@phdthesis{Fleszar2018,
  author    = {Fleszar, Krzysztof},
  title     = {Network-Design Problems in Graphs and on the Plane},
  edition   = {1. Auflage},
  publisher = {W{\"u}rzburg University Press},
  address   = {W{\"u}rzburg},
  isbn      = {978-3-95826-076-4 (Print)},
  doi       = {10.25972/WUP-978-3-95826-077-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154904},
  school      = {W{\"u}rzburg University Press},
  pages     = {xi, 204},
  year      = {2018},
  abstract  = {A network design problem defines an infinite set whose elements, called instances, describe relationships and network constraints. It asks for an algorithm that, given an instance of this set, designs a network that respects the given constraints and at the same time optimizes some given criterion. In my thesis, I develop algorithms whose solutions are optimum or close to an optimum value within some guaranteed bound. I also examine the computational complexity of these problems. Problems from two vast areas are considered: graphs and the Euclidean plane. In the Maximum Edge Disjoint Paths problem, we are given a graph and a subset of vertex pairs that are called terminal pairs. We are asked for a set of paths where the endpoints of each path form a terminal pair. The constraint is that any two paths share at most one inner vertex. The optimization criterion is to maximize the cardinality of the set. In the hard-capacitated k-Facility Location problem, we are given an integer k and a complete graph where the distances obey a given metric and where each node has two numerical values: a capacity and an opening cost. We are asked for a subset of k nodes, called facilities, and an assignment of all the nodes, called clients, to the facilities. The constraint is that the number of clients assigned to a facility cannot exceed the facility's capacity value. The optimization criterion is to minimize the total cost which consists of the total opening cost of the facilities and the total distance between the clients and the facilities they are assigned to. In the Stabbing problem, we are given a set of axis-aligned rectangles in the plane. We are asked for a set of horizontal line segments such that, for every rectangle, there is a line segment crossing its left and right edge. The optimization criterion is to minimize the total length of the line segments. In the k-Colored Non-Crossing Euclidean Steiner Forest problem, we are given an integer k and a finite set of points in the plane where each point has one of k colors. For every color, we are asked for a drawing that connects all the points of the same color. The constraint is that drawings of different colors are not allowed to cross each other. The optimization criterion is to minimize the total length of the drawings. In the Minimum Rectilinear Polygon for Given Angle Sequence problem, we are given an angle sequence of left (+90°) turns and right (-90°) turns. We are asked for an axis-parallel simple polygon where the angles of the vertices yield the given sequence when walking around the polygon in counter-clockwise manner. The optimization criteria considered are to minimize the perimeter, the area, and the size of the axis-parallel bounding box of the polygon.},
  subject      = {Euklidische Ebene},
  language  = {en}
}
@phdthesis{Wojtkowiak2018,
  author    = {Wojtkowiak, Harald},
  title     = {Planungssystem zur Steigerung der Autonomie von Kleinstsatelliten},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-163569},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Der Betrieb von Satelliten wird sich in Zukunft gravierend {\"a}ndern. Die bisher ausge{\"u}bte konventionelle Vorgehensweise, bei der die Planung der vom Satelliten auszuf{\"u}hrenden Aktivit{\"a}ten sowie die Kontrolle hier{\"u}ber ausschließlich vom Boden aus erfolgen, st{\"o}ßt bei heutigen Anwendungen an ihre Grenzen. Im schlimmsten Fall verhindert dieser Umstand sogar die Erschließung bisher ungenutzter M{\"o}glichkeiten. Der Gewinn eines Satelliten, sei es in Form wissenschaftlicher Daten oder der Vermarktung satellitengest{\"u}tzter Dienste, wird daher nicht optimal ausgesch{\"o}pft. Die Ursache f{\"u}r dieses Problem l{\"a}sst sich im Grunde auf eine ausschlaggebende Tatsache zur{\"u}ckf{\"u}hren: Konventionelle Satelliten k{\"o}nnen ihr Verhalten, d.h. die Folge ihrer T{\"a}tigkeiten, nicht eigenst{\"a}ndig anpassen. Stattdessen erstellt das Bedienpersonal am Boden - vor allem die Operatoren - mit Hilfe von Planungssoftware feste Ablaufpl{\"a}ne, die dann in Form von Kommandosequenzen von den Bodenstationen aus an die jeweiligen Satelliten hochgeladen werden. Dort werden die Befehle lediglich {\"u}berpr{\"u}ft, interpretiert und strikt ausgef{\"u}hrt. Die Abarbeitung erfolgt linear. Situationsbedingte {\"A}nderungen, wie sie vergleichsweise bei der Codeausf{\"u}hrung von Softwareprogrammen durch Kontrollkonstrukte, zum Beispiel Schleifen und Verzweigungen, {\"u}blich sind, sind typischerweise nicht vorgesehen. Der Operator ist daher die einzige Instanz, die das Verhalten des Satelliten mittels Kommandierung, per Upload, beeinflussen kann, und auch nur dann, wenn ein direkter Funkkontakt zwischen Satellit und Bodenstation besteht. Die dadurch m{\"o}glichen Reaktionszeiten des Satelliten liegen bestenfalls bei einigen Sekunden, falls er sich im Wirkungsbereich der Bodenstation befindet. Außerhalb des Kontaktfensters kann sich die Zeitschranke, gegeben durch den Orbit und die aktuelle Position des Satelliten, von einigen Minuten bis hin zu einigen Stunden erstrecken. Die Signallaufzeiten der Funk{\"u}bertragung verl{\"a}ngern die Reaktionszeiten um weitere Sekunden im erdnahen Bereich. Im interplanetaren Raum erstrecken sich die Zeitspannen aufgrund der immensen Entfernungen sogar auf mehrere Minuten. Dadurch bedingt liegt die derzeit technologisch m{\"o}gliche, bodengest{\"u}tzte, Reaktionszeit von Satelliten bestenfalls im Bereich von einigen Sekunden. Diese Einschr{\"a}nkung stellt ein schweres Hindernis f{\"u}r neuartige Satellitenmissionen, bei denen insbesondere nichtdeterministische und kurzzeitige Ph{\"a}nomene (z.B. Blitze und Meteoreintritte in die Erdatmosph{\"a}re) Gegenstand der Beobachtungen sind, dar. Die langen Reaktionszeiten des konventionellen Satellitenbetriebs verhindern die Realisierung solcher Missionen, da die verz{\"o}gerte Reaktion erst erfolgt, nachdem das zu beobachtende Ereignis bereits abgeschlossen ist. Die vorliegende Dissertation zeigt eine M{\"o}glichkeit, das durch die langen Reaktionszeiten entstandene Problem zu l{\"o}sen, auf. Im Zentrum des L{\"o}sungsansatzes steht dabei die Autonomie. Im Wesentlichen geht es dabei darum, den Satelliten mit der F{\"a}higkeit auszustatten, sein Verhalten, d.h. die Folge seiner T{\"a}tigkeiten, eigenst{\"a}ndig zu bestimmen bzw. zu {\"a}ndern. Dadurch wird die direkte Abh{\"a}ngigkeit des Satelliten vom Operator bei Reaktionen aufgehoben. Im Grunde wird der Satellit in die Lage versetzt, sich selbst zu kommandieren. Die Idee der Autonomie wurde im Rahmen der zugrunde liegenden Forschungsarbeiten umgesetzt. Das Ergebnis ist ein autonomes Planungssystem. Dabei handelt es sich um ein Softwaresystem, mit dem sich autonomes Verhalten im Satelliten realisieren l{\"a}sst. Es kann an unterschiedliche Satellitenmissionen angepasst werden. Ferner deckt es verschiedene Aspekte des autonomen Satellitenbetriebs, angefangen bei der generellen Entscheidungsfindung der T{\"a}tigkeiten, {\"u}ber die zeitliche Ablaufplanung unter Einbeziehung von Randbedingungen (z.B. Ressourcen) bis hin zur eigentlichen Ausf{\"u}hrung, d.h. Kommandierung, ab. Das Planungssystem kommt als Anwendung in ASAP, einer autonomen Sensorplattform, zum Einsatz. Es ist ein optisches System und dient der Detektion von kurzzeitigen Ph{\"a}nomenen und Ereignissen in der Erdatmosph{\"a}re. Die Forschungsarbeiten an dem autonomen Planungssystem, an ASAP sowie an anderen zu diesen in Bezug stehenden Systemen wurden an der Professur f{\"u}r Raumfahrttechnik des Lehrstuhls Informatik VIII der Julius-Maximilians-Universit{\"a}t W{\"u}rzburg durchgef{\"u}hrt.},
  subject      = {Planungssystem},
  language  = {de}
}
@phdthesis{Baier2018,
  author    = {Baier, Pablo A.},
  title     = {Simulator for Minimally Invasive Vascular Interventions: Hardware and Software},
  isbn      = {978-3-945459-22-5},
  doi       = {10.25972/OPUS-16119},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-161190},
  school      = {Universit{\"a}t W{\"u}rzburg},
  pages     = {118},
  year      = {2018},
  abstract  = {A complete simulation system is proposed that can be used as an educational tool by physicians in training basic skills of Minimally Invasive Vascular Interventions. In the first part, a surface model is developed to assemble arteries having a planar segmentation. It is based on Sweep Surfaces and can be extended to T- and Y-like bifurcations. A continuous force vector field is described, representing the interaction between the catheter and the surface. The computation time of the force field is almost unaffected when the resolution of the artery is increased. The mechanical properties of arteries play an essential role in the study of the circulatory system dynamics, which has been becoming increasingly important in the treatment of cardiovascular diseases. In Virtual Reality Simulators, it is crucial to have a tissue model that responds in real time. In this work, the arteries are discretized by a two dimensional mesh and the nodes are connected by three kinds of linear springs. Three tissue layers (Intima, Media, Adventitia) are considered and, starting from the stretch-energy density, some of the elasticity tensor components are calculated. The physical model linearizes and homogenizes the material response, but it still contemplates the geometric nonlinearity. In general, if the arterial stretch varies by 1\% or less, then the agreement between the linear and nonlinear models is trustworthy. In the last part, the physical model of the wire proposed by Konings is improved. As a result, a simpler and more stable method is obtained to calculate the equilibrium configuration of the wire. In addition, a geometrical method is developed to perform relaxations. It is particularly useful when the wire is hindered in the physical method because of the boundary conditions. The physical and the geometrical methods are merged, resulting in efficient relaxations. Tests show that the shape of the virtual wire agrees with the experiment. The proposed algorithm allows real-time executions and the hardware to assemble the simulator has a low cost.},
  subject      = {Computersimulation},
  language  = {en}
}
@article{ZimmererFischbachLatoschik2018,
  author    = {Zimmerer, Chris and Fischbach, Martin and Latoschik, Marc Erich},
  title     = {Semantic Fusion for Natural Multimodal Interfaces using Concurrent Augmented Transition Networks},
  series = {Multimodal Technologies and Interaction},
  volume    = {2},
  journal   = {Multimodal Technologies and Interaction},
  number    = {4},
  issn      = {2414-4088},
  doi       = {10.3390/mti2040081},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197573},
  year      = {2018},
  abstract  = {Semantic fusion is a central requirement of many multimodal interfaces. Procedural methods like finite-state transducers and augmented transition networks have proven to be beneficial to implement semantic fusion. They are compliant with rapid development cycles that are common for the development of user interfaces, in contrast to machine-learning approaches that require time-costly training and optimization. We identify seven fundamental requirements for the implementation of semantic fusion: Action derivation, continuous feedback, context-sensitivity, temporal relation support, access to the interaction context, as well as the support of chronologically unsorted and probabilistic input. A subsequent analysis reveals, however, that there is currently no solution for fulfilling the latter two requirements. As the main contribution of this article, we thus present the Concurrent Cursor concept to compensate these shortcomings. In addition, we showcase a reference implementation, the Concurrent Augmented Transition Network (cATN), that validates the concept's feasibility in a series of proof of concept demonstrations as well as through a comparative benchmark. The cATN fulfills all identified requirements and fills the lack amongst previous solutions. It supports the rapid prototyping of multimodal interfaces by means of five concrete traits: Its declarative nature, the recursiveness of the underlying transition network, the network abstraction constructs of its description language, the utilized semantic queries, and an abstraction layer for lexical information. Our reference implementation was and is used in various student projects, theses, as well as master-level courses. It is openly available and showcases that non-experts can effectively implement multimodal interfaces, even for non-trivial applications in mixed and virtual reality.},
  language  = {en}
}
@phdthesis{Budig2018,
  author    = {Budig, Benedikt},
  title     = {Extracting Spatial Information from Historical Maps: Algorithms and Interaction},
  edition   = {1. Auflage},
  publisher = {W{\"u}rzburg University Press},
  address   = {W{\"u}rzburg},
  isbn      = {978-3-95826-092-4},
  doi       = {10.25972/WUP-978-3-95826-093-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-160955},
  school      = {W{\"u}rzburg University Press},
  pages     = {viii, 160},
  year      = {2018},
  abstract  = {Historical maps are fascinating documents and a valuable source of information for scientists of various disciplines. Many of these maps are available as scanned bitmap images, but in order to make them searchable in useful ways, a structured representation of the contained information is desirable. This book deals with the extraction of spatial information from historical maps. This cannot be expected to be solved fully automatically (since it involves difficult semantics), but is also too tedious to be done manually at scale. The methodology used in this book combines the strengths of both computers and humans: it describes efficient algorithms to largely automate information extraction tasks and pairs these algorithms with smart user interactions to handle what is not understood by the algorithm. The effectiveness of this approach is shown for various kinds of spatial documents from the 16th to the early 20th century.},
  subject      = {Karte},
  language  = {en}
}
@misc{FunkenTscherner2018,
  author    = {Funken, Matthias and Tscherner, Michael},
  title     = {Jahresbericht 2017 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg},
  edition   = {1. Auflage},
  organization    = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168537},
  pages     = {68},
  year      = {2018},
  abstract  = {Eine {\"U}bersicht {\"u}ber die Aktivit{\"a}ten des Rechenzentrums im Jahr 2017.},
  subject      = {Julius-Maximilians-Universit{\"a}t W{\"u}rzburg},
  language  = {de}
}
@article{NaglerNaegeleGillietal.2018,
  author    = {Nagler, Matthias and N{\"a}gele, Thomas and Gilli, Christian and Fragner, Lena and Korte, Arthur and Platzer, Alexander and Farlow, Ashley and Nordborg, Magnus and Weckwerth, Wolfram},
  title     = {Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field},
  series = {Frontiers in Plant Science},
  volume    = {9},
  journal   = {Frontiers in Plant Science},
  number    = {1556},
  issn      = {1664-462X},
  doi       = {10.3389/fpls.2018.01556},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189560},
  year      = {2018},
  abstract  = {Experimental high-throughput analysis of molecular networks is a central approach to characterize the adaptation of plant metabolism to the environment. However, recent studies have demonstrated that it is hardly possible to predict in situ metabolic phenotypes from experiments under controlled conditions, such as growth chambers or greenhouses. This is particularly due to the high molecular variance of in situ samples induced by environmental fluctuations. An approach of functional metabolome interpretation of field samples would be desirable in order to be able to identify and trace back the impact of environmental changes on plant metabolism. To test the applicability of metabolomics studies for a characterization of plant populations in the field, we have identified and analyzed in situ samples of nearby grown natural populations of Arabidopsis thaliana in Austria. A. thaliana is the primary molecular biological model system in plant biology with one of the best functionally annotated genomes representing a reference system for all other plant genome projects. The genomes of these novel natural populations were sequenced and phylogenetically compared to a comprehensive genome database of A. thaliana ecotypes. Experimental results on primary and secondary metabolite profiling and genotypic variation were functionally integrated by a data mining strategy, which combines statistical output of metabolomics data with genome-derived biochemical pathway reconstruction and metabolic modeling. Correlations of biochemical model predictions and population-specific genetic variation indicated varying strategies of metabolic regulation on a population level which enabled the direct comparison, differentiation, and prediction of metabolic adaptation of the same species to different habitats. These differences were most pronounced at organic and amino acid metabolism as well as at the interface of primary and secondary metabolism and allowed for the direct classification of population-specific metabolic phenotypes within geographically contiguous sampling sites.},
  language  = {en}
}
@article{PetschkeStaab2018,
  author    = {Petschke, Danny and Staab, Torsten E.M.},
  title     = {DLTPulseGenerator: a library for the simulation of lifetime spectra based on detector-output pulses},
  series = {SoftwareX},
  volume    = {7},
  journal   = {SoftwareX},
  doi       = {10.1016/j.softx.2018.04.002},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-176883},
  pages     = {122-128},
  year      = {2018},
  abstract  = {The quantitative analysis of lifetime spectra relevant in both life and materials sciences presents one of the ill-posed inverse problems and, hence, leads to most stringent requirements on the hardware specifications and the analysis algorithms. Here we present DLTPulseGenerator, a library written in native C++ 11, which provides a simulation of lifetime spectra according to the measurement setup. The simulation is based on pairs of non-TTL detector output-pulses. Those pulses require the Constant Fraction Principle (CFD) for the determination of the exact timing signal and, thus, the calculation of the time difference i.e. the lifetime. To verify the functionality, simulation results were compared to experimentally obtained data using Positron Annihilation Lifetime Spectroscopy (PALS) on pure tin.},
  language  = {en}
}
@phdthesis{Ostermayer2017,
  author    = {Ostermayer, Ludwig},
  title     = {Integration of Prolog and Java with the Connector Architecture CAPJa},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150713},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {Modern software is often realized as a modular combination of subsystems for, e. g., knowledge management, visualization, verification, or the interaction with users. As a result, software libraries from possibly different programming languages have to work together. Even more complex the case is if different programming paradigms have to be combined. This type of diversification of programming languages and paradigms in just one software application can only be mastered by mechanisms for a seamless integration of the involved programming languages. However, the integration of the common logic programming language Prolog and the popular object-oriented programming language Java is complicated by various interoperability problems which stem on the one hand from the paradigmatic gap between the programming languages, and on the other hand, from the diversity of the available Prolog systems. The subject of the thesis is the investigation of novel mechanisms for the integration of logic programming in Prolog and object-oriented programming in Java. We are particularly interested in an object-oriented, uniform approach which is not specific to just one Prolog system. Therefore, we have first identified several important criteria for the seamless integration of Prolog and Java from the object-oriented perspective. The main contribution of the thesis is a novel integration framework called the Connector Architecture for Prolog and Java (CAPJa). The framework is completely implemented in Java and imposes no modifications to the Java Virtual Machine or Prolog. CAPJa provides a semi-automated mechanism for the integration of Prolog predicates into Java. For compact, readable, and object-oriented queries to Prolog, CAPJa exploits lambda expressions with conditional and relational operators in Java. The communication between Java and Prolog is based on a fully automated mapping of Java objects to Prolog terms, and vice versa. In Java, an extensible system of gateways provides connectivity with various Prolog system and, moreover, makes any connected Prolog system easily interchangeable, without major adaption in Java.},
  subject      = {Logische Programmierung},
  language  = {en}
}
@phdthesis{Aschenbrenner2017,
  author    = {Aschenbrenner, Doris},
  title     = {Human Robot Interaction Concepts for Human Supervisory Control and Telemaintenance Applications in an Industry 4.0 Environment},
  isbn      = {978-3-945459-18-8},
  doi       = {10.25972/OPUS-15052},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150520},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {While teleoperation of technical highly sophisticated systems has already been a wide field of research, especially for space and robotics applications, the automation industry has not yet benefited from its results. Besides the established fields of application, also production lines with industrial robots and the surrounding plant components are in need of being remotely accessible. This is especially critical for maintenance or if an unexpected problem cannot be solved by the local specialists. Special machine manufacturers, especially robotics companies, sell their technology worldwide. Some factories, for example in emerging economies, lack qualified personnel for repair and maintenance tasks. When a severe failure occurs, an expert of the manufacturer needs to fly there, which leads to long down times of the machine or even the whole production line. With the development of data networks, a huge part of those travels can be omitted, if appropriate teleoperation equipment is provided. This thesis describes the development of a telemaintenance system, which was established in an active production line for research purposes. The customer production site of Braun in Marktheidenfeld, a factory which belongs to Procter \& Gamble, consists of a six-axis cartesian industrial robot by KUKA Industries, a two-component injection molding system and an assembly unit. The plant produces plastic parts for electric toothbrushes. In the research projects "MainTelRob" and "Bayern.digital", during which this plant was utilised, the Zentrum f{\"u}r Telematik e.V. (ZfT) and its project partners develop novel technical approaches and procedures for modern telemaintenance. The term "telemaintenance" hereby refers to the integration of computer science and communication technologies into the maintenance strategy. It is particularly interesting for high-grade capital-intensive goods like industrial robots. Typical telemaintenance tasks are for example the analysis of a robot failure or difficult repair operations. The service department of KUKA Industries is responsible for the worldwide distributed customers who own more than one robot. Currently such tasks are offered via phone support and service staff which travels abroad. They want to expand their service activities on telemaintenance and struggle with the high demands of teleoperation especially regarding security infrastructure. In addition, the facility in Marktheidenfeld has to keep up with the high international standards of Procter \& Gamble and wants to minimize machine downtimes. Like 71.6 \% of all German companies, P\&G sees a huge potential for early information on their production system, but complains about the insufficient quality and the lack of currentness of data. The main research focus of this work lies on the human machine interface for all human tasks in a telemaintenance setup. This thesis provides own work in the use of a mobile device in context of maintenance, describes new tools on asynchronous remote analysis and puts all parts together in an integrated telemaintenance infrastructure. With the help of Augmented Reality, the user performance and satisfaction could be raised. A special regard is put upon the situation awareness of the remote expert realized by different camera viewpoints. In detail the work consists of: - Support of maintenance tasks with a mobile device - Development and evaluation of a context-aware inspection tool - Comparison of a new touch-based mobile robot programming device to the former teach pendant - Study on Augmented Reality support for repair tasks with a mobile device - Condition monitoring for a specific plant with industrial robot - Human computer interaction for remote analysis of a single plant cycle - A big data analysis tool for a multitude of cycles and similar plants - 3D process visualization for a specific plant cycle with additional virtual information - Network architecture in hardware, software and network infrastructure - Mobile device computer supported collaborative work for telemaintenance - Motor exchange telemaintenance example in running production environment - Augmented reality supported remote plant visualization for better situation awareness},
  subject      = {Fernwartung},
  language  = {en}
}
@phdthesis{Houshiar2017,
  author    = {Houshiar, Hamidreza},
  title     = {Documentation and mapping with 3D point cloud processing},
  isbn      = {978-3-945459-14-0},
  doi       = {10.25972/OPUS-14449},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144493},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {3D point clouds are a de facto standard for 3D documentation and modelling. The advances in laser scanning technology broadens the usability and access to 3D measurement systems. 3D point clouds are used in many disciplines such as robotics, 3D modelling, archeology and surveying. Scanners are able to acquire up to a million of points per second to represent the environment with a dense point cloud. This represents the captured environment with a very high degree of detail. The combination of laser scanning technology with photography adds color information to the point clouds. Thus the environment is represented more realistically. Full 3D models of environments, without any occlusion, require multiple scans. Merging point clouds is a challenging process. This thesis presents methods for point cloud registration based on the panorama images generated from the scans. Image representation of point clouds introduces 2D image processing methods to 3D point clouds. Several projection methods for the generation of panorama maps of point clouds are presented in this thesis. Additionally, methods for point cloud reduction and compression based on the panorama maps are proposed. Due to the large amounts of data generated from the 3D measurement systems these methods are necessary to improve the point cloud processing, transmission and archiving. This thesis introduces point cloud processing methods as a novel framework for the digitisation of archeological excavations. The framework replaces the conventional documentation methods for excavation sites. It employs point clouds for the generation of the digital documentation of an excavation with the help of an archeologist on-site. The 3D point cloud is used not only for data representation but also for analysis and knowledge generation. Finally, this thesis presents an autonomous indoor mobile mapping system. The mapping system focuses on the sensor placement planning method. Capturing a complete environment requires several scans. The sensor placement planning method solves for the minimum required scans to digitise large environments. Combining this method with a navigation system on a mobile robot platform enables it to acquire data fully autonomously. This thesis introduces a novel hole detection method for point clouds to detect obscured parts of a captured environment. The sensor placement planning method selects the next scan position with the most coverage of the obscured environment. This reduces the required number of scans. The navigation system on the robot platform consist of path planning, path following and obstacle avoidance. This guarantees the safe navigation of the mobile robot platform between the scan positions. The sensor placement planning method is designed as a stand alone process that could be used with a mobile robot platform for autonomous mapping of an environment or as an assistant tool for the surveyor on scanning projects.},
  subject      = {3D Punktwolke},
  language  = {en}
}
@article{KaltdorfSchulzeHelmprobstetal.2017,
  author    = {Kaltdorf, Kristin Verena and Schulze, Katja and Helmprobst, Frederik and Kollmannsberger, Philip and Dandekar, Thomas and Stigloher, Christian},
  title     = {Fiji macro 3D ART VeSElecT: 3D automated reconstruction tool for vesicle structures of electron tomograms},
  series = {PLoS Computational Biology},
  volume    = {13},
  journal   = {PLoS Computational Biology},
  number    = {1},
  doi       = {10.1371/journal.pcbi.1005317},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172112},
  year      = {2017},
  abstract  = {Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.},
  language  = {en}
}
@misc{OPUS4-15355,
  title     = {Jahresbericht 2016 des Rechenzentrums der Universit{\"a}t W{\"u}rzburg},
  edition   = {1. Auflage},
  organization    = {Rechenzentrum (Universit{\"a}t W{\"u}rzburg)},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-153558},
  pages     = {72},
  year      = {2017},
  abstract  = {Das Dokument umfasst eine j{\"a}hrliche Zusammenfassung der Aktivit{\"a}ten des Rechenzentrums als zentraler IT-Dienstleister der Universit{\"a}t W{\"u}rzburg},
  subject      = {Jahresbericht},
  language  = {de}
}
@article{vonMammenWagnerKnoteetal.2017,
  author    = {von Mammen, Sebastian Albrecht and Wagner, Daniel and Knote, Andreas and Taskin, Umut},
  title     = {Interactive simulations of biohybrid systems},
  series = {Frontiers in Robotics and AI},
  volume    = {4},
  journal   = {Frontiers in Robotics and AI},
  issn      = {2296-9144},
  doi       = {10.3389/frobt.2017.00050},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195755},
  year      = {2017},
  abstract  = {In this article, we present approaches to interactive simulations of biohybrid systems. These simulations are comprised of two major computational components: (1) agent-based developmental models that retrace organismal growth and unfolding of technical scaffoldings and (2) interfaces to explore these models interactively. Simulations of biohybrid systems allow us to fast forward and experience their evolution over time based on our design decisions involving the choice, configuration and initial states of the deployed biological and robotic actors as well as their interplay with the environment. We briefly introduce the concept of swarm grammars, an agent-based extension of L-systems for retracing growth processes and structural artifacts. Next, we review an early augmented reality prototype for designing and projecting biohybrid system simulations into real space. In addition to models that retrace plant behaviors, we specify swarm grammar agents to braid structures in a self-organizing manner. Based on this model, both robotic and plant-driven braiding processes can be experienced and explored in virtual worlds. We present an according user interface for use in virtual reality. As we present interactive models concerning rather diverse description levels, we only ensured their principal capacity for interaction but did not consider efficiency analyzes beyond prototypic operation. We conclude this article with an outlook on future works on melding reality and virtuality to drive the design and deployment of biohybrid systems.},
  language  = {en}
}
@article{FisselerMuellerWeichert2017,
  author    = {Fisseler, Denis and M{\"u}ller, Gerfrid G. W. and Weichert, Frank},
  title     = {Web-Based scientific exploration and analysis of 3D scanned cuneiform datasets for collaborative research},
  series = {Informatics},
  volume    = {4},
  journal   = {Informatics},
  number    = {4},
  issn      = {2227-9709},
  doi       = {10.3390/informatics4040044},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197958},
  pages     = {44},
  year      = {2017},
  abstract  = {The three-dimensional cuneiform script is one of the oldest known writing systems and a central object of research in Ancient Near Eastern Studies and Hittitology. An important step towards the understanding of the cuneiform script is the provision of opportunities and tools for joint analysis. This paper presents an approach that contributes to this challenge: a collaborative compatible web-based scientific exploration and analysis of 3D scanned cuneiform fragments. The WebGL -based concept incorporates methods for compressed web-based content delivery of large 3D datasets and high quality visualization. To maximize accessibility and to promote acceptance of 3D techniques in the field of Hittitology, the introduced concept is integrated into the Hethitologie-Portal Mainz, an established leading online research resource in the field of Hittitology, which until now exclusively included 2D content. The paper shows that increasing the availability of 3D scanned archaeological data through a web-based interface can provide significant scientific value while at the same time finding a trade-off between copyright induced restrictions and scientific usability.},
  language  = {en}
}
@article{KunzLiangNillaetal.2016,
  author    = {Kunz, Meik and Liang, Chunguang and Nilla, Santosh and Cecil, Alexander and Dandekar, Thomas},
  title     = {The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development},
  series = {Database},
  volume    = {2016},
  journal   = {Database},
  doi       = {10.1093/database/baw041},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147369},
  pages     = {baw041},
  year      = {2016},
  abstract  = {The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure-activity relationships.},
  language  = {en}
}
@article{AliMontenegro2016,
  author    = {Ali, Qasim and Montenegro, Sergio},
  title     = {Decentralized control for scalable quadcopter formations},
  series = {International Journal of Aerospace Engineering},
  volume    = {2016},
  journal   = {International Journal of Aerospace Engineering},
  doi       = {10.1155/2016/9108983},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146704},
  pages     = {9108983},
  year      = {2016},
  abstract  = {An innovative framework has been developed for teamwork of two quadcopter formations, each having its specified formation geometry, assigned task, and matching control scheme. Position control for quadcopters in one of the formations has been implemented through a Linear Quadratic Regulator Proportional Integral (LQR PI) control scheme based on explicit model following scheme. Quadcopters in the other formation are controlled through LQR PI servomechanism control scheme. These two control schemes are compared in terms of their performance and control effort. Both formations are commanded by respective ground stations through virtual leaders. Quadcopters in formations are able to track desired trajectories as well as hovering at desired points for selected time duration. In case of communication loss between ground station and any of the quadcopters, the neighboring quadcopter provides the command data, received from the ground station, to the affected unit. Proposed control schemes have been validated through extensive simulations using MATLAB®/Simulink® that provided favorable results.},
  language  = {en}
}
@article{AliMontenegro2016,
  author    = {Ali, Qasim and Montenegro, Sergio},
  title     = {Explicit Model Following Distributed Control Scheme for Formation Flying of Mini UAVs},
  series = {IEEE Access},
  volume    = {4},
  journal   = {IEEE Access},
  number    = {397-406},
  doi       = {10.1109/ACCESS.2016.2517203},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146061},
  year      = {2016},
  abstract  = {A centralized heterogeneous formation flight position control scheme has been formulated using an explicit model following design, based on a Linear Quadratic Regulator Proportional Integral (LQR PI) controller. The leader quadcopter is a stable reference model with desired dynamics whose output is perfectly tracked by the two wingmen quadcopters. The leader itself is controlled through the pole placement control method with desired stability characteristics, while the two followers are controlled through a robust and adaptive LQR PI control method. Selected 3-D formation geometry and static stability are maintained under a number of possible perturbations. With this control scheme, formation geometry may also be switched to any arbitrary shape during flight, provided a suitable collision avoidance mechanism is incorporated. In case of communication loss between the leader and any of the followers, the other follower provides the data, received from the leader, to the affected follower. The stability of the closed-loop system has been analyzed using singular values. The proposed approach for the tightly coupled formation flight of mini unmanned aerial vehicles has been validated with the help of extensive simulations using MATLAB/Simulink, which provided promising results.},
  language  = {en}
}
@article{LugrinLatoschikHabeletal.2016,
  author    = {Lugrin, Jean-Luc and Latoschik, Marc Erich and Habel, Michael and Roth, Daniel and Seufert, Christian and Grafe, Silke},
  title     = {Breaking Bad Behaviors: A New Tool for Learning Classroom Management Using Virtual Reality},
  series = {Frontiers in ICT},
  volume    = {3},
  journal   = {Frontiers in ICT},
  number    = {26},
  doi       = {10.3389/fict.2016.00026},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147945},
  year      = {2016},
  abstract  = {This article presents an immersive virtual reality (VR) system for training classroom management skills, with a specific focus on learning to manage disruptive student behavior in face-to-face, one-to-many teaching scenarios. The core of the system is a real-time 3D virtual simulation of a classroom populated by twenty-four semi-autonomous virtual students. The system has been designed as a companion tool for classroom management seminars in a syllabus for primary and secondary school teachers. This will allow lecturers to link theory with practice using the medium of VR. The system is therefore designed for two users: a trainee teacher and an instructor supervising the training session. The teacher is immersed in a real-time 3D simulation of a classroom by means of a head-mounted display and headphone. The instructor operates a graphical desktop console, which renders a view of the class and the teacher whose avatar movements are captured by a marker less tracking system. This console includes a 2D graphics menu with convenient behavior and feedback control mechanisms to provide human-guided training sessions. The system is built using low-cost consumer hardware and software. Its architecture and technical design are described in detail. A first evaluation confirms its conformance to critical usability requirements (i.e., safety and comfort, believability, simplicity, acceptability, extensibility, affordability, and mobility). Our initial results are promising and constitute the necessary first step toward a possible investigation of the efficiency and effectiveness of such a system in terms of learning outcomes and experience.},
  language  = {en}
}
@article{AnkenbrandWeberBeckeretal.2016,
  author    = {Ankenbrand, Markus J. and Weber, Lorenz and Becker, Dirk and F{\"o}rster, Frank and Bemm, Felix},
  title     = {TBro: visualization and management of de novo transcriptomes},
  series = {Database},
  volume    = {2016},
  journal   = {Database},
  doi       = {10.1093/database/baw146},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147954},
  pages     = {baw146},
  year      = {2016},
  abstract  = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.},
  language  = {en}
}