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  <doc>
    <id>1097</id>
    <completedYear/>
    <publishedYear>2007</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2007-08-17</publishedDate>
    <thesisDateAccepted>2007-07-18</thesisDateAccepted>
    <title language="eng">Skeleton-based visualization of massive voxel objects with network-like architecture</title>
    <title language="deu">Skelettbasierte Visualisierung großer Voxel-Objekte mit netzwerkartiger Architektur</title>
    <abstract language="eng">This work introduces novel internal and external memory algorithms for computing voxel skeletons of massive voxel objects with complex network-like architecture and for converting these voxel skeletons to piecewise linear geometry, that is triangle meshes and piecewise straight lines. The presented techniques help to tackle the challenge of visualizing and analyzing 3d images of increasing size and complexity, which are becoming more and more important in, for example, biological and medical research. Section 2.3.1 contributes to the theoretical foundations of thinning algorithms with a discussion of homotopic thinning in the grid cell model. The grid cell model explicitly represents a cell complex built of faces, edges, and vertices shared between voxels. A characterization of pairs of cells to be deleted is much simpler than characterizations of simple voxels were before. The grid cell model resolves topologically unclear voxel configurations at junctions and locked voxel configurations causing, for example, interior voxels in sets of non-simple voxels. A general conclusion is that the grid cell model is superior to indecomposable voxels for algorithms that need detailed control of topology. Section 2.3.2 introduces a noise-insensitive measure based on the geodesic distance along the boundary to compute two-dimensional skeletons. The measure is able to retain thin object structures if they are geometrically important while ignoring noise on the object's boundary. This combination of properties is not known of other measures. The measure is also used to guide erosion in a thinning process from the boundary towards lines centered within plate-like structures. Geodesic distance based quantities seem to be well suited to robustly identify one- and two-dimensional skeletons. Chapter 6 applies the method to visualization of bone micro-architecture. Chapter 3 describes a novel geometry generation scheme for representing voxel skeletons, which retracts voxel skeletons to piecewise linear geometry per dual cube. The generated triangle meshes and graphs provide a link to geometry processing and efficient rendering of voxel skeletons. The scheme creates non-closed surfaces with boundaries, which contain fewer triangles than a representation of voxel skeletons using closed surfaces like small cubes or iso-surfaces. A conclusion is that thinking specifically about voxel skeleton configurations instead of generic voxel configurations helps to deal with the topological implications. The geometry generation is one foundation of the applications presented in Chapter 6. Chapter 5 presents a novel external memory algorithm for distance ordered homotopic thinning. The presented method extends known algorithms for computing chamfer distance transformations and thinning to execute I/O-efficiently when input is larger than the available main memory. The applied block-wise decomposition schemes are quite simple. Yet it was necessary to carefully analyze effects of block boundaries to devise globally correct external memory variants of known algorithms. In general, doing so is superior to naive block-wise processing ignoring boundary effects. Chapter 6 applies the algorithms in a novel method based on confocal microscopy for quantitative study of micro-vascular networks in the field of microcirculation.</abstract>
    <abstract language="deu">Die vorliegende Arbeit führt I/O-effiziente Algorithmen und Standard-Algorithmen zur Berechnung von Voxel-Skeletten aus großen Voxel-Objekten mit komplexer, netzwerkartiger Struktur und zur Umwandlung solcher Voxel-Skelette in stückweise-lineare Geometrie ein. Die vorgestellten Techniken werden zur Visualisierung und Analyse komplexer drei-dimensionaler Bilddaten, beispielsweise aus Biologie und Medizin, eingesetzt. Abschnitt 2.3.1 leistet mit der Diskussion von topologischem Thinning im Grid-Cell-Modell einen Beitrag zu den theoretischen Grundlagen von Thinning-Algorithmen. Im Grid-Cell-Modell wird ein Voxel-Objekt als Zellkomplex dargestellt, der aus den Ecken, Kanten, Flächen und den eingeschlossenen Volumina der Voxel gebildet wird. Topologisch unklare Situationen an Verzweigungen und blockierte Voxel-Kombinationen werden aufgelöst. Die Charakterisierung von Zellpaaren, die im Thinning-Prozess entfernt werden dürfen, ist einfacher als bekannte Charakterisierungen von so genannten "Simple Voxels". Eine wesentliche Schlussfolgerung ist, dass das Grid-Cell-Modell atomaren Voxeln überlegen ist, wenn Algorithmen detaillierte Kontrolle über Topologie benötigen. Abschnitt 2.3.2 präsentiert ein rauschunempfindliches Maß, das den geodätischen Abstand entlang der Oberfläche verwendet, um zweidimensionale Skelette zu berechnen, welche dünne, aber geometrisch bedeutsame, Strukturen des Objekts rauschunempfindlich abbilden. Das Maß wird im weiteren mit Thinning kombiniert, um die Erosion von Voxeln auf Linien zuzusteuern, die zentriert in plattenförmigen Strukturen liegen. Maße, die auf dem geodätischen Abstand aufbauen, scheinen sehr geeignet zu sein, um ein- und zwei-dimensionale Skelette bei vorhandenem Rauschen zu identifizieren. Eine theoretische Begründung für diese Beobachtung steht noch aus. In Abschnitt 6 werden die diskutierten Methoden zur Visualisierung von Knochenfeinstruktur eingesetzt. Abschnitt 3 beschreibt eine Methode, um Voxel-Skelette durch kontrollierte Retraktion in eine stückweise-lineare geometrische Darstellung umzuwandeln, die als Eingabe für Geometrieverarbeitung und effizientes Rendering von Voxel-Skeletten dient. Es zeigt sich, dass eine detaillierte Betrachtung der topologischen Eigenschaften eines Voxel-Skeletts einer Betrachtung von allgemeinen Voxel-Konfigurationen für die Umwandlung zu einer geometrischen Darstellung überlegen ist. Die diskutierte Methode bildet die Grundlage für die Anwendungen, die in Abschnitt 6 diskutiert werden. Abschnitt 5 führt einen I/O-effizienten Algorithmus für Thinning ein. Die vorgestellte Methode erweitert bekannte Algorithmen zur Berechung von Chamfer-Distanztransformationen und Thinning so, dass diese effizient ausführbar sind, wenn die Eingabedaten den verfügbaren Hauptspeicher übersteigen. Der Einfluss der Blockgrenzen auf die Algorithmen wurde analysiert, um global korrekte Ergebnisse sicherzustellen. Eine detaillierte Analyse ist einer naiven Zerlegung, die die Einflüsse von Blockgrenzen vernachlässigt, überlegen. In Abschnitt 6 wird, aufbauend auf den I/O-effizienten Algorithmen, ein Verfahren zur quantitativen Analyse von Mikrogefäßnetzwerken diskutiert.</abstract>
    <identifier type="opus3-id">1134</identifier>
    <identifier type="urn">urn:nbn:de:kobv:517-opus-14888</identifier>
    <identifier type="url">http://opus.kobv.de/ubp/volltexte/2007/1488/</identifier>
    <author>Steffen Prohaska</author>
    <submitter>Steffen Prohaska</submitter>
    <advisor>Jürgen Döllner</advisor>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Visualisierung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Bilddatenanalyse</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Skelettberechnung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Geometrieerzeugung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>I/O-effiziente Algorithmen</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>visualization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image data analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>skeletonization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>geometry generation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>external memory algorithms</value>
    </subject>
    <collection role="ddc" number="004">Datenverarbeitung; Informatik</collection>
    <collection role="ccs" number="J.3">LIFE AND MEDICAL SCIENCES</collection>
    <collection role="ccs" number="I.3.5">Computational Geometry and Object Modeling</collection>
    <collection role="ccs" number="I.3.8">Applications</collection>
    <collection role="ccs" number="I.4.7">Feature Measurement</collection>
    <collection role="ccs" number="I.4.10">Image Representation</collection>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Universität Potsdam</thesisGrantor>
    <file>https://opus4.kobv.de/opus4-zib/files/1097/prohaska_diss_lowres.pdf</file>
  </doc>
  <doc>
    <id>1110</id>
    <completedYear/>
    <publishedYear>2008</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2009-01-22</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Variational and statistical shape modeling for 3D geometry reconstruction</title>
    <abstract language="eng">The reconstruction of geometric shapes plays an important role in many biomedical applications. One example is the patient-specific, computer-aided planning of complex interventions, which requires the generation of explicitly represented geometric models of anatomical structures from medical image data. Only solutions that require minimal interaction by medical personnel are likely to enter clinical routine. Another example is the planning of surgical corrections of deformities where the target shape is unknown. Surgeons are often forced to resort to subjective criteria. These applications still pose highly challenging reconstruction problems, which are addressed in this thesis. The fundamental hypothesis, pursued in this thesis, is that the problems can be solved by incorporating a-priori knowledge about shape and other application-specific characteristics. Here, we focus mainly on the aspect of geometric shape analysis. The basic idea is to capture the most essential variations of a certain class of geometric objects via statistical shape models, which model typical features contained in a given population, and restrict the outcome of a reconstruction algorithm (more or less) to the space spanned by such models. A fundamental prerequisite for performing statistical shape analysis on a set of different objects is the identification of corresponding points on their associated surfaces. This problem is particularly difficult to solve if the shapes stem from different individuals. The reason lies in the basic difficulty of defining suitable measures of similarity. In this thesis, we divide the correspondence problem into feature and non-feature matching. The feature part depends on the application, while the non-feature part can be characterized by a purely geometric description. We propose two different approaches. The first approach has proved useful in many applications. Yet, it suffers from some practical limitations and does not yield a measure of similarity. Our second, variational, approach is designed to overcome these limitations. In it, we propose to minimize an invariant stretching measure, constrained by previously computed features. An important property, which sets our method apart from previous work, is that it does not require the computation of a global surface parameterization.</abstract>
    <identifier type="opus3-id">1151</identifier>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000005805</identifier>
    <enrichment key="SourceTitle">Appeared as Lamecker, Hans: Variational and statistical shape modeling for 3D geometry reconstruction. Dr. Hut Verlag, 2008. 171 S. ISBN 978-3-89963-878-3</enrichment>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Hans Lamecker</author>
    <submitter>unknown unknown</submitter>
    <advisor>Peter Deuflhard</advisor>
    <advisor>Martin Rumpf</advisor>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>correspondence problem</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>surface matching</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image segmentation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>model-based shape reconstruction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>2d-3d shape reconstruction</value>
    </subject>
    <collection role="ddc" number="510">Mathematik</collection>
    <collection role="ccs" number="I.4">IMAGE PROCESSING AND COMPUTER VISION (REVISED)</collection>
    <collection role="msc" number="68U01">General</collection>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="lamecker">Lamecker, Hans</collection>
    <collection role="projects" number="FacialGrowth">FacialGrowth</collection>
    <collection role="projects" number="IKG-FacialMorphology">IKG-FacialMorphology</collection>
    <collection role="projects" number="MATHEON-F2">MATHEON-F2</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>4145</id>
    <completedYear>2005</completedYear>
    <publishedYear>2005</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation>Technische Universität Berlin</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computer assisted osteotomy planning in cranio-maxillofacial surgery under consideration of facial soft tissue changes</title>
    <additionalTitle language="deu">Computergestützte Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung</additionalTitle>
    <identifier type="url">www.dr.hut-verlag.de/titelMedizininformatik.html</identifier>
    <author>Stefan Zachow</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="persons" number="zachow">Zachow, Stefan</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4151</id>
    <completedYear>2004</completedYear>
    <publishedYear>2004</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Visualization of General Relativistic Tensor Fields via a Fiber Bundle Data Model</title>
    <note>ISBN 3-86541-108-8</note>
    <author>Werner Benger</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>4153</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Efficient Visualization and Reconstruction of 3D Geometric from Neuro-Biological Confocal Microscope Scans</title>
    <author>Malte (née Zöckler)</author>
    <advisor>Peter Deuflhard</advisor>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="projects" number="VNL">VNL</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>4113</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation>Freie Universität Berlin</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Lagrangian feature extraction in two-dimensional unsteady flows</title>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Jens Kasten</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="compvis">Vergleichende Visualisierung</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>4114</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation>Freie Universität Berlin</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Computational discrete Morse theory</title>
    <author>Jan Reininghaus</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="compvis">Vergleichende Visualisierung</collection>
    <collection role="projects" number="CVT">CVT</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Otto-von-Guericke-Universität Magdeburg</thesisGrantor>
  </doc>
  <doc>
    <id>4129</id>
    <completedYear>2009</completedYear>
    <publishedYear>2009</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Extraction of Vortex Structures in 3D Flow Fields</title>
    <author>Jan Sahner</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Otto-von-Guericke-Universität Magdeburg</thesisGrantor>
  </doc>
  <doc>
    <id>4135</id>
    <completedYear>2008</completedYear>
    <publishedYear>2008</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation>Zuse Institute Berlin and Otto-von-Guericke-Universität Magdeburg, Fakultät für Informatik</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Extraction of Topological Structures in 2D and 3D Vector Fields</title>
    <author>Tino Weinkauf</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="projects" number="FLOW-ANALYSISII">FLOW-ANALYSISII</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4136</id>
    <completedYear>2008</completedYear>
    <publishedYear>2008</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation>Freie Universität Berlin, Fachbereich Mathematik und Informatik (P. Deuflhard), Der Andere Verlag, Tönning</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Analysis and Visualization of Molecular Conformations</title>
    <author>Johannes Schmidt-Ehrenberg</author>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="visalgo">Visual Data Analysis in Science and Engineering</collection>
    <collection role="projects" number="MOLVIS">MOLVIS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4245</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>XIV, 157 S.</pageNumber>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2013-07-03</publishedDate>
    <thesisDateAccepted>2013-05-02</thesisDateAccepted>
    <title language="eng">Three-Dimensional Second-Order Tensor Fields: Exploratory Visualization and Anisotropic Sampling</title>
    <abstract language="eng">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.</abstract>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000094629</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <advisor>Ingrid Hotz</advisor>
    <author>Andrea Kratz</author>
    <submitter>Regine Kossick</submitter>
    <advisor>Markus Hadwiger</advisor>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>visualization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>tensors of second order</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>exploratory visualization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>anisotropic sampling of tensor fields</value>
    </subject>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="compvis">Vergleichende Visualisierung</collection>
    <collection role="persons" number="kratz">Kratz, Andrea</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisPublisher>Freie Universität Berlin</thesisPublisher>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>4452</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2013-09-13</publishedDate>
    <thesisDateAccepted>2013-09-13</thesisDateAccepted>
    <title language="eng">Deformable Meshes for Accurate Automatic Segmentation of Medical Image Data</title>
    <enrichment key="PeerReviewed">no</enrichment>
    <advisor>Bernd Fischer †</advisor>
    <author>Dagmar Kainmüller</author>
    <submitter>Stefan Zachow</submitter>
    <advisor>Jan Modersitzki</advisor>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="projects" number="MATHEON-F2">MATHEON-F2</collection>
    <collection role="projects" number="SFB760-SiBiLL">SFB760-SiBiLL</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Universität zu Lübeck</thesisGrantor>
  </doc>
  <doc>
    <id>5487</id>
    <completedYear/>
    <publishedYear>2014</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2014-05-05</thesisDateAccepted>
    <title language="eng">Concepts and Algorithms for the Deformation, Analysis, and Compression of Digital Shapes</title>
    <abstract language="eng">This thesis concerns model reduction techniques for the efficient numerical treatment&#13;
of physical systems governing the deformation behavior of geometrically complex shapes.&#13;
We present new strategies for the construction of simplified,&#13;
low-dimensional models that capture the main features of the original complex system&#13;
and are suitable for use in interactive computer graphics applications.&#13;
To demonstrate the effectiveness of the new techniques we propose frameworks&#13;
for real-time simulation and interactive deformation-based modeling&#13;
of elastic solids and shells and compare them to alternative approaches.&#13;
In addition, we investigate differential operators that are derived from&#13;
the physical models and hence can serve as alternatives to the Laplace-Beltrami&#13;
operator for applications in modal shape analysis.&#13;
Furthermore, this thesis addresses the compression of digital shapes.&#13;
In particular, we present a lossless compression scheme that is adapted to&#13;
the special characteristics of adaptively refined, hierarchical meshes.</abstract>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000096721</identifier>
    <identifier type="doi">10.17169/refubium-4697</identifier>
    <identifier type="urn">urn:nbn:de:kobv:188-fudissthesis000000096721-7</identifier>
    <enrichment key="FulltextUrl">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000096721</enrichment>
    <advisor>Konrad Polthier</advisor>
    <author>Christoph von Tycowicz</author>
    <submitter>Christoph von Tycowicz</submitter>
    <collection role="msc" number="53-XX">DIFFERENTIAL GEOMETRY (For differential topology, see 57Rxx. For foundational questions of differentiable manifolds, see 58Axx)</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="vontycowicz">Tycowicz, Christoph von</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>5225</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>179</pageNumber>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2013-04-19</thesisDateAccepted>
    <title language="eng">Lagrangian Methods for Visualization and Analysis of Time-dependent Vector Fields</title>
    <abstract language="eng">Time-dependent vector fields are of high relevance to describe a wide range&#13;
of physical phenomena based on particle motion, including stall effects in&#13;
technical engineering, blood flow anomalies, and atmospheric mass trans-&#13;
port. The efficient analysis and fundamental understanding of intrinsic field&#13;
properties can lead to significant improvements when interacting with such&#13;
phenomena based on the available field data. So called Lagrangian methods&#13;
are a particularly established technique for this purpose. They are based on&#13;
the evaluation of time-dependent particle trajectories.&#13;
This work will present an overview of the state of the art in time-dependent&#13;
vector field analysis and visualization, with special focus on topology-oriented&#13;
and Lagrangian methods. The first core aspect of this work is the introduction&#13;
of a novel concept for a more objective and qualitative benchmark of existing&#13;
Lagrangian approaches. Based on this benchmark, this work contributes&#13;
and evaluates a set of novel concepts, that offer new perspectives towards&#13;
established approaches with respect to computational handling, quality and&#13;
efficiency. The second core aspect is the empirical application and validation&#13;
of Lagrangian methods with respect to practically relevant analysis scenarios.&#13;
Each application case includes an introduction into the underlying problem&#13;
statement and an efficient solution using Lagrangian methods. The validation&#13;
focuses on the comparison with existing flow analysis concepts and aspects&#13;
of the quantitative evaluation in each case. Together, both topics of this work&#13;
contribute towards a more consistent formalization, but also to the improved&#13;
applicability of Lagrangian methods.</abstract>
    <identifier type="url">http://edoc2.bibliothek.uni-halle.de/hs/id/31067</identifier>
    <identifier type="urn">urn:nbn:de:gbv:ma9:1-4177</identifier>
    <advisor>Prof. Dr. Holger Theisel</advisor>
    <author>Alexander Kuhn</author>
    <submitter>Alexander Kuhn</submitter>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Flow Visualization, Time-dependent Vector Fields</value>
    </subject>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Otto-von-Guericke-Universität Magdeburg</thesisGrantor>
  </doc>
  <doc>
    <id>5241</id>
    <completedYear/>
    <publishedYear>2006</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2006-12-12</thesisDateAccepted>
    <title language="deu">Modellgebundene Cranioplastie - Operationstechnik zur Umformung frühkindlicher Schädeldeformitäten unter Verwendung dreidimensionaler Standardformmodelle aus MRT-basierten Rekonstruktionen nicht deformierter Kinder</title>
    <advisor>Ernst-Johannes Haberl</advisor>
    <author>Maja Zöckler</author>
    <submitter>Stefan Zachow</submitter>
    <advisor>Hans Lamecker</advisor>
    <advisor>Stefan Zachow</advisor>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="projects" number="Cranio">Cranio</collection>
    <collection role="projects" number="MATHEON-F2">MATHEON-F2</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Charité – Universitätsmedizin Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>5260</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2013-11-19</thesisDateAccepted>
    <title language="deu">Erstellung eines statistischen Formmodells des Mittelgesichts zur Planung individueller Templates für die navigationsgestützte Rekonstruktion des Mittelgesichtsschädels</title>
    <advisor>Nils-Claudius Gellrich</advisor>
    <author>Kim Kubiack</author>
    <submitter>Stefan Zachow</submitter>
    <advisor>Stefan Zachow</advisor>
    <advisor>Enno-Ludwig Barth</advisor>
    <advisor>Alexander Schramm</advisor>
    <advisor>Harald Essig</advisor>
    <advisor>Hans Lamecker</advisor>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="projects" number="FacialSurgery">FacialSurgery</collection>
    <collection role="projects" number="MATHEON-F2">MATHEON-F2</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Medizinische Hochschule Hannover</thesisGrantor>
  </doc>
  <doc>
    <id>5261</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2011-06-28</thesisDateAccepted>
    <title language="deu">Das Konzept der Rhinorespiratorischen Homöostase – ein neuer theoretischer Ansatz für die Diskussion physiologischer und physikalischer Zusammenhänge bei der Nasenatmung</title>
    <identifier type="url">http://www.freidok.uni-freiburg.de/volltexte/8177/pdf/Hildebrandt_Dissertation.pdf</identifier>
    <advisor>Werner Heppt</advisor>
    <author>Thomas Hildebrandt</author>
    <submitter>Stefan Zachow</submitter>
    <advisor>Stefan Zachow</advisor>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="projects" number="Rhino-CFD">Rhino-CFD</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Albert-Ludwigs-Universität Freiburg</thesisGrantor>
  </doc>
  <doc>
    <id>6319</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Visual Analysis of Atomic Structures Based on the Hard-Sphere Model</title>
    <abstract language="eng">Visualization and Analysis of atomic compositions is essential to understand&#13;
the structure and functionality of molecules. There exist versatile areas of applications, from fundamental researches in biophysics and materials science to&#13;
drug development in pharmaceutics. For most applications, the hard-sphere&#13;
model is the most often used molecular model. Although the model is a quite&#13;
simple approximation of reality, it enables investigating important physical&#13;
properties in a purely geometrical manner. Furthermore, large data sets with&#13;
thousands up to millions of atoms can be visualized and analyzed. In addition to an adequate and efficient visualization of the data, the extraction of&#13;
important structures plays a major role. For the investigation of biomolecules,&#13;
such as proteins, especially the analysis of cavities and their dynamics is of&#13;
high interest. Substrates can bind in cavities, thereby inducing changes in&#13;
the function of the protein. Another example is the transport of substrates&#13;
through membrane proteins by the dynamics of the cavities. For both, the&#13;
visualization as well as the analysis of cavities, the following contributions&#13;
will be presented in this thesis:&#13;
1. The rendering of smooth molecular surfaces for the analysis of cavities&#13;
is accelerated and visually improved, which allows showing dynamic&#13;
proteins. On the other hand, techniques are proposed to interactively&#13;
render large static biological structures and inorganic materials up to&#13;
atomic resolution for the first time.&#13;
2. A Voronoi-based method is presented to extract molecular cavities. The&#13;
procedure comes with a high geometrical accuracy by a comparatively&#13;
fast computation time. Additionally, new methods are presented to visualize and highlight the cavities within the molecular structure. In a&#13;
further step, the techniques are extended for dynamic molecular data to&#13;
trace cavities over time and visualize topological changes.&#13;
3. To further improve the accuracy of the approaches mentioned above, a&#13;
new molecular surface model is presented that shows the accessibility&#13;
of a substrate. For the first time, the structure and dynamics of the substrate as hard-sphere model is considered for the accessibility computation. In addition to the definition of the surface, an efficient algorithm&#13;
for its computation is proposed, which additionally allows extracting&#13;
cavities.&#13;
The presented algorithms are demonstrated on different molecular data&#13;
sets. The data sets are either the result of physical or biological experiments&#13;
or molecular dynamics simulations.</abstract>
    <identifier type="urn">urn:nbn:de:0297-zib-63190</identifier>
    <advisor>Christof Schütte</advisor>
    <author>Norbert Lindow</author>
    <submitter>Norbert Lindow</submitter>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="projects" number="MOL-ANALYSIS">MOL-ANALYSIS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
    <file>https://opus4.kobv.de/opus4-zib/files/6319/thesis-lindow.pdf</file>
  </doc>
  <doc>
    <id>6370</id>
    <completedYear/>
    <publishedYear>2004</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2004-11-01</thesisDateAccepted>
    <title language="eng">Metabolic Pathways</title>
    <identifier type="url">http://publications.imp.fu-berlin.de/10/</identifier>
    <advisor> unknown</advisor>
    <author>Tim Conrad</author>
    <submitter>Paulina Bressel</submitter>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="conrad">Conrad, Tim</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Monash University Melbourne</thesisGrantor>
  </doc>
  <doc>
    <id>5720</id>
    <completedYear>2015</completedYear>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2015-12-11</completedDate>
    <publishedDate>2015-12-11</publishedDate>
    <thesisDateAccepted>2015-11-12</thesisDateAccepted>
    <title language="eng">Visual computing techniques for the reconstruction and analysis of anatomically realistic neural networks</title>
    <abstract language="eng">To understand how the brain translates sensory input into behavior, one needs to identify, at the cellular level, the involved neural circuitry and the electrical signals it carries. This thesis describes methods and tools that enable neuroscientists to obtain important anatomical data, including neuron numbers and shapes, from 3D microscopy images. On this basis, tools have been developed to create and visually analyze anatomically realistic 3D models of neural networks:&#13;
&#13;
1. An automatic segmentation method for determining the number and location of neuron cell bodies in 3D microscopy images. Application of this method yields a difference of merely ∼4% between automatically and manually counted cells, which is sufficiently accurate for application in large-scale counting experiments.&#13;
&#13;
2. A method for the automatic alignment of 3D section volumes containing filamentous structures. To this end, an existing point-matching-based method has been adapted such that sections containing neuron and microtubule fragments could be successfully aligned.&#13;
&#13;
3. The Filament Editor, a 3D proof-editing tool for visual verification and correction of automatically traced filaments. The usefulness of the Filament Editor is demonstrated by applying it in a validated neuron reconstruction pipeline to create 3D models of long-range and complex neuronal branches.&#13;
&#13;
4. The tool NeuroNet, which is used to assemble an anatomical model of a neural network representing the rat barrel cortex (or subnetworks therein, e.g. individual cortical columns), based on reconstructed anatomical data, such as neuron distributions and 3D morphologies. The tool estimates synaptic connectivity between neurons based on structural overlap between axons and dendrites.&#13;
&#13;
5. A framework for the interactive visual analysis of synaptic connectivity in such networks at multiple scales. It works from the level of neuron populations down to individual synapse positions on dendritic trees. It comprises the Cortical Column Connectivity Viewer, developed to analyze synaptic connections between neuron populations within and between cortical columns.&#13;
&#13;
The usefulness of these methods is demonstrated by applying them to reconstruct and analyze neural networks in the rat barrel cortex. Finally, I describe several applications of these methods and tools by neuroscientists, yielding significant biological findings regarding neuron anatomy and connectivity.</abstract>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000100938</identifier>
    <advisor>Christof Schütte</advisor>
    <author>Vincent J. Dercksen</author>
    <submitter>Vincent J. Dercksen</submitter>
    <advisor>Markus Hadwiger</advisor>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>3D reconstruction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image segmentation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neural network</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neuron tracing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>connectome</value>
    </subject>
    <collection role="ccs" number="E.">Data</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="projects" number="NeuroConnect">NeuroConnect</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>5789</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2015-07-15</thesisDateAccepted>
    <title language="eng">Reconstruction of Microtubule Centerlines from Electron Tomograms</title>
    <abstract language="eng">The organization of the mitotic spindle, a structure that separates the chromosomes during cell division, is an active research topic in molecular cell biology. It is composed of microtubules, elongated tubular macromolecules with a diameter of 25 nm. The only volumetric imaging technique that is available to a wide community and provides the required resolution to capture details about microtubules is electron tomography. However, the automatic detection of microtubules in electron tomograms is a difficult task due to the low contrast of the data. Furthermore, thick samples have to be cut into 300 nm thin sections before electron tomography can be applied. Software for automatically segmentation and stitching of the microtubules are not available and therefore these tasks have to be performed manually.&#13;
&#13;
Unfortunately, manual segmentation is time consuming for large samples and manual stitching of the tomograms is often infeasible due to the lack of prominent features for registration. Conclusions drawn from electron tomographic data is currently mostly based on either small samples containing few microtubules or single sections of complex structures. Consequently, simple properties, such as the length of microtubules in the spindle or their number, are still unknown for most model organisms.&#13;
&#13;
In this thesis, we present methods for 1) an automatic segmentation of microtubule centerlines in electron tomograms, and 2) an automatic stitching of the lines extracted from serial sections. For the centerline segmentation, we use 3D template matching and exploit knowledge about shape of microtubules and microscopy artifacts to design the templates. For the registration of the lines, we present a way to model the orientation of lines as a mixture of Fisher-Mises distributions where we estimate transformation parameters with the expectation maximization algorithm. The final line matching problem is formulated in terms of a probabilistic graphical model. To find the correct correspondences of line ends, we use belief propagation. We handle the poor convergence properties of this algorithm by detecting ambiguous and conflicting assignments of lines automatically. An expert can then influence the final output of the algorithm by solving conflicts manually.&#13;
&#13;
A detailed error analysis on true biological data and assessment of the reliability of the results is the prerequisite for analyzing the resulting line representations of the microtubules. To this end, the developed workflow for segmenting and stitching of microtubule centerlines is evaluated on plasticembedded samples of C. elegans early embryos and of spindles from X. laevis egg extracts. Our results suggest that the output of the presented algorithms together with little manual correction is of sufficient quality to allow a detailed analysis of dense microtubule networks. Finally, we exemplarily show results for the centrosome of a C. elegans mitotic spindle.</abstract>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000100915</identifier>
    <advisor>Knut Reinert</advisor>
    <author>Britta Weber</author>
    <submitter>Vincent J. Dercksen</submitter>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>microtubules</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>electron tomography</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>c.elegans</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>image processing</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>graphical model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>gaussian mixture model</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>template matching</value>
    </subject>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="projects" number="MICROTUBULES">MICROTUBULES</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>5790</id>
    <completedYear/>
    <publishedYear>2015</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2015-05-27</thesisDateAccepted>
    <title language="eng">Modeling, Quantification and Visualization of Probabilistic Features in Fields with Uncertainties</title>
    <abstract language="deu">Eine grundlegende Eigenschaft von naturwissenschaftlichen Daten ist, dass der wahre Wert einer Größe nicht beliebig genau bestimmbar ist. Es ist lediglich möglich, ihn durch Intervalle einzugrenzen oder die Unsicherheit durch eine Wahrscheinlichkeitsverteilung zu charakterisieren. Dies gilt für alle reellwertigen Daten, sowohl für Mess-, als auch für Simulationsergebnisse. Beispiele sind Messungen von grundlegenden physikalischen Größen wie Geschwindigkeit oder auch langfristige Temperaturvorhersagen, die durch Klimamodelle berechnet werden. Die Unsicherheit von Ergebnissen ist eine wichtige Information, die in Natur- und Ingenieurwissenschaften häufig durch Konfidenzintervalle in 1D-Plots und Tabellen angezeigt wird. Im Gegensatz dazu ist es bisher bei der Visualisierung von 2D- und 3D-Daten mithilfe von Standardmethoden meist unmöglich, die Datenunsicherheit zu repräsentieren.&#13;
&#13;
Diese Arbeit stellt wahrscheinlichkeitstheoretisch fundierte Methoden vor, die die Analyse und Visualisierung von Skalar-, Vektor- und Tensorfeldern mit Unsicherheiten ermöglichen. Der Fokus liegt dabei auf der Extraktion von raumzeitlichen geometrischen und topologischen Merkmalen aus den Feldern (z.B. Isokonturen und kritische Punkte). Wir nutzen parametrische und nichtparametrische Zufallsfelder, um Variabilität und räumliche Korrelation mathematisch zu modellieren. Die Wahrscheinlichkeitsverteilungen werden aus Ensemble-Datensätzen geschätzt, die mehrere Simulationsergebnisse (z.B. basierend auf variierenden Simulationsparametern) zusammenfassen. Wir untersuchen die Konditionszahlen von Merkmalsextraktionsmethoden, um die Sensitivität, d.h. die Verstärkung oder Abschwächung der Unsicherheit der Ergebnisse relativ zu Unsicherheiten in den Eingangsdaten abzuschätzen. Wir stellen einen allgemeiner Ansatz für die probabilistische Merkmalsextraktion vor, der die Basis für die Berechnung räumlicher Wahrscheinlichkeitsverteilungen von verschiedenen Merkmalen in Skalar-, Vektor- und Tensorfeldern bildet. In diesem Framework werden Wahrscheinlichkeiten für die Existenz von Merkmalen aus lokalen Randverteilungen und formalen Merkmalsdefinitionen berechnet. Numerisch können die Wahrscheinlichkeiten durch Monte-Carlo­-Integration bestimmt werden. Um den hohen Rechenaufwand dieses Ansatzes zu vermeiden, schlagen wir schnelle Berechnungsmethoden vor, wobei Merkmalswahrscheinlichkeiten näherungsweise mit Hilfe von Surrogatfunktionen bzw. Lookup-Tabellen geschätzt werden. Die vorgeschlagenen Methoden werden anhand von Daten aus Klima- und Biofluidmechaniksimulationen sowie aus der medizinischen Bildgebung qualitativ und quantitativ evaluiert.</abstract>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000099462?lang=en</identifier>
    <advisor>Christof Schütte</advisor>
    <author>Kai Pöthkow</author>
    <submitter>Vincent J. Dercksen</submitter>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>uncertainty quantification</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>feature extraction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>probability</value>
    </subject>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="projects" number="UncertaintyVis">UncertaintyVis</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
  <doc>
    <id>1043</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2005-12-31</completedDate>
    <publishedDate>2005-12-31</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Computergestützte 3D Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung</title>
    <title language="eng">Computer assisted 3D osteotomy planning in cranio-maxillofacial surgery under consideration of facial soft tissue arrangement</title>
    <abstract language="deu">In der Arbeit wird die computergestützte Planung von chirurgisch gesetzten Knochenfrakturen bzw. Knochenschnitten (sogenannten Osteotomien) an dreidimensionalen, computergrafischen Schädelmodellen, sowie die Umpositionierung separierter knöcherner Segmente im Kontext der rekonstruktiven MKG-Chirurgie behandelt. Durch die 3D Modellierung und Visualisierung anatomischer Strukturen, sowie der 3D Osteotomie- und Umstellungsplanung unter Einbeziehung der resultierenden Weichgewebedeformation wird den Chirurgen ein Werkzeug an die Hand gegeben, mit dem eine Therapieplanung am Computer durchgeführt und diese in Hinblick auf Funktion und Ästhetik bewertet werden kann. Unterschiedliche Strategien können dabei erprobt und in ihrer Auswirkung erfasst werden. Dazu wird ein methodischer Ansatz vorgestellt, der zum einen die chirurgische Planung im Vergleich zu existierenden Ansätzen deutlich verbessert und zum anderen eine robuste Weichgewebeprognose, durch den Einsatz geeigneter Planungsmodelle und eines physikalisch basierten Weichgewebemodells unter Nutzung numerischer Lösungsverfahren in die Planung integriert. Die Visualisierung der Planungsergebnisse erlaubt sowohl eine anschauliche und überzeugende, präoperative Patientenaufklärung, als auch die Demonstration möglicher Vorgehensweisen und deren Auswirkungen für die chirurgische Ausbildung. Ferner ergänzen die Planungsdaten die Falldokumentation und liefern einen Beitrag zur Qualitätssicherung. Die Arbeit ist in sieben Kapitel gegliedert und wie folgt strukturiert: Zuerst wird die medizinische Aufgabenstellung bei der chirurgischen Rekonstruktion von Knochenfehlbildungen und -fehlstellungen in der kraniofazialen Chirurgie sowie die daraus resultierenden Anforderungen an die Therapieplanung beschrieben. Anschließend folgt ein umfassender Überblick über entsprechende Vorarbeiten zur computergestützten Planung knochenverlagernder Operationen und eine kritische Bestandsaufnahme der noch vorhandenen Defizite. Nach der Vorstellung des eigenen Planungsansatzes wird die Generierung individueller, qualitativ hochwertiger 3D Planungsmodelle aus tomografischen Bilddaten beschrieben, die den Anforderungen an eine intuitive, 3D Planung von Umstellungsosteotomien entsprechen und eine Simulation der daraus resultierenden Weichgewebedeformation mittels der Finite-Elemente Methode (FEM) ermöglichen. Die Methoden der 3D Schnittplanung an computergrafischen Modellen werden analysiert und eine 3D Osteotomieplanung an polygonalen Schädelmodellen entwickelt, die es ermöglicht, intuitiv durch Definition von Schnittlinien am 3D Knochenmodell, eine den chirurgischen Anforderungen entsprechende Schnittplanung unter Berücksichtigung von Risikostrukturen durchzuführen. Separierte Knochensegmente lassen sich im Anschluss interaktiv umpositionieren und die resultierende Gesamtanordnung hinsichtlich einer funktionellen Rehabilitation bewerten. Aufgrund des in dieser Arbeit gewählten, physikalisch basierten Modellierungsansatzes kann unter Berücksichtigung des gesamten Weichgewebevolumens aus der Knochenverlagerung direkt die resultierende Gesichtsform berechnet werden. Dies wird anhand von 13 exemplarischen Fallstudien anschaulich demonstriert, wobei die Prognosequalität mittels postoperativer Fotografien und postoperativer CT-Daten überprüft und belegt wird. Die Arbeit wird mit einem Ausblick auf erweiterte Modellierungsansätze und einem Konzept für eine integrierte, klinisch einsetzbare Planungsumgebung abgeschlossen.</abstract>
    <abstract language="eng">In cranio-maxillofacial surgery, physicians are often faced with skeletal malformations that require complex bone relocations. Especially in severe cases of congenital dysgnathia (misalignment of upper and lower jaw) or hemifacial microsomia (asymmetric bone and tissue development), where multiple bone segments are to be mobilized and relocated simultaneously and in relation to each other, careful preoperative planning is mandatory. At present in clinical routine not all possible strategies can be planned and assessed with regard to functional rehabilitation. Moreover, the aesthetic outcome, i.e. the postoperative facial appearance, can only be estimated by a surgeon's experience and hardly communicated to the patient. On this account, a preoperative planning of complex osteotomies with bone relocations on a computerized model of a patient's head, including a reliable three-dimensional prediction and visualization of the post-surgical facial appearance is a highly appreciated possibility cranio-maxillofacial surgeons are longing for. This work, being performed at Zuse Institute Berlin (ZIB), addresses such a computer based 3D~surgery planning. A processing pipeline has been established and a simulation environment has been developed on basis of the software Amira, enabling a surgeon to perform bone cuts and bone rearrangements in an intuitive manner on virtual patient models. In addition, a prediction of the patients' postoperative appearance according to the relocated bone can be simulated and visualized realistically. For a meaningful planning of surgical procedures, anatomically correct patient models providing all relevant details are reconstructed from tomographic data with high fidelity. These patient models reliably represent bony structures as well as the facial soft tissue. Unstructured volumetric grids of the soft tissue are generated for a fast and efficient numerical solution of partial differential equations, describing tissue deformation on the foundation of 3D elastomechanics. The planning of osteotomies (bone cuts) for the mobilization and relocation of bone segments is performed in accordance to the planning on basis of life size replicas of a patient's skull, i.e. stereolitographic models. Osteotomy lines can be drawn on top of the polygonal planning models using suitable input devices. After evaluation of the consequence of a planned cut with regard to vulnerable inner structures (nerves, teeth etc.) the model is separated accordingly. A relocation of bone segments can be performed unrestrictedly in 3D or restricted to a translation or rotation within arbitrarily chosen planes under consideration of cephalometric guidelines. Bone and tooth collisions can be evaluated for functional analysis or orthodontic treatment planning with possible integration of digitized dental plaster casts. As a result of the preoperative planning, a single transformation matrix, encoding translation and rotation, or a sequence of such matrices are provided for each bone segment. Both the osteotomy paths and the transformation parameters can finally be used for intra-operative navigation. In the course of the planning, the relocated positions of bone segments serve as an input for the simulation of the resulting soft tissue deformation. Since bone and surrounding soft tissue share common boundaries that are either fixed or translocated, the resulting configuration of the entire tissue volume can be computed from the given boundary displacements by numerical minimization of the internal strain energy on basis of a biomechanical model, using a finite-element approach. In collaboration with different surgeons and hospitals more than 25 treatments have been accompanied by preoperative planning so far ranging from mandibular and midfacial hypoplasia to complex hemifacial microsomia. 13 of these cases are presented within this work. Simulation results were validated on the basis of photographs as well as of postoperative CT data, showing a good correlation between simulation and postoperative outcome. Further aspects of improving the modeling approach are discussed. It has been demonstrated that 3D~osteotomy planning on virtual patient models can be performed intuitively, and that 3D~tissue deformation for cranio-maxillofacial osteotomy planning can be predicted numerically without using heuristic ratios. It can be stated that by using 3D~planning software, a surgeon gains a better spatial understanding of complex dysplasia, and the 3D~soft tissue prediction gives an additional criterion for the assessment of the planned strategy. It turned out that, especially in complex cases such as hemifacial microsomia or for decisions bet­ween mono- and bimaxillary advancements, a 3D~planning aid is extremely helpful. The conclusion is, that images and animations created within the planning phase provide a valuable planning criterion for maxillofacial surgeons as well as a demonstrative information for patients and their relatives, thus greatly enhancing patient information, as well as surgical education. All data that result from the planning are also important for documentation and quality assurance. 3D osteotomy planning, including soft tissue prediction, likely will become a new paradigm of plastic and reconstructive surgery planning in the future. An assortment of results can be found under: http://www.zib.de/visual/medical/projects</abstract>
    <identifier type="isbn">3899631986</identifier>
    <identifier type="opus3-id">1071</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-10432</identifier>
    <enrichment key="SourceTitle">Ersch. als Buchveröffentlichung: Computergestützte 3D Osteotomieplanung in der Mund-Kiefer-Gesichtschirurgie unter Berücksichtigung der räumlichen Weichgewebeanordnung, (2005), Dr. Hut, ISBN 3-89963-198-6</enrichment>
    <author>Stefan Zachow</author>
    <submitter>Stefan Zachow</submitter>
    <advisor>Heinz Lemke</advisor>
    <advisor>Bernhard Preim</advisor>
    <advisor>Hans-Florian Zeilhofer</advisor>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>MKG-Chirurgie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Mund-Kiefer-Gesichtschirurgie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Therapieplanung</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Osteotomie</value>
    </subject>
    <subject>
      <language>deu</language>
      <type>uncontrolled</type>
      <value>Weichgewebeprädiktion</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>computer assisted surgery</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>therapy planning</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>osteotomy</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>soft tissue prediction</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>CAS</value>
    </subject>
    <collection role="ddc" number="620">Ingenieurwissenschaften und zugeordnete Tätigkeiten</collection>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="zachow">Zachow, Stefan</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Technische Universität Berlin</thesisGrantor>
    <file>https://opus4.kobv.de/opus4-zib/files/1043/zachow_diss_2005.pdf</file>
  </doc>
  <doc>
    <id>1048</id>
    <completedYear>2007</completedYear>
    <publishedYear>2007</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2007-12-19</completedDate>
    <publishedDate>2007-12-19</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Point-Based Algorithm for Multiple 3D Surface Alignment of Drug-Sized Molecules</title>
    <abstract language="eng">One crucial step in virtual drug design is the identification of new lead structures with respect to a pharmacological target molecule. The search for new lead structures is often done with the help of a pharmacophore, which carries the essential structural as well as physico-chemical properties that a molecule needs to have in order to bind to the target molecule. In the absence of the target molecule, such a pharmacophore can be established by comparison of a set of active compounds. In order to identify their common features,a multiple alignment of all or most of the active compounds is necessary. Moreover, since the “outer shape” of the molecules plays a major role in the interaction between drug and target, an alignment algorithm aiming at the identification of common binding properties needs to consider the molecule’s “outer shape”, which can be approximated by the solvent excluded surface. In this thesis, we present a new approach to molecular surface alignment based on a discrete representation of shape as well as physico-chemical properties by points distributed on the solvent excluded surface. We propose a new method to distribute points regularly on a surface w.r.t. a smoothly varying point density given on that surface. Since the point distribution algorithm is not restricted to molecular surfaces, it might also be of interest for other applications. For the computation of pairwise surface alignments, we extend an existing point matching scheme to surface points, and we develop an efficient data structure speeding up the computation by a factor of three. Moreover, we present an approach to compute multiple alignments from pairwise alignments, which is able to handle a large number of surface points. All algorithms are evaluated on two sets of molecules: eight thermolysin inhibitors and seven HIV-1 protease inhibitors. Finally, we compare the results obtained from surface alignment with the results obtained by applying an atom alignment approach.</abstract>
    <abstract language="deu">Die Identifizierung neuer Leitstrukturen (lead structures) zur Entwicklung optimierter Wirkstoffe ist ein äußerst wichtiger Schritt in der virtuellen Wirkstoffentwicklung (virtual drug design). Die Suche nach neuen Leitstrukturen wird oft mit Hilfe eines Pharmakophor-Modells durchgeführt, welches die wichtigsten strukturellen wie auch physiko-chemischen Eigenschaften eines bindenden Moleküls in sich vereint. Ist das Zielmolekül (target) nicht bekannt, kann das Pharmakophor-Modell mit Hilfe des Vergleiches aktiver Moleküle erstellt werden. Hier ist insbesondere die gleichzeitige Überlagerung (multiple alignment) aller oder nahezu aller Moleküle notwendig. Da bei der Interaktion zweier Moleküle die "äußere Form" der Moleküle eine besondere Rolle spielt, sollte diese von jedem Überlagerungsalgorithmus, der sich mit der Identifizierung von Bindungseigenschaften befasst, berücksichtigt werden. Dabei kann die "äußere Form" durch eine bestimmte Art von molekularer Oberfläche approximiert werden, die man als solvent excluded surface bezeichnet. In dieser Arbeit stellen wir einen neuen Ansatz zur Überlagerung molekularer Oberflächen dar, der auf einer diskreten Repräsentation sowohl der Form als auch der molekularen Eigenschaften mittels Punkten beruht. Um die Punkte auf der molekularen Oberfläche möglichst regulär entsprechend einer gegebenen Punktdichte zu verteilen, entwickeln wir eine neue Methode. Diese Methode ist nicht auf Moleküloberflächen beschränkt und könnte daher auch für andere Anwendungen von Interesse sein. Basierend auf einem bekannten Point-Matching Verfahren entwickeln wir einen Point-Matching Algorithmus für Oberflächenpunkte. Dazu erarbeiten wir u.a. eine effiziente Datenstruktur, die den Algorithmus um einen Faktor von drei beschleunigt. Darüberhinaus stellen wir einen Ansatz vor, der Mehrfachüberlagerungen (multiple alignments) aus paarweisen Überlagerungen berechnet. Die Herausforderung besteht hierbei vor allem in der großen Anzahl von Punkten, die berücksichtigt werden muss. Die vorgestellten Algorithmen werden an zwei Gruppen von Molekülen evaluiert, wobei die erste Gruppe aus acht Thermolysin Inhibitoren besteht, die zweite aus sieben HIV-1 Protease Inhibitoren. Darüberhinaus vergleichen wir die Ergebnisse der Oberflächenüberlagerung mit denen einer Atommittelpunktüberlagerung.</abstract>
    <identifier type="opus3-id">1077</identifier>
    <identifier type="urn">urn:nbn:de:kobv:188-fudissthesis000000002759-2</identifier>
    <identifier type="url">http://www.diss.fu-berlin.de/diss/receive/FUDISS_thesis_000000002759</identifier>
    <author>Daniel Baum</author>
    <advisor>Peter Deuflhard</advisor>
    <advisor>Joachim Selbig</advisor>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>molecular surface alignment</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>point-based approximation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>multiple alignment</value>
    </subject>
    <collection role="ddc" number="004">Datenverarbeitung; Informatik</collection>
    <collection role="ccs" number="J.3">LIFE AND MEDICAL SCIENCES</collection>
    <collection role="ccs" number="I.4.9">Applications</collection>
    <collection role="msc" number="68U07">Computer-aided design [See also 65D17]</collection>
    <collection role="msc" number="92C40">Biochemistry, molecular biology</collection>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="projects" number="MOLVIS">MOLVIS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisPublisher>Freie Universität Berlin</thesisPublisher>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
    <file>https://opus4.kobv.de/opus4-zib/files/1048/Baum_Dissertation_2007.pdf</file>
  </doc>
  <doc>
    <id>1057</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2005-09-20</completedDate>
    <publishedDate>2005-09-20</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Accelerated Volume Rendering on Structured Adaptive Meshes</title>
    <abstract language="eng">Multi-scale phenomena are abundant in many application fields. Representing and numerically simulating such processes is a challenging task since quite different scales have to be resolved, which often requires enormous amounts of storage and computational power. An important strategy in this context is adaptivity, i.e. local adjustment of the spatio-temporal resolution to the details to be resolved. A standard representation therefore are hierarchical, locally refined grids. A specific adaptive approach for solving partial differential equations, usually called AMR (Adaptive Mesh Refinement), was introduced in 1984. The basic idea is to combine the simplicity of structured grids and the advantages of local refinement. In this numerical scheme the computations are started on a set of coarse, potentially overlapping structured grids, that cover the computational domain. Local error criteria are applied to detect regions that require higher resolution. These are covered by subgrids with decreasing mesh spacing, which do not replace, but rather overlap the refined regions of the coarser patches. The equations are advanced on the finer subgrids and the refinement procedure recursively continues until all cells fulfill the considered error criteria, giving rise to a hierarchy of nested levels of refinement. In 1989 a variant of this scheme, called Structured Adaptive Mesh Refinement (SAMR), which reduces some of the complexity of the original approach, was proposed. While the separate subgrids in the AMR scheme could be rotated against each other, in SAMR they are aligned with the major axes of the coordinate system, which for example simplifies the computation of fluxes of (conserved) quantities through the cell faces. SAMR has become more and more popular in the last decade, and nowadays it is applied in many domains like hydrodynamics, meteorology and in particular in cosmology and relativistic astrophysics. Due to this growing popularity, an increasing number of scientists is in need of appropriate interactive visualization techniques to interpret and analyze AMR simulation data. Tools for both, 2D analysis to quantitatively convey the information within single slices and 3D representations to apprehend the overall structure are required. In this thesis we develop direct and indirect volume visualization algorithms for scalar fields that are defined on structured Adaptive Mesh Refinement (SAMR) grids. In particular algorithms for planar slicing and the display of height fields, C0-continuous isosurface extraction, software-, and hardware-based direct volume rendering and temporal interpolation for cell-, and vertex-centered data on unrestricted SAMR grids are proposed. Additionally we investigate the applicability of SAMR data structures for accelerated software-, and hardware-based volume rendering of large 3D scalar data.</abstract>
    <identifier type="opus3-id">1086</identifier>
    <identifier type="urn">urn:nbn:de:kobv:188-2005002769</identifier>
    <author>Ralf Kähler</author>
    <advisor>Peter Deuflhard</advisor>
    <advisor>Edward Seidel</advisor>
    <advisor>Konrad Polthier</advisor>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Visualization</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Volume Rendering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Adaptive Mesh Refinement Data</value>
    </subject>
    <collection role="ddc" number="510">Mathematik</collection>
    <collection role="ccs" number="I.3.3">Picture/Image Generation</collection>
    <collection role="ccs" number="I.3.7">Three-Dimensional Graphics and Realism</collection>
    <collection role="collections" number="">Dissertationen</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
    <file>https://opus4.kobv.de/opus4-zib/files/1057/Kaehler_Diss.pdf</file>
  </doc>
  <doc>
    <id>8835</id>
    <completedYear/>
    <publishedYear>2022</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>doctoralthesis</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>2022-11-14</thesisDateAccepted>
    <title language="eng">Efficient Riemannian Statistical Shape Analysis with Applications in Disease Assessment</title>
    <abstract language="eng">In this work, we address the challenge of developing statistical shape models that account for the non-Euclidean nature inherent to (anatomical) shape variation and at the same time offer fast, numerically robust processing and as much invariance as possible regarding translation and rotation, i.e. Euclidean motion.&#13;
With the aim of doing that we formulate a continuous and physically motivated notion of shape space based on deformation gradients. We follow two different tracks endowing this differential representation with a Riemannian structure to establish a statistical shape model. (1) We derive a model based on differential coordinates as elements in GL(3)+. To this end, we adapt the notion of bi-invariant means employing an affine connection structure on GL(3)+. Furthermore, we perform second-order statistics based on a family of Riemannian metrics providing the most possible invariance, viz. GL(3)+-left-invariance and O(3)-right-invariance. (2) We endow the differential coordinates with a non-Euclidean structure, that stems from a product Lie group of stretches and rotations. This structure admits a bi-invariant metric and thus allows for a consistent analysis via manifold-valued Riemannian statistics. This work further presents a novel shape representation based on discrete fundamental forms that is naturally invariant under Euclidean motion, namely the fundamental coordinates. We endow this representation with a Lie group structure that admits bi-invariant metrics and therefore allows for consistent analysis using manifold-valued statistics based on the Riemannian framework. Furthermore, we derive a simple, efficient, robust, yet accurate (i.e. without resorting to model approximations) solver for the inverse problem that allows for interactive applications. Beyond statistical shape modeling the proposed framework is amenable for surface processing such as quasi-isometric flattening. Additionally, the last part of the thesis aims on shape-based, continuous disease stratification to provide means that objectify disease assessment over the current clinical practice of ordinal grading systems. Therefore, we derive the geodesic B-score, a generalization of the of the Euclidean B-score, in order to assess knee osteoarthritis. In this context we present a Newton-type fixed point iteration for projection onto geodesics in shape space. On the application side, we show that the derived geodesic B-score features, in comparison to its Euclidean counterpart, an improved predictive performance on assessing the risk of total knee replacement surgery.</abstract>
    <identifier type="doi">10.17169/refubium-36729</identifier>
    <identifier type="urn">urn:nbn:de:kobv:188-refubium-37016-3</identifier>
    <enrichment key="opus.source">publish</enrichment>
    <enrichment key="FulltextUrl">http://d-nb.info/1274080460/34</enrichment>
    <advisor>Christof Schütte</advisor>
    <submitter>Felix Ambellan</submitter>
    <author>Felix Ambellan</author>
    <advisor>Christoph von Tycowicz</advisor>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="vontycowicz">Tycowicz, Christoph von</collection>
    <collection role="persons" number="ambellan">Ambellan, Felix</collection>
    <collection role="projects" number="MathPlus-TrU-1">MathPlus-TrU-1</collection>
    <collection role="projects" number="BIFOLD">BIFOLD</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <thesisGrantor>Freie Universität Berlin</thesisGrantor>
  </doc>
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