPad Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17731 SN - 1438-0064 ER -