TY - THES A1 - Dill, Sabrina T1 - Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection N2 - In this thesis we investigate the task of automatically detecting phases in surgical workflow in endoscopic video data. For this, we employ deep learning approaches that solely rely on frame-wise visual information, instead of using additional signals or handcrafted features. While previous work has mainly focused on tool presence and temporal information for this task, we reason that additional global information about the context of a frame might benefit the phase detection task. We propose novel deep learning architectures: a convolutional neural network (CNN) based model for the tool detection task only, called Clf-Net, as well as a model which performs joint (context) feature learning and tool classification to incorporate information about the context, which we name Context-Clf-Net. For the phase detection task lower-dimensional feature vectors are extracted, which are used as input to recurrent neural networks in order to enforce temporal constraints. We compare the performance of an online model, which only considers previous frames up to the current time step, to that of an offline model that has access to past and future information. Experimental results indicate that the tool detection task benefits strongly from the introduction of context information, as we outperform both Clf-Net results and stateof-the-art methods. Regarding the phase detection task our results do not surpass state-of-the-art methods. Furthermore, no improvement of using features learned by the Context-Clf-Net is observed in the phase detection task for both online and offline versions Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81745 ER - TY - THES A1 - Schotte, Merlind T1 - Finite-Elemente-Techniken zur mechanischen Stabilitätsanalyse der Hyomandibula von Rochen N2 - Haie und Rochen sind die einzigen Wirbeltiere, die sich durch ein Knorpelskelett auszeichnen, das mit winzigen mineralisierten Elementen bedeckt ist, die sogenannten Tesserae. Obwohl dieser mineralisierte Knorpel seit hunderten von Millionen Jahren ein charakteristisches Merkmal dieser Tiere ist, ist der funktionelle Vorteil dieses Gewebestruktur bisher unklar geblieben. In dieser Masterarbeit wird diese Struktur mithilfe der Finite-Elemente-Methode(FEM) untersucht, wobei biologische Informationen zu den Muskeln und der geometrischen Gegebenheiten aus einem hochaufgelösten, kontrastgefärbten μCT-Scan einer Stechrochenhyomandibula verwendet werden. Für die Analyse werden Computer-Aided-Design(CAD)-Modelle und FE-Modelle konstruiert sowie vorhandene Methoden erweitert, um bei den Berechnungen die Charakteristika des biologischen Objektes bestmöglich zu berücksichtigen. Die Modelle bauen auf einer Segmentierung der Hyomandibula auf, wobei die mehreren tausend Tesserae in diesem Datensatz bereits voneinander isoliert sind. Für die Modellierung der Hyomandibula wird als erstes ein CAD-Modell konstruiert. Bei dieser Konstruktion wird eine Tesserae-Mittelfläche erstellt und im Anschluss nach innen und außen verschoben. Der nächste Schritt basiert auf dem Einbau von Zwischenwänden, die die Tesserae voneinander separieren. Auf Grundlage dieses Modells wird ein Tetraedergitter generiert, das die Basis für den zweiten Teil dieser Arbeit darstellt - die Berechnungen mit der FEM. Die wesentliche Aufgabe des zweiten Teils beinhaltet die Konstruktion eines FE-Modells, das in die lineare FEM einzuordnen ist. In dieses fließen die Randbedingungen und die Materialeigenschaften des Skelettelements ein. Mithilfe der FEM lassen sich die durch Krafteinwirkung auftretenden Verschiebungen und Spannungen der Hyomandibula ermitteln. Die Ergebnisse geben Rückschlüsse über das Verhalten des Materials, die Besonderheiten der Geometrie und damit über die Stabilität des Objektes. Der dritte Teil der Abschlussarbeit beschäftigt sich mit zusätzlichen Anpassungen und Änderungen der Modelle (CAD-Modell und FE-Modell), um diese Resultate mit dem Modell zu vergleichen, das der Biologie am nächsten kommt. Diese Anpassungen beinhalten das Variieren der Dicke der mineralisierten Schicht, die Konstellation des Materials und den Abstand zwischen den Tesserae. Die Ergebnisse zeigen, dass sowohl die Tesserae-Struktur als auch die zwischen den Tesserae liegenden Kollagenfasern vermutlich keinen Einfluss auf die Mechanik und dementsprechend die Stabilität haben. Jedoch lassen die unterschiedlichen Resultate im Fall verschieden gewählter Tesserae-Dicken annehmen, dass diese sehr wohl einen Einfluss besitzen. N2 - Sharks and rays are the only vertebrates characterized by a peculiar cartilage skeleton covered with minute mineralized tiles called tesserae. Although this tessellated cartilage has been a defining feature of this lineage for hundreds of millions of years, the functional advantage of this tissue design has remained obscure. In this Master’s thesis, the finite element method (FEM) is used to investigate the role of tiling in the skeleton, using biological information on the muscles and shape from a high-resolution, contrast-stained μCT-scan of a stingray hyomandibula. For this purpose, computer aided design (CAD) models and FE models are constructed and existing methods will be extended to take the best possible account of the characteristics of the biological object. The analysis builds from a segmentation of the hyomandibula, with the dataset’s several thousand tesserae pre-isolated from one another. For the modeling of the hyomandibula a CAD model is constructed. In this construction, a medial surface is created using the tesserae which is subsequently moved to the inside and outside. The next step is to integrate partition walls separating the tesserae elements. Based on this model, a tetrahedral grid is then generated, which is the content of the second part of this thesis, the calculation with the FEM. A finite element model is constructed including boundary conditions and material properties of the skeletal element to compute the results using the linear FEM theory. The FEM is used to determine the displacements and stresses resulting from biological forces acting on the hyomandibula. The results allow conclusions of the material behavior, geometric characteristics (tesselation) and therefore the object stability. Important contributions of this thesis are additional adjustments and changes to the models (CAD model and FE model) to make it more appropriate to study the biological data at hand. The tesserae thickness, the length of the collagenious fibres and the constellation of the material are the parameters, which are changed. In contrast to the tesserae thicknesses, the results suggest that both the arrangement of the tesserae and its interposed collagen fibers have no substantial influence on the mechanics. Y1 - 2018 ER - TY - CHAP A1 - Paetsch, Olaf T1 - Möglichkeiten und Grenzen automatischer Merkmalserkennung am Beispiel von Risserkennungen in 3D-CT-Aufnahmen von Betonproben N2 - Die Auswertungen der großen Datenmengen moderner bildgebender Verfahren der ZfP können manuell kaum noch bewältigt werden. Hochauflösende 3D-CT-Aufnahmen bestehen oft aus über 1000 Schichtbildern mit einer Datenmenge von mehreren Gigabytes. Aktuelle Computer können diese zwar problemlos visualisieren und erlauben somit eine visuelle Inspektion, aber die möglichst vollständige Erkennung bestimmter Merkmale in den Daten und deren qualitative wie quantitative Auswertung ist durch Experten manuell nicht mehr zu bewältigen. Das gilt insbesondere im Kontext der Schadensaufklärung für die quantitative Analyse verschiedenartig induzierter Risse in Betonen (z.B. durch mechanische Belastungen sowie Frost, Sulfat und Alkali-Kieselsäure-Reaktion). Eine dazu notwendige Segmentierung und Merkmalserkennung kann nur automatisch durchgeführt werden. Dabei ergibt sich (auch fast automatisch) die Frage nach der Verlässlichkeit der verwendeten Algorithmen. Inwieweit kann man davon ausgehen, dass alle gesuchten Merkmale auch tatsächlich gefunden worden sind? Sind die gefundenen Merkmale quantitativ auswertbar und wie wirken sich Parameteränderungen auf die Ergebnisse aus? Sollten immer dieselben, einmal mit gutem Ergebnis angewandten, Parameter auch bei anderen Proben zur besseren Vergleichbarkeit genutzt werden? Anhand eines Risserkennungsalgorithmus basierend auf Formerkennung und Bildverarbeitung wird die Problematik diskutiert. Als Grundlage zur Bewertung des Ansatzes dienen 3D-CT-Aufnahmen von geschädigten Betonprobekörpern und Datensätze, in denen sich aufgrund ihres homogenen Aufbaus mit einfachen Mitteln Risse sicher und eindeutig erkennen lassen. Zur Auswertung der erkannten Risse gehört auch deren Einbettung in das umliegende Material. Das erfordert neben einer automatischen Risserkennung auch eine Segmentierung des gesamten Probekörpers in Zementsteinmatrix, Gesteinskörnung und Porenraum. Da eine solche Segmentierung aufgrund der Datenmenge nur schwer manuell erfolgen kann, werden erste Ergebnisse aus einer Segmentierung mit Hilfe selbstlernender Convolutional Neural Networks gezeigt. Y1 - 2018 PB - iCT 2019 CY - https://www.ndt.net/article/ctc2019/papers/iCT2019_Full_paper_29.pdf ER - TY - THES A1 - Dill, Sabrina Patricia T1 - Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection Y1 - 2018 ER - TY - JOUR A1 - Hettich, G. A1 - Schierjott, R. A. A1 - Schilling, C. A1 - Maas, A. A1 - Ramm, Heiko A1 - Bindernagel, Matthias A1 - Lamecker, Hans A1 - Grupp, T. M. T1 - Validation of a Statistical Shape Model for Acetabular Bone Defect Analysis JF - ISTA 2018 London Abstract Book N2 - Acetabular bone defects are still challenging to quantify. Numerous classification schemes have been proposed to categorize the diverse kinds of defects. However, these classification schemes are mainly descriptive and hence it remains difficult to apply them in pre-clinical testing, implant development and pre-operative planning. By reconstructing the native situation of a defect pelvis using a Statistical Shape Model (SSM), a more quantitative analysis of the bone defects could be performed. The aim of this study is to develop such a SSM and to validate its accuracy using relevant clinical scenarios and parameters. Y1 - 2018 ER - TY - JOUR A1 - Zhang, Wei A1 - Hartmann, Carsten A1 - von Kleist, Max T1 - Optimal control of Markov jump processes: Asymptotic analysis, algorithms and applications to the modeling of chemical reaction systems JF - Communications in Mathematical Sciences N2 - Markov jump processes are widely used to model natural and engineered processes. In the context of biological or chemical applications one typically refers to the chemical master equation (CME), which models the evolution of the probability mass of any copy-number combination of the interacting particles. When many interacting particles (“species”) are considered, the complexity of the CME quickly increases, making direct numerical simulations impossible. This is even more problematic when one aims at controlling the Markov jump processes defined by the CME. In this work, we study both open loop and feedback optimal control problems of the Markov jump processes in the case that the controls can only be switched at fixed control stages. Based on Kurtz’s limit theorems, we prove the convergence of the respective control value functions of the underlying Markov decision problem as the copy numbers of the species go to infinity. In the case of the optimal control problem on a finite time-horizon, we propose a hybrid control policy algorithm to overcome the difficulties due to the curse of dimensionality when the copy number of the involved species is large. Two numerical examples demonstrate the suitability of both the analysis and the proposed algorithms. Y1 - 2018 U6 - https://doi.org/10.4310/CMS.2018.v16.n2.a1 SP - 293 EP - 331 ER - TY - JOUR A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-dimensional reconstruction and quantification of dislocation substructures from transmission electron microscopy stereo pairs JF - Ultramicroscopy N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (>300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3% and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. Y1 - 2018 U6 - https://doi.org/10.1016/j.ultramic.2018.08.015 VL - 195 SP - 157 EP - 170 ER - TY - JOUR A1 - Kork, F. A1 - Spies, Claudia A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 ER - TY - JOUR A1 - Obermeier, Patrick A1 - Heim, A. A1 - Biere, Barbara A1 - Hage, E. A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Clinical characteristics and disease severity associated with adenovirus infections in infants and children - discovery of a novel adenovirus, HAdV-D80 JF - Clinical Infectious Diseases Y1 - 2018 ER - TY - JOUR A1 - Alchikh, Maren A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Ma, Xiaolin A1 - Broberg, Eeva K. A1 - Penttinen, P. A1 - Reiche, J. A1 - Biere, Barbara A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection JF - Clinical Microbiology and Infection Y1 - 2018 U6 - https://doi.org/10.1016/j.cmi.2018.05.023 IS - 06/18 SP - 1 EP - 1 ER - TY - JOUR A1 - Mireles, Victor A1 - Conrad, Tim T1 - Reusable building blocks in biological systems JF - Journal of the Royal Society Interface N2 - One of the most widely recognized features of biological systems is their modularity. The modules that constitute biological systems are said to be redeployed and combined across several conditions, thus acting as building blocks. In this work, we analyse to what extent are these building blocks reusable as compared with those found in randomized versions of a system. We develop a notion of decompositions of systems into phenotypic building blocks, which allows them to overlap while maximizing the number of times a building block is reused across several conditions. Different biological systems present building blocks whose reusability ranges from single use (e.g. condition specific) to constitutive, although their average reusability is not always higher than random equivalents of the system. These decompositions reveal a distinct distribution of building block sizes in real biological systems. This distribution stems, in part, from the peculiar usage pattern of the elements of biological systems, and constitutes a new angle to study the evolution of modularity. Y1 - 2018 U6 - https://doi.org/10.1098/rsif.2018.0595 VL - 15 IS - 149 SP - 1 EP - 10 ER - TY - JOUR A1 - Ma, Xiaolin A1 - Conrad, Tim A1 - Alchikh, Maren A1 - Reiche, J. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review JF - Medical Virology N2 - Studies have shown that the predictive value of “clinical diagnoses” of influenza and other respiratory viral infections is low, especially in children. In routine care, pediatricians often resort to clinical diagnoses, even in the absence of robust evidence‐based criteria. We used a dual approach to identify clinical characteristics that may help to differentiate infections with common pathogens including influenza, respiratory syncytial virus, adenovirus, metapneumovirus, rhinovirus, bocavirus‐1, coronaviruses, or parainfluenza virus: (a) systematic review and meta‐analysis of 47 clinical studies published in Medline (June 1996 to March 2017, PROSPERO registration number: CRD42017059557) comprising 49 858 individuals and (b) data‐driven analysis of an inception cohort of 6073 children with ILI (aged 0‐18 years, 56% male, December 2009 to March 2015) examined at the point of care in addition to blinded PCR testing. We determined pooled odds ratios for the literature analysis and compared these to odds ratios based on the clinical cohort dataset. This combined analysis suggested significant associations between influenza and fever or headache, as well as between respiratory syncytial virus infection and cough, dyspnea, and wheezing. Similarly, literature and cohort data agreed on significant associations between HMPV infection and cough, as well as adenovirus infection and fever. Importantly, none of the abovementioned features were unique to any particular pathogen but were also observed in association with other respiratory viruses. In summary, our “real‐world” dataset confirmed published literature trends, but no individual feature allows any particular type of viral infection to be ruled in or ruled out. For the time being, laboratory confirmation remains essential. More research is needed to develop scientifically validated decision models to inform best practice guidelines and targeted diagnostic algorithms. Y1 - 2018 U6 - https://doi.org/10.1002/rmv.1997 VL - 28 IS - 5 SP - 1 EP - 12 ER - TY - JOUR A1 - Hoffmann, Rene A1 - Lemanis, Robert A1 - Wulff, Lena A1 - Zachow, Stefan A1 - Lukeneder, Alexander A1 - Klug, Christian A1 - Keupp, Helmut T1 - Traumatic events in the life of the deep-sea cephalopod mollusc, the coleoid Spirula spirula JF - ScienceDirect: Deep Sea Research Part I - Oceanographic Research N2 - Here, we report on different types of shell pathologies of the enigmatic deep-sea (mesopelagic) cephalopod Spirula spirula. For the first time, we apply non-invasive imaging methods to: document trauma-induced changes in shell shapes, reconstruct the different causes and effects of these pathologies, unravel the etiology, and attempt to quantify the efficiency of the buoyancy apparatus. We have analysed 2D and 3D shell parameters from eleven shells collected as beach findings from the Canary Islands (Gran Canaria and Fuerteventura), West-Australia, and the Maldives. All shells were scanned with a nanotom-m computer tomograph. Seven shells were likely injured by predator attacks: fishes, cephalopods or crustaceans, one specimen was infested by an endoparasite (potentially Digenea) and one shell shows signs of inflammation and one shell shows large fluctuations of chamber volumes without any signs of pathology. These fluctuations are potential indicators of a stressed environment. Pathological shells represent the most deviant morphologies of a single species and can therefore be regarded as morphological end-members. The changes in the shell volume / chamber volume ratio were assessed in order to evaluate the functional tolerance of the buoyancy apparatus showing that these had little effect. Y1 - 2018 U6 - https://doi.org/10.1016/j.dsr.2018.10.007 VL - 142 IS - 12 SP - 127 EP - 144 ER - TY - CHAP A1 - Knötel, David A1 - Becker, Carola A1 - Scholtz, Gerhard A1 - Baum, Daniel T1 - Global and Local Mesh Morphing for Complex Biological Objects from microCT Data T2 - Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) N2 - We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations. Y1 - 2018 U6 - https://doi.org/10.2312/vcbm.20181243 SP - 179 EP - 183 CY - Granada, Spain ER - TY - GEN A1 - Knötel, David A1 - Becker, Carola A1 - Scholtz, Gerhard A1 - Baum, Daniel T1 - Global and Local Mesh Morphing for Complex Biological Objects from microCT Data N2 - We show how biologically coherent mesh models of animals can be created from μCT data to generate artificial yet naturally looking intermediate objects. The whole pipeline of processing algorithms is presented, starting from generating topologically equivalent surface meshes, followed by solving the correspondence problem, and, finally, creating a surface morphing. In this pipeline, we address all the challenges that are due to dealing with complex biological, non-isometric objects. For biological objects it is often particularly important to obtain deformations that look as realistic as possible. In addition, spatially non-uniform shape morphings that only change one part of the surface and keep the rest as stable as possible are of interest for evolutionary studies, since functional modules often change independently from one another. We use Poisson interpolation for this purpose and show that it is well suited to generate both global and local shape deformations. T3 - ZIB-Report - 18-53 KW - Mesh interpolation KW - Geometry processing KW - microCT Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70618 SN - 1438-0064 ER - TY - CHAP A1 - Dennstedt, Anne A1 - Gaslain, Fabrice A1 - Bartsch, Marion A1 - Guipont, Vincent A1 - Maurel, Vincent T1 - Crack Morphology in a Columnar Thermal Barrier Coating System N2 - Ceramic layers are used as thermal barrier coatings (TBCs) on metallic substrates. During thermal transients, the thermal expansion mismatch between coating and substrate drives failure of the TBC mainly by interfacial cracking. Laser Shock Adhesion Test (LASAT) provides stresses at the ceramic/metal interface enabling controlled interfacial cracking. For achieving a clear understanding of the influence of local morphology on interfacial toughness, this study aims at characterizing the 3D morphology of a crack at the interface between metal and an EB-PVD TBC having a columnar structure. Cracks were produced by LASAT and documented further in SE and BSE image stacks collected simultaneously during subsequent slice and view operations using a focus ion beam (FIB) and a scanning electron microscope (FIB slice & view). The segmented 3D data gives clear understanding of the columnar structure of the ceramic and of the interaction between the crack and the TBC microstructure. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69385 ER - TY - CHAP A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Coconu, Liviu A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - An 1834 mediterranean garden in Berlin – engaged from 2004, 2018, 2032, and 2202 T2 - PerDis ’18 – 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - In 2004, a team of researchers realized a semi-immersive interactive gallery installation, visualizing an 1834 Mediterranean garden, introduced as “italienisches Kunststück” (Italian legerdemain) by Peter Joseph Lenné. The park was originally realized on the grounds of Schloss Sanssouci in Potsdam, Germany. The installation centered on highly detailed renderings of hundreds of plants projected upon a panoramic display. Interactivity was expressed with a tangible interface which (while presently dated) we believe remains without near-precedent then or since. We present the installation (experienced by roughly 20,000 visitors), focusing on the interaction aspects. We introduce new book and table/door-format mockups. Drawing upon a heuristic of the scientist-philosopher Freeman Dyson, we consider grounded future prospect variations in the contexts of 2018, 2032, and 2202. We see this exercise as prospectively generalizing to a variety of similar and widely diverse application domains. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3205894 SP - no. 12 PB - ACM CY - New York, NY, USA ER - TY - CHAP A1 - Coconu, Liviu A1 - Ullmer, Brygg A1 - Paar, Philip A1 - Liu, Jing A1 - Konkel, Miriam A1 - Hege, Hans-Christian T1 - A smartphone-based tangible interaction approach for landscape visualization. T2 - PerDis ’18 Proceedings of the 7th ACM International Symposium on Pervasive Displays, Munich, Germany, June 6-8, 2018 N2 - The use of tangible interfaces for navigation of landscape scenery – for example, lost places re-created in 3D – has been pursued and articulated as a promising, impactful application of interactive visualization. In this demonstration, we present a modern, low-cost implementation of a previously-realized multimodal gallery installation. Our demonstration centers upon the versatile usage of a smartphone for sensing, navigating, and (optionally) displaying element on a physical surface in tandem with a larger, more immersive display. Y1 - 2018 U6 - https://doi.org/10.1145/3205873.3210707 SP - no. 23 PB - ACM CY - New York, NY, USA ER - TY - GEN A1 - Agudo Jácome, Leonardo A1 - Hege, Hans-Christian A1 - Paetsch, Olaf A1 - Pöthkow, Kai T1 - Three-Dimensional Reconstruction and Quantification of Dislocation Substructures from Transmission Electron Microscopy Stereo-Pairs N2 - A great amount of material properties is strongly influenced by dislocations, the carriers of plastic deformation. It is therefore paramount to have appropriate tools to quantify dislocation substructures with regard to their features, e.g., dislocation density, Burgers vectors or line direction. While the transmission electron microscope (TEM) has been the most widely-used equipment implemented to investigate dislocations, it usually is limited to the two-dimensional (2D) observation of three-dimensional (3D) structures. We reconstruct, visualize and quantify 3D dislocation substructure models from only two TEM images (stereo-pairs) and assess the results. The reconstruction is based on the manual interactive tracing of filiform objects on both images of the stereo-pair. The reconstruction and quantification method are demonstrated on dark field (DF) scanning (S)TEM micrographs of dislocation substructures imaged under diffraction contrast conditions. For this purpose, thick regions (> 300 nm) of TEM foils are analyzed, which are extracted from a Ni-base superalloy single crystal after high temperature creep deformation. It is shown how the method allows 3D quantification from stereo-pairs in a wide range of tilt conditions, achieving line length and orientation uncertainties of 3 % and 7°, respectively. Parameters that affect the quality of such reconstructions are discussed. T3 - ZIB-Report - 18-50 KW - dislocation, diffraction contrast, scanning transmission electron microscopy, stereoscopy, visualization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70339 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 -