TY - CHAP A1 - Hege, Hans-Christian A1 - Stüben, Hinnerk T1 - Vectorization and Parallelization of Irregular Problems via Graph Coloring T2 - Proc. of the ACM Int. Conf. on Supercomputing Y1 - 1991 U6 - https://doi.org/10.1145/109025.109042 SP - 47 EP - 56 CY - Cologne ER - TY - THES A1 - Lange, Martin T1 - Shadow Volumes für dynamische Dreiecksnetze auf CPU und GPU Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/Lange-MA_2012.pdf ER - TY - THES A1 - Tenbusch, Tobias T1 - Rendering von Partikeleffekten in einem Deferred Renderer Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/Tenbusch-MA_2012.pdf ER - TY - THES A1 - Papazov, Chavdar T1 - Morphing zwischen triangulierten Nicht-Mannigfaltigkeiten unter Berücksichtigung topologischer Änderungen Y1 - 2007 ER - TY - THES A1 - Zilske, Michael T1 - Adaptive remeshing of non-manifold triangulations T2 - Adaptives Remeshing von nicht-mannigfaltigen Dreicksnetzen Y1 - 2007 ER - TY - THES A1 - Schudoma, Christian T1 - A Fragment Based Approach to RNA Threading Y1 - 2006 ER - TY - THES A1 - Beckmann, Philipp T1 - Consistent Cell-Decomposition of Homeomorphic Simplicial Surfaces Y1 - 2006 ER - TY - THES A1 - Clasen, Malte T1 - Beleuchtung von Landschaften in interaktiver Darstellung Y1 - 2005 ER - TY - THES A1 - Zachow, Stefan T1 - Computer assisted osteotomy planning in cranio-maxillofacial surgery under consideration of facial soft tissue changes T2 - Computergestützte Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung Y1 - 2005 UR - www.dr.hut-verlag.de/titelMedizininformatik.html ER - TY - GEN A1 - Wenckebach, Thomas T1 - Das Korrespondenzproblem für Statistische 3D-Formmodelle in biomedizinischen Anwendungen Y1 - 2004 ER - TY - THES A1 - Wenckebach, Thomas T1 - Volumetrische Registrierung zur medizinischen Bildanalyse Y1 - 2004 ER - TY - THES A1 - Schudoma, Christian T1 - Application of a Combined Sequence and Structure Alignment for RNA 3D Modeling Y1 - 2004 ER - TY - THES A1 - Baumeister, Timm T1 - Modellierung der freien Solvatisierungsenthalpie und Anwendung als Scoringfunktion Y1 - 2004 ER - TY - THES A1 - Benger, Werner T1 - Visualization of General Relativistic Tensor Fields via a Fiber Bundle Data Model Y1 - 2004 N1 - ISBN 3-86541-108-8 ER - TY - THES A1 - Adolfson, Jon A1 - Helgesson, Johan T1 - Generation of Smooth Non-Manifold Surfaces from Segmented Image Data Y1 - 2004 ER - TY - THES A1 - (née Zöckler), Malte T1 - Efficient Visualization and Reconstruction of 3D Geometric from Neuro-Biological Confocal Microscope Scans Y1 - 2003 ER - TY - THES A1 - Trepczynski, Adam T1 - Schnittmodellierung auf triangulierten Polygonoberflächen Y1 - 2002 ER - TY - THES A1 - Sander, Oliver T1 - Constructing Boundary and Interface Parametrizations for Finite Element Solvers Y1 - 2001 ER - TY - THES A1 - Zaharescu, Valentin-Florian T1 - Semi-automatic Volume Slices Alignment for 3D Reconstruction and Analysis Y1 - 2001 ER - TY - THES A1 - Coconu, Liviu T1 - Semi-automatic Segmentation of Bronchoscopic Images Y1 - 2001 ER - TY - THES A1 - Westerhoff, Natascha T1 - Geometrische Methoden zur 3D-Segmentierung Y1 - 1999 ER - TY - THES A1 - Preis, Philipp T1 - Sichtbarkeitsorientiertes Picking in Direct Volume Renderings mit Beleuchtungsmodellen Y1 - 2012 UR - http://www.zib.de/visual/publications/thesis/preis_MA.pdf ER - TY - THES A1 - Malinowski, Jana T1 - Ein kontinuierliches Optimierungsverfahren für die Segmentierung medizinischer Bilddaten mit Hilfe von Formmodellen Y1 - 2012 ER - TY - THES A1 - Nguyen, The Duy T1 - Automatic segmentation for dental operation planning Y1 - 2012 ER - TY - THES A1 - Orgiu, Sara T1 - Automatic liver segmentation in contrast enhanced CT data using 3D free-form deformation based on optimal graph searching Y1 - 2012 ER - TY - THES A1 - Ruben, Karl T1 - Kugelpackungen in arbiträr geformten Volumina T1 - Sphere Packings in Arbitrarily Bounded Volumes Y1 - 2012 ER - TY - THES A1 - Surma, Alexander T1 - Automatisierte Registrierung von 2D-Daten in 3-dimensionalen Volumen mit Hilfe von ZIBAmira T1 - Automated Registration of 2D Data in 3-dimensional Volumina using ZIBAmira Y1 - 2012 ER - TY - THES A1 - Ehlke, Moritz T1 - Simulating X-ray images from deformable shape and intensity models on the GPU Y1 - 2012 ER - TY - THES A1 - Kahnt, Max T1 - Generation of constrained high-quality multi-material tetrahedral meshes Y1 - 2012 ER - TY - THES A1 - Kasten, Jens T1 - Lagrangian feature extraction in two-dimensional unsteady flows Y1 - 2012 ER - TY - THES A1 - Reininghaus, Jan T1 - Computational discrete Morse theory Y1 - 2012 ER - TY - THES A1 - Winkler, Charlotte T1 - Graph-Cut Segmentation for 3D Single-Plane Illumination Microscopy Images Y1 - 2009 ER - TY - THES A1 - van den Bruck, Nils T1 - Techniken zur Artefaktreduktion für GPU-basiertes Ray Casting Y1 - 2009 ER - TY - THES A1 - Gensel, Maria T1 - Visualisierungsmethoden zur Verdeutlichung der räumlichen Beziehungen zwischen linien- und flächenartigen Strukturen am Beispiel neurobiologischer Daten Y1 - 2009 ER - TY - THES A1 - Sahner, Jan T1 - Extraction of Vortex Structures in 3D Flow Fields Y1 - 2009 ER - TY - THES A1 - Lienhard, Matthias T1 - Aufbau und Analyse eines statistischen Formmodells des Gehirns der Honigbiene Apis Mellifera Y1 - 2008 ER - TY - THES A1 - Singer, Jochen T1 - Entwicklung einer Anpassungsstrategie zur Autosegmentierung des Gehirns der Honigbiene Apis mellifera mittels eines statistischen Formmodells Y1 - 2008 ER - TY - THES A1 - Wade, Moritz T1 - Automatic Textbook-Like Layout of Biological Networks Y1 - 2008 ER - TY - THES A1 - Weber, Britta T1 - Merkmalskurven auf triangulierten Oberflächen Y1 - 2008 ER - TY - THES A1 - Weinkauf, Tino T1 - Extraction of Topological Structures in 2D and 3D Vector Fields Y1 - 2008 ER - TY - THES A1 - Schmidt-Ehrenberg, Johannes T1 - Analysis and Visualization of Molecular Conformations Y1 - 2008 ER - TY - THES A1 - Kettlitz, Nino T1 - Anisotropes Sampling in der Tensorfeldvisualisierung Y1 - 2011 ER - TY - THES A1 - Retzlaff, Michelle T1 - Brushing and Linking Methods by the Example of Tensor Visualization Y1 - 2011 ER - TY - THES A1 - Seidel, Paul T1 - Interaktive Visualisierung und Filterung großer Volumendaten mittels Volumenrendering Y1 - 2011 ER - TY - THES A1 - Schuberth, Sebastian T1 - High-Performance Tomographic Reconstruction using OpenCL Y1 - 2011 ER - TY - THES A1 - Wittmers, Antonia T1 - Ein Werkzeug zur Erzeugung konsistenter Netze auf triangulierten Oberflächen Y1 - 2011 ER - TY - THES A1 - Zobel, Valentin T1 - Spectral Analysis of the Hodge Laplacian on Discrete Manifolds Y1 - 2010 ER - TY - THES A1 - Lindow, Norbert T1 - Dynamische Moleküloberflächen T1 - Dynamic Molecular Surfaces Y1 - 2010 ER - TY - THES A1 - Nietfeld, Jan T1 - Oberflächenrekonstruktion aus nicht-parallelen Konturdaten Y1 - 2010 ER - TY - THES A1 - Löwen, Christian T1 - Parallele Berechnung kombinatorischer Vektorfelder mit CUDA Y1 - 2009 ER - TY - THES A1 - Brenner, Thomas T1 - Volume Rendering - Ein Projektionsansatz für den Cray T3D Y1 - 1996 ER - TY - THES A1 - Battke, Henrik T1 - Entwicklung textur-basierter Verfahren zur Vektorfeldvisualisierung Y1 - 1996 ER - TY - THES A1 - Anders, Thomas T1 - Effiziente Algorihmen zur Isoflächengenerierung aus Volumendaten Y1 - 1996 ER - TY - THES A1 - Höllerer, Tobias T1 - Volume Rendering auf irregulären Gittern - Theorie und Implementierung Y1 - 1995 ER - TY - BOOK ED - Hege, Hans-Christian T1 - Visualization and Mathematics T3 - Book Series Y1 - 2010 PB - Springer-Verlag ER - TY - BOOK ED - Hege, Hans-Christian T1 - VideoMath T3 - Video Series Y1 - 2010 PB - Springer-Verlag ER - TY - GEN ED - Hege, Hans-Christian ED - Machiraju, Raghu ED - Laidlaw, David T1 - Volume Graphics and Point-Based Graphics Y1 - 2010 N1 - Collection of selected and extended papers of international IEEE/EG Symposia Volume Graphics and Point-Based Graphics 2008, Special Section in IEEE Trans. Vis. Comput. Graph., 16:4, pp. 529-608, 2010 ER - TY - BOOK ED - Hege, Hans-Christian ED - Hotz, Ingrid ED - Munzner, Tamara T1 - EuroVis 2009 Y1 - 2009 PB - Blackwell Publishing ER - TY - BOOK ED - Scheuermann, Gerik ED - Hege, Hans-Christian ED - Polthier, Konrad T1 - Topology-based Methods in Visualization II T3 - Mathematics and Visualization Y1 - 2009 SN - 978-3-540-88605-1 PB - Springer ER - TY - BOOK ED - Hege, Hans-Christian ED - Laidlaw, David ED - Pajarola, Renato ED - Staadt, Oliver T1 - Volume and Point-Based Graphics 2008 Y1 - 2008 SN - 978-3-905674-12-5 PB - Eurographics Association ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric intensity models for accurate simulation of X-ray images N2 - We present an efficient GPU-based method to generate virtual X-ray images from tetrahedral meshes which are associated with attenuation values. In addition, a novel approach is proposed that performs the model deformation on the GPU. The tetrahedral grids are derived from volumetric statistical shape and intensity models (SSIMs) and describe anatomical structures. Our research targets at reconstructing 3D anatomical shapes by comparing virtual X-ray images generated using our novel approach with clinical data while varying the shape and density of the SSIM in an optimization process. We assume that a deformed SSIM adequately represents an anatomy of interest when the similarity between the virtual and the clinical X-ray image is maximized. The OpenGL implementation presented here generates accurate (virtual) X-ray images at interactive rates, thus qualifying it for its use in the reconstruction process. T3 - ZIB-Report - 12-40 KW - Digitally Reconstructed Radiograph (DRR), Anatomy Reconstruction, Statistical Shape and Intensity Model (SSIM), GPU acceleration Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16580 SN - 1438-0064 ER - TY - THES A1 - Kratz, Andrea T1 - Three-Dimensional Second-Order Tensor Fields: Exploratory Visualization and Anisotropic Sampling N2 - Tensors provide a powerful mathematical language to describe physical phenomena. Consequently, they have a long tradition in physics and appear in various application areas, either as intermediate product or as output of simulations or measurements. The potential of tensors to describe complex anisotropic behavior, however, concurrently complicates their interpretation. The central research question of this thesis is how three-dimensional tensor fields of second order are visualized effectively so that, as a long term goal, their interpretation becomes easier. The focus of this thesis lies on the class of indefinite tensors. The methods that are proposed in this thesis fall into two main categories: (1.) the interactive exploration of the three-dimensional tensor data, and (2.) the geometric reduction of the data to two-dimensional planes or triangulated surfaces. In both cases, possible visualization approaches are presented. For interactive exploration of the data, we propose to combine diagram views with three-dimensional hybrid visualizations. We show that this facilitates familiarizing with the data and leads to exciting analytic queries. If a geometric data reduction is possible, we focus on glyph- and texture-based methods. In this context, the thesis is concerned with methods to improve their quality. Therefore, we propose two algorithms for the efficient creation of anisotropic sample distributions. Moreover, we present a novel visualization method that works on planar slices as well as on triangulated surfaces. The basic idea of this method is to use anisotropic sample distributions for the efficient computation of anisotropic Voronoi cells, which then are used as base elements for texture mapping. Hence, the usage of textures to encode the tensor’s various degrees of freedom becomes possible. We evaluate our methods for the interactive exploration on stress tensor fields from structure simulations. To show the ffectiveness of novel visualization methods, various datasets are presented. KW - visualization KW - tensors of second order KW - exploratory visualization KW - anisotropic sampling of tensor fields Y1 - 2013 UR - http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094629 ER - TY - GEN A1 - Wiebel, Alexander A1 - Müller, Cornelius A1 - Garth, Christoph A1 - Knösche, Thomas ED - Westin, Carl-Frederic ED - Burgeth, Bernhard ED - Vilanova, Anna T1 - A System for Combined Visualization of EEG and Diffusion Tensor Imaging Tractography Data T2 - Visualization and Processing of Tensors and Higher-Order Descriptors for Multi-field Data Y1 - 2014 SP - 325 EP - 337 PB - Springer ER - TY - GEN A1 - Ramm, Heiko A1 - Morillo Victoria, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Visual Support for Positioning Hearing Implants N2 - We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit. T3 - ZIB-Report - 13-53 KW - bone anchored hearing implant KW - surgery planning KW - segmentation KW - visualization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42495 SN - 1438-0064 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 - Kuhn, Alexander A1 - Engelke, Wito A1 - Rössl, Christian A1 - Hadwiger, Markus A1 - Theisel, Holger T1 - Time Line Cell Tracking for the Approximation of Lagrangian Coherent Structures with Subgrid Accuracy N2 - Lagrangian Coherent Structures (LCS) have become a widespread and powerful method to describe dynamic motion patterns in time-dependent flow fields. The standard way to extract LCS is to compute height ridges in the Finite Time Lyapunov Exponent (FTLE) field. In this work, we present an alternative method to approximate Lagrangian features for 2D unsteady flow fields that achieves subgrid accuracy without additional particle sampling. We obtain this by a geometric reconstruction of the flow map using additional material constraints for the available samples. In comparison to the standard method, this allows for a more accurate global approximation of LCS on sparse grids and for long integration intervals. The proposed algorithm works directly on a set of given particle trajectories and without additional flow map derivatives. We demonstrate its application for a set of computational fluid dynamic examples, as well as trajectories acquired by Lagrangian methods, and discuss its benefits and limitations. T3 - ZIB-Report - 13-71 KW - time-dependent vector fields KW - flow field visualization KW - Lagrangian Coherent Structures (LCS) KW - finite-time Lyapunov exponents (FTLE) KW - time lines Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43050 SN - 1438-0064 ER - TY - GEN A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology N2 - Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator. T3 - ZIB-Report - 13-75 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43157 SN - 1438-0064 ER - TY - JOUR A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology JF - NeuroInformatics Y1 - 2014 U6 - https://doi.org/10.1007/s12021-013-9213-2 VL - 12 IS - 2 SP - 325 EP - 339 PB - Springer US ER - TY - GEN A1 - Egger, Robert A1 - Dercksen, Vincent J. A1 - Kock, Christiaan P.J. A1 - Oberlaender, Marcel ED - Cuntz, Hermann ED - Remme, Michiel W.H. ED - Torben-Nielsen, Benjamin T1 - Reverse Engineering the 3D Structure and Sensory-Evoked Signal Flow of Rat Vibrissal Cortex T2 - The Computing Dendrite Y1 - 2014 U6 - https://doi.org/10.1007/978-1-4614-8094-5_8 VL - 11 SP - 127 EP - 145 PB - Springer CY - New York ER - TY - CHAP A1 - Hlawitschka, Mario A1 - Hotz, Ingrid A1 - Kratz, Andrea A1 - Marai, G. Elisabeta A1 - Moreno, Rodrigo A1 - Scheuermann, Gerik A1 - Stommel, Markus A1 - Wiebel, Alexander A1 - Zhang, Eugene ED - Westin, Carl-Frederic ED - Burgeth, Bernhard ED - Vilanova, Anna T1 - Top Challenges in the Visualization of Engineering Tensor Fields T2 - Visualization and Processing of Tensors and Higher-Order Descriptors for Multi-Field Data Y1 - 2014 SP - 3 EP - 15 PB - Springer ER - TY - JOUR A1 - Hoch, Hannelore A1 - Wessel, Andreas A1 - Asche, Manfred A1 - Baum, Daniel A1 - Beckmann, Felix A1 - Bräunig, Peter A1 - Ehrig, Karsten A1 - Mühlethaler, Roland A1 - Riesemeier, Heinrich A1 - Staude, Andreas A1 - Stelbrink, Björn A1 - Wachmann, Ekkehard A1 - Weintraub, Phyllis A1 - Wipfler, Benjamin A1 - Wolff, Carsten A1 - Zilch, Mathias T1 - Non-Sexual Abdominal Appendages in Adult Insects Challenge a 300 Million Year Old Bauplan JF - Current Biology Y1 - 2014 U6 - https://doi.org/10.1016/j.cub.2013.11.040 VL - 24 IS - 1 SP - R16 EP - R17 ER - TY - JOUR A1 - Conrad, Tim A1 - Genzel, Martin A1 - Cvetkovic, Nada A1 - Wulkow, Niklas A1 - Vybiral, Jan A1 - Kutyniok, Gitta A1 - Schütte, Christof T1 - Sparse Proteomics Analysis – a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data JF - BMC Bioinformatics N2 - Motivation: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested how MS spectra dier between patients of different classes, for example spectra from healthy patients vs. spectra from patients having a particular disease. Machine learning algorithms are needed to (a) identify these discriminating features and (b) classify unknown spectra based on this feature set. Since the acquired data is usually noisy, the algorithms should be robust to noise and outliers, and the identied feature set should be as small as possible. Results: We present a new algorithm, Sparse Proteomics Analysis (SPA), based on the theory of Compressed Sensing that allows to identify a minimal discriminating set of features from mass spectrometry data-sets. We show how our method performs on artificial and real-world data-sets. Y1 - 2017 U6 - https://doi.org/10.1186/s12859-017-1565-4 VL - 18 IS - 160 SP - 1 EP - 20 ER - TY - JOUR A1 - Seeber, L. A1 - Conrad, Tim A1 - Hoppe, Christian A1 - Obermeier, Patrick A1 - Chen, X. A1 - Karsch, K. A1 - Muehlhans, S. A1 - Tief, Franziska A1 - Boettcher, Sindy A1 - Diedrich, S. A1 - Schweiger, Brunhilde A1 - Rath, Barbara T1 - Educating parents about the vaccination status of their children: A user-centered mobile application JF - Preventive Medicine Reports N2 - Parents are often uncertain about the vaccination status of their children. In times of vaccine hesitancy, vaccination programs could benefit from active patient participation. The Vaccination App (VAccApp) was developed by the Vienna Vaccine Safety Initiative, enabling parents to learn about the vaccination status of their children, including 25 different routine, special indication and travel vaccines listed in the WHO Immunization Certificate of Vaccination (WHO-ICV). Between 2012 and 2014, the VAccApp was validated in a hospital-based quality management program in Berlin, Germany, in collaboration with the Robert Koch Institute. Parents of 178 children were asked to transfer the immunization data of their children from the WHO-ICV into the VAccApp. The respective WHO-ICV was photocopied for independent, professional data entry (gold standard). Demonstrating the status quo in vaccine information reporting, a Recall Group of 278 parents underwent structured interviews for verbal immunization histories, without the respective WHO-ICV. Only 9% of the Recall Group were able to provide a complete vaccination status; on average 39% of the questions were answered correctly. Using the WHO-ICV with the help of the VAccApp resulted in 62% of parents providing a complete vaccination status; on average 95% of the questions were answered correctly. After using the VAccApp, parents were more likely to remember key aspects of the vaccination history. User-friendly mobile applications empower parents to take a closer look at the vaccination record, thereby taking an active role in providing accurate vaccination histories. Parents may become motivated to ask informed questions and to keep vaccinations up-to-date. Y1 - 2017 U6 - https://doi.org/10.1016/j.pmedr.2017.01.002 VL - 5 SP - 241 EP - 250 ER - TY - GEN A1 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. T3 - ZIB-Report - 19-13 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72699 SN - 1438-0064 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging (MRI) that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs).The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures.The shape models and neural networks employed are trained using data from the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets from the SKI10 challenge.For the first time, an accuracy equivalent to the inter-observer variability of human readers is achieved in this challenge.Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We make the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation.In conclusion, combining localized classification via CNNs with statistical anatomical knowledge via SSMs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. T3 - ZIB-Report - 19-06 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72704 SN - 1438-0064 N1 - Innovation Excellence Award 2020 ER - TY - GEN A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures N2 - The analysis and visualization of nucleic acids (RNA and DNA) play an increasingly important role due to the growing number of known 3-dimensional structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. For the first time, we present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization. T3 - ZIB-Report - 18-33 KW - ribonucleic acids KW - DNA KW - RNA KW - secondary & tertiary structures KW - interactive rendering KW - ray casting KW - brushing & linking Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69704 SN - 1438-0064 ER - TY - JOUR A1 - Lindow, Norbert A1 - Baum, Daniel A1 - Leborgne, Morgan A1 - Hege, Hans-Christian T1 - Interactive Visualization of RNA and DNA Structures JF - IEEE Transactions on Visualization and Computer Graphics N2 - The analysis and visualization of nucleic acids (RNA and DNA) is playing an increasingly important role due to their fundamental importance for all forms of life and the growing number of known 3D structures of such molecules. The great complexity of these structures, in particular, those of RNA, demands interactive visualization to get deeper insights into the relationship between the 2D secondary structure motifs and their 3D tertiary structures. Over the last decades, a lot of research in molecular visualization has focused on the visual exploration of protein structures while nucleic acids have only been marginally addressed. In contrast to proteins, which are composed of amino acids, the ingredients of nucleic acids are nucleotides. They form structuring patterns that differ from those of proteins and, hence, also require different visualization and exploration techniques. In order to support interactive exploration of nucleic acids, the computation of secondary structure motifs as well as their visualization in 2D and 3D must be fast. Therefore, in this paper, we focus on the performance of both the computation and visualization of nucleic acid structure. We present a ray casting-based visualization of RNA and DNA secondary and tertiary structures, which enables for the first time real-time visualization of even large molecular dynamics trajectories. Furthermore, we provide a detailed description of all important aspects to visualize nucleic acid secondary and tertiary structures. With this, we close an important gap in molecular visualization. Y1 - 2019 U6 - https://doi.org/10.1109/TVCG.2018.2864507 VL - 25 IS - 1 SP - 967 EP - 976 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 - 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 - 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 - GEN A1 - Sakurai, Daisuke A1 - Ono, Kenji A1 - Carr, Hamish A1 - Nonaka, Jorji A1 - Kawanabe, Tomohiro ED - Carr, Hamish ED - Fujishiro, Issei ED - Sadlo, Filip ED - Takahashi, Shigeo T1 - Flexible Fiber Surfaces: A Reeb-Free Approach T2 - Topological Methods in Data Analysis and Visualization V N2 - The fiber surface generalizes the popular isosurface to multi-fields, so that pre-images can be visualized as surfaces. As with the isosurface, however, the fiber surface suffers from visual occlusion. We propose to avoid such occlusion by restricting the components to only the relevant ones with a new component-wise flexing algorithm. The approach, flexible fiber surface, generalizes the manipulation idea found in the flexible isosurface for the fiber surface. The flexible isosurface in the original form, however, relies on the contour tree. For the fiber surface, this corresponds to the Reeb space, which is challenging for both the computation and user interaction. We thus take a Reeb-free approach, in which one does not compute the Reeb space. Under this constraint, we generalize a few selected interactions in the flexible isosurface and discuss the implication of the restriction. Y1 - 2019 PB - Springer ER - TY - GEN A1 - Sakurai, Daisuke A1 - Ono, Kenji A1 - Carr, Hamish A1 - Nonaka, Jorji A1 - Kawanabe, Tomohiro T1 - Flexible Fiber Surfaces: A Reeb-Free Approach N2 - The fiber surface generalizes the popular isosurface to multi-fields, so that pre-images can be visualized as surfaces. As with the isosurface, however, the fiber surface suffers from visual occlusion. We propose to avoid such occlusion by restricting the components to only the relevant ones with a new component-wise flexing algorithm. The approach, flexible fiber surface, generalizes the manipulation idea found in the flexible isosurface for the fiber surface. The flexible isosurface in the original form, however, relies on the contour tree. For the fiber surface, this corresponds to the Reeb space, which is challenging for both the computation and user interaction. We thus take a Reeb-free approach, in which one does not compute the Reeb space. Under this constraint, we generalize a few selected interactions in the flexible isosurface and discuss the implication of the restriction. T3 - ZIB-Report - 19-09 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72599 SN - 1438-0064 ER - TY - GEN A1 - Sakurai, Daisuke A1 - Hege, Hans-Christian A1 - Kuhn, Alexander A1 - Rust, Henning A1 - Kern, Bastian A1 - Breitkopf, Tom-Lukas T1 - An Application-Oriented Framework for Feature Tracking in Atmospheric Sciences N2 - In atmospheric sciences, sizes of data sets grow continuously due to increasing resolutions. A central task is the comparison of spatiotemporal fields, to assess different simulations and to compare simulations with observations. A significant information reduction is possible by focusing on geometric-topological features of the fields or on derived meteorological objects. Due to the huge size of the data sets, spatial features have to be extracted in time slices and traced over time. Fields with chaotic component, i.e. without 1:1 spatiotemporal correspondences, can be compared by looking upon statistics of feature properties. Feature extraction, however, requires a clear mathematical definition of the features – which many meteorological objects still lack. Traditionally, object extractions are often heuristic, defined only by implemented algorithms, and thus are not comparable. This work surveys our framework designed for efficient development of feature tracking methods and for testing new feature definitions. The framework supports well-established visualization practices and is being used by atmospheric researchers to diagnose and compare data. T3 - ZIB-Report - 17-50 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72617 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 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan ED - Rea, Paul M. T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy T2 - Biomedical Visualisation N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. Y1 - 2019 SN - 978-3-030-19384-3 SN - 978-3-030-19385-0 U6 - https://doi.org/10.1007/978-3-030-19385-0_5 VL - 3 IS - 1156 SP - 67 EP - 84 PB - Springer Nature Switzerland AG ET - 1 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Schmidt, Nora Laura A1 - Lamecker, Hans A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - The Healthy Nasal Cavity - Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon’s Perspective JF - Facial Plastic Surgery N2 - Functional surgery on the nasal framework requires referential criteria to objectively assess nasal breathing for indication and follow-up. Thismotivated us to generate amean geometry of the nasal cavity based on a statistical shape model. In this study, the authors could demonstrate that the introduced nasal cavity’s mean geometry features characteristics of the inner shape and airflow, which are commonly observed in symptom-free subjects. Therefore, the mean geometry might serve as a reference-like model when one considers qualitative aspects. However, to facilitate quantitative considerations and statistical inference, further research is necessary. Additionally, the authorswere able to obtain details about the importance of the isthmus nasi and the inferior turbinate for the intranasal airstream. KW - statistical shape model KW - nasal cavity KW - nasal breathing KW - nasal airflow KW - isthmus nasi KW - inferior turbinate Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677721 VL - 35 IS - 1 SP - 9 EP - 13 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Goubergrits, Leonid T1 - Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery JF - Facial Plastic Surgery N2 - Successful functional surgery on the nasal framework requires reliable and comprehensive diagnosis. In this regard, the authors introduce a new methodology: Digital Analysis of Nasal Airflow (diANA). It is based on computational fluid dynamics, a statistical shape model of the healthy nasal cavity and rhinologic expertise. diANA necessitates an anonymized tomographic dataset of the paranasal sinuses including the complete nasal cavity and, when available, clinical information. The principle of diANA is to compare the morphology and the respective airflow of an individual nose with those of a reference. This enablesmorphometric aberrations and consecutive flow field anomalies to localize and quantify within a patient’s nasal cavity. Finally, an elaborated expert opinion with instructive visualizations is provided. Using diANA might support surgeons in decision-making, avoiding unnecessary surgery, gaining more precision, and target-orientation for indicated operations. KW - nasal airflow simulation KW - nasal breathing KW - statistical shape model KW - diANA KW - nasal obstruction KW - rhinorespiratory homeostasis Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677720 VL - 35 IS - 1 SP - 1 EP - 8 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 - THES A1 - Prendke, Mona T1 - Comparison of 2D and 3D CNNs for Classification of Knee MRI Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72439 ER - TY - THES A1 - Dill, Sabrina Patricia T1 - Joint Feature Learning and Classification - Deep Learning for Surgical Phase Detection Y1 - 2018 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 - 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 - 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 - CHAP A1 - Jayrannejad, Fahrnaz A1 - Conrad, Tim T1 - Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining T2 - Springer Lecture Notes in Artificial Intelligence N2 - Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set. Y1 - 2017 SP - studi ER - TY - CHAP A1 - Tack, Alexander A1 - Zachow, Stefan T1 - Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative T2 - IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) N2 - Volumetry of cartilage of the knee is needed for knee osteoarthritis (KOA) assessment. It is typically performed manually in a tedious and subjective process. We developed a method for an automated, segmentation-based quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data and cartilage volumetry readings performed by clinical experts for 1378 subjects provided by the Osteoarthritis Initiative. It was shown that 3D CNNs are able to achieve volume measures comparable to the magnitude of variation between expert readings and the real in vivo situation. In the future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as longitudinal analysis of KOA progression. Y1 - 2019 U6 - https://doi.org/10.1109/ISBI.2019.8759201 SP - 40 EP - 43 ER - TY - THES A1 - Herter, Felix T1 - Supervised Classification of Microtubule Ends: An Evaluation of Machine Learning Approaches N2 - Aim of this thesis was to evaluate the performance of three popular machine learning methods – decision trees, support vector machines, and neural networks – on a supervised image classification task from the domain of cell biology. Specifically, the task was to classify microtubule ends in electron tomography images as open or closed. Microtubules are filamentous macromolecules of the cytoskeleton. Distribution of their end types is of interest to cell biologists as it allows to analyze microtubule nucleation sites. Currently classification is done manually by domain experts, which is a difficult task due to the low signal-to-noise ratio and the abundance of microtubules in a single cell. Automating this tedious and error prone task would be beneficial to both efficiency and consistency. Images of microtubule ends were obtained from electron tomography reconstructions of mitotic spindles. As ground truth data for training and testing four independent expert classifications for the same samples from different tomograms were used. Image information around microtubule ends was extracted in various formats for further processing. For all classifiers we considered how the performance varies when different preprocessing techniques (per-feature and per-image standardization) are applied. or decision trees and support vector machines we also evaluated the effect of training on a) imbalanced versus under- and over-sampled data and b) image-based vs feature-based input for specifically designed features. The results show that for decision trees and support vector machines classification on features outperforms classification on images. Both methods give most equalized per-class accuracies when the training data was undersampled and when preprocessed with per-image standardization prior to features extraction. Neural networks gave the best results when no preprocessing was applied. The final decision tree, support vector machine, and neural network obtained accuracies on the test set for (open,closed ) samples of (62%, 72%), (66%, 70%), and (61%, 78%) respectively, when considering all samples where at least one expert assigned a label. Restricting the test set to samples with at least three agreeing expert labels raised these to (78%, 84%), (74%, 92%), and (82%, 88%). It can be observed that many samples misclassified by the algorithms were also difficult to classify for the experts. Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68395 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 - 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 - THES A1 - Gidey, Henok Hagos T1 - Automated Hip Knee Ankle Angle Determination using Convolutional Neural Networks N2 - Advanced osteoarthritis is a leading cause of knee replacement and loss of functionality. Early detection of risk factors plays an important role in the application of preventive measures. One of the risk factors is the leg alignment which influences the speed of knee cartilage degradation. The ’gold standard’ measurement of leg alignment is done by determining the Hip Knee Ankle (HKA) angle from full lower limb radiographs. Convolutional Neural Networks (CNNs) have gained popularity recently in computer vision. In this thesis we developed methods using CNNs to determine HKA angles from full lower limb radiographs. We trained the CNNs using data from the Osteoarthritis Initiative (OAI). We evaluated our method’s performance by evaluating its agreement to experts measurement and its reliability. Our best performing method shows excellent agreement and reliability levels. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71263 ER - TY - JOUR A1 - Ozel, Mehmet Neset A1 - Kulkarni, Abhishek A1 - Hasan, Amr A1 - Brummer, Josephine A1 - Moldenhauer, Marian A1 - Daumann, Ilsa-Maria A1 - Wolfenberg, Heike A1 - Dercksen, Vincent J. A1 - Kiral, Ferdi Ridvan A1 - Weiser, Martin A1 - Prohaska, Steffen A1 - von Kleist, Max A1 - Hiesinger, Peter Robin T1 - Serial synapse formation through filopodial competition for synaptic seeding factors JF - Developmental Cell N2 - Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses. Y1 - 2019 U6 - https://doi.org/10.1016/j.devcel.2019.06.014 VL - 50 IS - 4 SP - 447 EP - 461 ER -