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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>1103</id>
    <completedYear/>
    <publishedYear>2008</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2008-12-12</completedDate>
    <publishedDate>2008-12-12</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Dual Streamline Seeding - Method and Implementation</title>
    <abstract language="eng">This work introduces a novel streamline seeding technique based on dual streamlines that are orthogonal to the vector field, instead of tangential. The greedy algorithm presented here produces a net of orthogonal streamlines that is iteratively refined resulting in good domain coverage and a high degree of continuity and uniformity. The algorithm is easy to implement and efficient, and it naturally extends to curved surfaces.</abstract>
    <abstract language="deu">In dieser Arbeit wird eine neue Strategie zur Platzierung von Stromlinien vorgestellt. Hierzu werden zusätzliche duale Stromlinien verwendet, die --im Gegensatz zur üblichen Definition-- orthogonal zum Vektorfeld verlaufen. Der vorgestellte Greedy-Algorithmus berechnet ein Netz aus orthogonalen Stromlinien, welches iterativ verfeinert wird, was zu einer guten Abdeckung der Domäne und einer gleichmäßigen Verteilung der Stromlinien führt. Es handelt sich um einen einfach zu implementierenden und effizienten Algorithmus, der direkt auf gekrümmten Oberflächen anwendbar ist.</abstract>
    <identifier type="serial">08-49</identifier>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="opus3-id">1141</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-11032</identifier>
    <enrichment key="SourceTitle">Appeared in: Proceedings of the IEEE Pacific Visualization Symposium (P. Eades, T. Ertl und H.-W. Shen, Hg.), 2009, S. 9–16.</enrichment>
    <author>Olufemi Rosanwo</author>
    <submitter>unknown unknown</submitter>
    <author>Christoph Petz</author>
    <author>Steffen Prohaska</author>
    <author>Ingrid Hotz</author>
    <author>Hans-Christian Hege</author>
    <series>
      <title>ZIB-Report</title>
      <number>08-49</number>
    </series>
    <collection role="ddc" number="004">Datenverarbeitung; Informatik</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="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="FLOW-VIS">FLOW-VIS</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1103/DualSeeding.pdf</file>
  </doc>
  <doc>
    <id>1425</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2011-11-05</completedDate>
    <publishedDate>2011-11-05</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Level of Detail for Trees Using Clustered Ellipsoids</title>
    <abstract language="eng">We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="serial">11-41</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-14251</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Malte Clasen</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Philip Paar</author>
    <author>Steffen Prohaska</author>
    <series>
      <title>ZIB-Report</title>
      <number>11-41</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>level of detail</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>rendering</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>natural scene</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Gaussian mixture model</value>
    </subject>
    <collection role="ccs" number="I.">Computing Methodologies</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1425/zibreport.pdf</file>
  </doc>
  <doc>
    <id>1773</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-12-02</completedDate>
    <publishedDate>2013-12-02</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">iCon.text – a customizable iPad app for kiosk applications in museum exhibitions</title>
    <abstract language="eng">We present iCon.text, a kiosk platform for the iPad centered around artefacts, whose content and layout can be tailored without programming skills for specific museum exhibitions. The central metaphor to access information is a virtual postcard with one front and a customizable number of back sides that provide details about exhibits to museum visitors in textual and image form. Back sides can link to others cards. Access to these postcards is possible through one or more navigation views that can be navigated to from a navigation bar.&#13;
The entry point to the application is designed as a multitouch interactive pile of cards in a playful manner that allows visitors of any age an easy approach to the presentation and interaction metaphor. To directly access a certain postcard, a mosaic view can be uitilized to provide an overview about all available exhibits. A category view groups postcards into themes. Locating artefacts on a zoomable map or exhibition floor plan allows for conveying information about spatial contexts between different objects and their location. Furthermore, contexts can be illustrated with a two stage view comprising an overview and corresponding detail views to provide further insights into the spatial, temporal, and thematic contexts of artefacts. The application scaffolding allows the design of bilingual presentations to support exhibitions with an international audience. The logo of the presenting institution or exhibition can be incorporated to display the the kiosk's corporate design branding and to access an imprint or further informations. Usage is logged into files to provide a basis for extracting statistical information about the usage.&#13;
The details about the exhibits are presented as images and as such impose no limit to the design choices made by the content provider or exhibition designer.&#13;
The application (enhanced with a panoramic view) has been integrated successfully into a large special exhibition about the ancient city of Pergamon 2011/2012 at the Pergamon Museum Berlin within the interdisciplinary project "Berlin Sculpture Network".</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-17731</identifier>
    <enrichment key="SourceTitle">Appeared in:  EVA , Berlin Nov. 2012, pp. 150-155. Gesellschaft zur Förderung angewandter Informatik</enrichment>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Marco Klindt</author>
    <submitter>Marco Klindt</submitter>
    <author>Daniel Baum</author>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-07</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>HCI</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Cultural Heritage</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Kiosk application</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>iPad</value>
    </subject>
    <collection role="ccs" number="H.5.1">Multimedia Information Systems</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="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="klindt">Klindt, Marco</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/1773/ZIB-Report-13-07.pdf</file>
  </doc>
  <doc>
    <id>3924</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>7</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace>Banff, Alberta, Canada</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A Virtual Laboratory for Assessment of Bone Biopsies</title>
    <parentTitle language="eng">14th IAA Humans in Space Symposium</parentTitle>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <author>Michael Giehl</author>
    <author>Wolfgang Gowin</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>3925</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace>Banff, Alberta, Canada</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantification of Changes in Spatial Structure of Human Bone Biopsies Using 3D Measures of Complexity</title>
    <parentTitle language="eng">14th IAA Humans in Space Symposium</parentTitle>
    <author>Peter Saparin</author>
    <author>Wolfgang Gowin</author>
    <author>Alexei Zaikin</author>
    <author>Jesper Thomsen</author>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <author>Jürgen Kurths</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>3927</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace>Berlin-Adlershof</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Interactive Visualization to Support Quantification of Bone Biopsies</title>
    <parentTitle language="eng">2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’</parentTitle>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <author>Michael Giehl</author>
    <author>Wolfgang Gowin</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>3928</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace>Berlin-Adlershof</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantification of changes in human bone structure at different skeletal locations using measures of complexity</title>
    <parentTitle language="eng">2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’</parentTitle>
    <author>Peter Saparin</author>
    <author>Wolfgang Gowin</author>
    <author>Alexei Zaikin</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="institutes" number="medplan">Therapy Planning</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>3932</id>
    <completedYear>2003</completedYear>
    <publishedYear>2003</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
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    <title language="eng">Architectural Reasons for the Femoral Neck Fracture Location</title>
    <parentTitle language="eng">2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’</parentTitle>
    <author>Wolfgang Gowin</author>
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    <author>Stefan Belle</author>
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    <title language="eng">2D and 3D bone modelling for analysis of changes in the bone architecture and for evaluation of structural measures.</title>
    <parentTitle language="eng">2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’</parentTitle>
    <author>Alexei Zaikin</author>
    <author>Peter Saparin</author>
    <author>Steffen Prohaska</author>
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    <author>Wolfgang Gowin</author>
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    <title language="eng">Comparison between Static Histomorphometric Measures Conducted by Traditionally 2D Histomorphometry and 3D μ-CT in Human Tibial Biopsies</title>
    <parentTitle language="eng">2nd European Congress ’Achievements in Space Medicine into Health Care Practice and Industry’</parentTitle>
    <author>Jesper Thomsen</author>
    <author>Bruno Koller</author>
    <author>Andreas Laib</author>
    <author>Steffen Prohaska</author>
    <author>Michael Giehl</author>
    <author>Wolfgang Gowin</author>
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    <language>eng</language>
    <pageFirst>145</pageFirst>
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    <title language="eng">Distributed visualization and analysis of fluid dynamics data</title>
    <parentTitle language="eng">Proc. Fourth International Symposium on Advanced Fluid Information and Transdisciplinary Fluid Integration</parentTitle>
    <author>Hans-Christian Hege</author>
    <author>Tino Weinkauf</author>
    <author>Steffen Prohaska</author>
    <author>Andrei Hutanu</author>
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    <publisherName>Kanazawa University</publisherName>
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    <title language="eng">From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models</title>
    <parentTitle language="eng">Proceedings of the Japan Korea Computer Graphics Conference 2002</parentTitle>
    <author>Hans-Christian Hege</author>
    <author>Hartmut Schirmacher</author>
    <author>Malte Westerhoff</author>
    <author>Hans Lamecker</author>
    <author>Steffen Prohaska</author>
    <author>Stefan Zachow</author>
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    <language>eng</language>
    <pageFirst>171</pageFirst>
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    <title language="eng">Visual Analysis of Trabecular Bone Structure</title>
    <parentTitle language="eng">Journal of Gravitational Physiology</parentTitle>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <author>Michael Giehl</author>
    <author>Wolfgang Gowin</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
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    <id>3958</id>
    <completedYear>2002</completedYear>
    <publishedYear>2002</publishedYear>
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    <language>eng</language>
    <pageFirst/>
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    <title language="eng">Regional Structural Skeletal Discordance Assessed by Measures of Complexity</title>
    <author>Wolfgang Gowin</author>
    <author>Peter Saparin</author>
    <author>Dieter Felsenberg</author>
    <author>Jürgen Kurths</author>
    <author>Alexei Zaikin</author>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
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    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
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    <id>3959</id>
    <completedYear>2002</completedYear>
    <publishedYear>2002</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>175</pageFirst>
    <pageLast>176</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>9</volume>
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    <completedDate>--</completedDate>
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    <title language="eng">Bone Modeling and Structural Measures of Complexity</title>
    <parentTitle language="eng">Journal of Gravitational Physiology</parentTitle>
    <identifier type="doi">10.1016/j.actaastro.2005.01.007</identifier>
    <author>Alexei Zaikin</author>
    <author>Peter Saparin</author>
    <author>Steffen Prohaska</author>
    <author>Jürgen Kurths</author>
    <author>Wolfgang Gowin</author>
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    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
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  <doc>
    <id>3960</id>
    <completedYear>2002</completedYear>
    <publishedYear>2002</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>26</pageFirst>
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    <edition/>
    <issue/>
    <volume>73</volume>
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    <title language="eng">Femoral Neck Fractures: Reasons for the Most Common Location of Fractures</title>
    <parentTitle language="eng">Acta Orthop. Scand. (Suppl. 304)</parentTitle>
    <author>Wolfgang Gowin</author>
    <author>Peter Saparin</author>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <author>Dieter Felsenberg</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
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    <id>3833</id>
    <completedYear>2006</completedYear>
    <publishedYear>2006</publishedYear>
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    <language>eng</language>
    <pageFirst>15</pageFirst>
    <pageLast>32</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>13</volume>
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    <title language="eng">A novel three-dimensional computer assisted method for a quantitative study of microvascular networks of the human cerebral cortex</title>
    <parentTitle language="eng">Microcirculation</parentTitle>
    <author>Francis Cassot</author>
    <author>Frederic Lauwers</author>
    <author>Céline Fouard</author>
    <author>Steffen Prohaska</author>
    <author>Valerie Lauwer-Cances</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
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  <doc>
    <id>3946</id>
    <completedYear>2002</completedYear>
    <publishedYear>2002</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>29</pageFirst>
    <pageLast>36</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName>IEEE Computer Society Press</publisherName>
    <publisherPlace>Boston MA, USA</publisherPlace>
    <creatingCorporation/>
    <contributingCorporation>IEEE Computer Society</contributingCorporation>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
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    <title language="eng">Fast Visualization of Plane-Like Structures in Voxel Data</title>
    <parentTitle language="eng">Proceedings of IEEE Visualization 2002</parentTitle>
    <identifier type="doi">10.1109/VISUAL.2002.1183753</identifier>
    <author>Steffen Prohaska</author>
    <editor>Robert J. Moorhead</editor>
    <author>Hans-Christian Hege</author>
    <editor>Markus Gross</editor>
    <editor>Kenneth I. Joy</editor>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
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  <doc>
    <id>4251</id>
    <completedYear/>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
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    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2013-09-19</completedDate>
    <publishedDate>2013-09-19</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Definition, Extraction, and Validation of Pore Structures in Porous Materials</title>
    <abstract language="eng">An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-42510</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <enrichment key="SourceTitle">Appeared in: Topological Methods in Data Analysis and Visualization III</enrichment>
    <author>Ulrike Homberg</author>
    <submitter>Ulrike Homberg</submitter>
    <author>Daniel Baum</author>
    <author>Alexander Wiebel</author>
    <author>Steffen Prohaska</author>
    <author>Hans-Christian Hege</author>
    <series>
      <title>ZIB-Report</title>
      <number>13-56</number>
    </series>
    <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="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
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    <file>https://opus4.kobv.de/opus4-zib/files/4251/ZR-13-56.pdf</file>
  </doc>
  <doc>
    <id>7300</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>066001</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue>6</issue>
    <volume>24</volume>
    <type>article</type>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
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    <title language="eng">3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent</title>
    <abstract language="eng">Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.</abstract>
    <parentTitle language="eng">Journal of Biomedical Optics</parentTitle>
    <identifier type="doi">10.1117/1.JBO.24.6.066001</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2019-04-24</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-72995</enrichment>
    <author>Jens Buchmann</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Bernhard Kaplan</author>
    <author>Samuel Powell</author>
    <author>Steffen Prohaska</author>
    <author>Jan Laufer</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="dfg-photom">dfg-photom</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>7299</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
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    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2019-04-25</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">3D quantitative photoacoustic tomography using an adjoint radiance Monte Carlo model and gradient descent</title>
    <abstract language="eng">Quantitative photoacoustic tomography aims to recover maps of the local concentrations of tissue chromophores from multispectral images. While model-based inversion schemes are promising approaches, major challenges to their practical implementation include the unknown fluence distribution and the scale of the inverse problem. This paper describes an inversion scheme based on a radiance Monte Carlo model and an adjoint-assisted gradient optimization that incorporates fluence-dependent step sizes and adaptive moment estimation. The inversion is shown to recover absolute chromophore concentrations, blood oxygen saturation and the Grüneisen parameter from in silico 3D phantom images for different radiance approximations. The scattering coefficient was assumed to be homogeneous and known a priori.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-72995</identifier>
    <identifier type="doi">10.1117/1.JBO.24.6.066001</identifier>
    <enrichment key="SourceTitle">Appeared in: Journal of Biomedical Optics, 24, p. 066001, 2019</enrichment>
    <author>Jens Buchmann</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Bernhard Kaplan</author>
    <author>Samuel Powell</author>
    <author>Steffen Prohaska</author>
    <author>Jan Laufer</author>
    <series>
      <title>ZIB-Report</title>
      <number>19-16</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>quantitative photoacoustic imaging</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>blood oxygen saturation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>inverse problem</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>model-based inversion</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Monte Carlo</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spectral unmixing</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
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    <file>https://opus4.kobv.de/opus4-zib/files/7299/zibreport-19-16_v1.pdf</file>
  </doc>
  <doc>
    <id>7129</id>
    <completedYear/>
    <publishedYear>2019</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>447</pageFirst>
    <pageLast>461</pageLast>
    <pageNumber/>
    <edition/>
    <issue>4</issue>
    <volume>50</volume>
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    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Serial synapse formation through filopodial competition for synaptic seeding factors</title>
    <abstract language="eng">Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.</abstract>
    <parentTitle language="eng">Developmental Cell</parentTitle>
    <identifier type="doi">10.1016/j.devcel.2019.06.014</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="SourceTitle">appeared also as bioRxiv preprint https://doi.org/10.1101/506378</enrichment>
    <enrichment key="AcceptedDate">2019-06-21</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-74397</enrichment>
    <author>Mehmet Neset Ozel</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Abhishek Kulkarni</author>
    <author>Amr Hasan</author>
    <author>Josephine Brummer</author>
    <author>Marian Moldenhauer</author>
    <author>Ilsa-Maria Daumann</author>
    <author>Heike Wolfenberg</author>
    <author>Vincent J. Dercksen</author>
    <author>Ferdi Ridvan Kiral</author>
    <author>Martin Weiser</author>
    <author>Steffen Prohaska</author>
    <author>Max von Kleist</author>
    <author>Peter Robin Hiesinger</author>
    <collection role="institutes" number="num">Numerical Mathematics</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="persons" number="weiser">Weiser, Martin</collection>
    <collection role="projects" number="FU-Images">FU-Images</collection>
    <collection role="projects" number="GC-Dynamics">GC-Dynamics</collection>
    <collection role="projects" number="BrainWiring">BrainWiring</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6202</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2017-03-30</completedDate>
    <publishedDate>2017-03-30</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration</title>
    <abstract language="eng">Surface structuring of titanium-based implants with appropriate nanotopographies can significantly modulate their impact on the biological behavior of cells populating these implants.  Implant assisted bone tissue repair and regeneration require functional adhesion and expansion of bone progenitors. The surface nanotopography of implant materials used to support bone healing and its effect on cell behavior, in particular cell adhesion, spreading, expansion, and motility, is still not clearly understood.  The aim of this study is to investigate preosteoblast proliferation, adhesion, morphology, and migration on different titanium materials with similar surface chemistry, but distinct nanotopographical features. Sonochemical treatment and anodic oxidation were employed to fabricate disordered – mesoporous titania (TMS), and ordered – titania nanotubular (TNT) topographies respectively.  The morphological evaluation revealed a surface dependent shape, thickness, and spreading of cells owing to different adherence behavior. Cells were polygonal-shaped and well-spread on glass and TMS, but displayed an elongated fibroblast-like morphology on TNT surfaces. The cells on glass however, were much flatter than on nanostructured surfaces. Both nanostructured surfaces impaired cell adhesion, but TMS was more favorable for cell growth due to its support of cell attachment and spreading in contrast to TNT. Quantitative wound healing assay in combination with live-cell imaging revealed that cells seeded on TMS surfaces migrated in close proximity to neighboring cells and less directed when compared to the migratory behavior on other surfaces. The results indicate distinctly different cell adhesion and migration on ordered and disordered titania nanotopographies, providing important information that could be used in optimizing titanium-based scaffold design to foster bone tissue growth and repair.</abstract>
    <parentTitle language="eng">Advanced Healthcare Materials</parentTitle>
    <identifier type="doi">10.1002/adhm.201601244</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-63053</enrichment>
    <author>Yulia Zhukova</author>
    <submitter>Marc Osterland</submitter>
    <author>Christian Hiepen</author>
    <author>Petra Knaus</author>
    <author>Marc Osterland</author>
    <author>Steffen Prohaska</author>
    <author>John W. C. Dunlop</author>
    <author>Peter Fratzl</author>
    <author>Ekaterina V. Skorb</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="FU-Images">FU-Images</collection>
    <collection role="projects" number="Cellmigration">Cellmigration</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4576</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Osteocytes number and volume in osteoporotic and in healthy bone biopsies analysed using Synchrotron CT: a pilot study</title>
    <parentTitle language="eng">Proc. ISB 2011</parentTitle>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Zully Ritter</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Steffen Prohaska</author>
    <author>R. Brand</author>
    <author>A. Friedmann</author>
    <author>Hans-Christian Hege</author>
    <author>Jürgen Goebbels</author>
    <author>Dieter Felsenberg</author>
    <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="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="hege">Hege, Hans-Christian</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4579</id>
    <completedYear/>
    <publishedYear>2011</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira</title>
    <parentTitle language="deu">Proc. DGZfP-Jahrestagung 2011</parentTitle>
    <enrichment key="PeerReviewed">no</enrichment>
    <author>Doreen Streicher</author>
    <submitter>Olaf Paetsch</submitter>
    <author>Olaf Paetsch</author>
    <author>Robert Seiler</author>
    <author>Steffen Prohaska</author>
    <author>Martin Krause</author>
    <author>Christian Boller</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="paetsch">Paetsch, Olaf</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="BAM-ECHOBETONVIZ">BAM-ECHOBETONVIZ</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4385</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computer-Tomographie</title>
    <parentTitle language="deu">Tagungsband der DACH Jahrestagung 2012</parentTitle>
    <enrichment key="PeerReviewed">No</enrichment>
    <enrichment key="FulltextUrl">http://www.ndt.net/article/dgzfp2012/papers/mo2b2.pdf</enrichment>
    <author>Olaf Paetsch</author>
    <author>Daniel Baum</author>
    <author>Karsten Ehrig</author>
    <author>Dietmar Meinel</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="paetsch">Paetsch, Olaf</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="BAM-RISSBETON">BAM-RISSBETON</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4386</id>
    <completedYear>2013</completedYear>
    <publishedYear>2013</publishedYear>
    <thesisYearAccepted/>
    <language>deu</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="deu">3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben</title>
    <parentTitle language="deu">Tagungsband der DGZfP Jahrestagung 2013</parentTitle>
    <enrichment key="PeerReviewed">No</enrichment>
    <enrichment key="FulltextUrl">http://www.ndt.net/article/dgzfp2013/papers/poster12.pdf</enrichment>
    <author>Olaf Paetsch</author>
    <author>Daniel Baum</author>
    <author>David Breßler</author>
    <author>Karsten Ehrig</author>
    <author>Dietmar Meinel</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="paetsch">Paetsch, Olaf</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="BAM-RISSBETON">BAM-RISSBETON</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>4387</id>
    <completedYear>2012</completedYear>
    <publishedYear>2012</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>321</pageFirst>
    <pageLast>330</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>conferenceobject</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography</title>
    <parentTitle language="eng">Proceedings of Conference on Industrial Computed Tomography</parentTitle>
    <enrichment key="PeerReviewed">No</enrichment>
    <author>Olaf Paetsch</author>
    <author>Daniel Baum</author>
    <author>Karsten Ehrig</author>
    <author>Dietmar Meinel</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="paetsch">Paetsch, Olaf</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="BAM-RISSBETON">BAM-RISSBETON</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>5967</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2016-06-15</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases</title>
    <abstract language="eng">Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches.&#13;
&#13;
We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-59672</identifier>
    <identifier type="doi">10.1016/j.neuron.2016.06.012</identifier>
    <enrichment key="SourceTitle">appeared also as bioRxiv preprint http://dx.doi.org/10.1101/006346 and in revised form in Neuron</enrichment>
    <author>Marta Costa</author>
    <submitter>Steffen Prohaska</submitter>
    <author>James D. Manton</author>
    <author>Aaron D. Ostrovsky</author>
    <author>Steffen Prohaska</author>
    <author>Gregory S.X.E. Jefferis</author>
    <series>
      <title>ZIB-Report</title>
      <number>16-34</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neuroinformatics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>NBLAST</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>neuron similarity</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cell type</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>clustering</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="68-XX">COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section -04 in that area)</collection>
    <collection role="msc" number="92-XX">BIOLOGY AND OTHER NATURAL SCIENCES</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/5967/zibreport-16-34_v1.pdf</file>
  </doc>
  <doc>
    <id>5968</id>
    <completedYear/>
    <publishedYear>2016</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>293</pageFirst>
    <pageLast>311</pageLast>
    <pageNumber/>
    <edition/>
    <issue>2</issue>
    <volume>91</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases</title>
    <abstract language="eng">Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish.</abstract>
    <parentTitle language="eng">Neuron</parentTitle>
    <identifier type="doi">10.1016/j.neuron.2016.06.012</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-59672</enrichment>
    <enrichment key="SourceTitle">appeared also as bioRxiv preprint https://doi.org/10.1101/006346</enrichment>
    <author>Marta Costa</author>
    <submitter>Steffen Prohaska</submitter>
    <author>James D. Manton</author>
    <author>Aaron D. Ostrovsky</author>
    <author>Steffen Prohaska</author>
    <author>Gregory S.X.E. Jefferis</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="no-project">no-project</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6985</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2018-08-07</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A switch in microtubule orientation during C. elegans meiosis</title>
    <abstract language="eng">In oocytes of many organisms, meiotic spindles form in the absence of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-69855</identifier>
    <submitter>Norbert Lindow</submitter>
    <author>Stefanie Redemann</author>
    <author>Ina Lantzsch</author>
    <author>Norbert Lindow</author>
    <author>Steffen Prohaska</author>
    <author>Martin Srayko</author>
    <author>Thomas Müller-Reichert</author>
    <series>
      <title>ZIB-Report</title>
      <number>18-34</number>
    </series>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6985/zib-report-v1.pdf</file>
  </doc>
  <doc>
    <id>6986</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">A switch in microtubule orientation during C. elegans meiosis</title>
    <abstract language="eng">In oocytes of many organisms, meiotic spindles form in the absence&#13;
of centrosomes [1–5]. Such female meiotic spindles have a pointed appearance in metaphase with microtubules focused at acentrosomal spindle poles. At anaphase, the microtubules of acentrosomal spindles then transition to an inter- chromosomal array, while the spindle poles disappear. This transition is currently not understood. Previous studies have focused on this inter- chromosomal microtubule array and proposed a pushing model to drive chromosome segregation [6, 7]. This model includes an end-on orientation of microtubules with chromosomes. Alternatively, chromosomes were thought to associate along bundles of microtubules [8, 9]. Starting with metaphase, this second model proposed a pure lateral chromosome-to-microtubule association up to the final meiotic stages of anaphase. Here we applied large-scale electron tomography [10] of staged C. elegans oocytes in meiosis to analyze the orientation of microtubules in respect to chromosomes. We show that microtubules at metaphase I are primarily oriented laterally to the chromosomes and that microtubules switch to an end-on orientation during progression through anaphase. We further show that this switch in microtubule orientation involves a kinesin-13 microtubule depolymerase, KLP-7, which removes laterally associated microtubules around chromosomes. From this we conclude that both lateral and end-on modes of microtubule-to-chromosome orientations are successively used in C. elegans oocytes to segregate meiotic chromosomes.</abstract>
    <parentTitle language="eng">Current Biology</parentTitle>
    <identifier type="doi">10.1016/j.cub.2018.07.012</identifier>
    <identifier type="issn">0960-9822</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2018-07-05</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-69855</enrichment>
    <author>Stefanie Redemann</author>
    <submitter>Norbert Lindow</submitter>
    <author>Ina Lantzsch</author>
    <author>Norbert Lindow</author>
    <author>Steffen Prohaska</author>
    <author>Martin Srayko</author>
    <author>Thomas Müller-Reichert</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6937</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>45</pageFirst>
    <pageLast>64</pageLast>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>145</volume>
    <type>bookpart</type>
    <publisherName>Academic Press</publisherName>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantification of three-dimensional spindle architecture</title>
    <abstract language="eng">Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional (3D) architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. 3D reconstruction of microtubules, however, is only the first step toward biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.</abstract>
    <parentTitle language="eng">Methods in Cell Biology Part B</parentTitle>
    <identifier type="doi">10.1016/bs.mcb.2018.03.012</identifier>
    <identifier type="issn">0091-679X</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-66562</enrichment>
    <author>Norbert Lindow</author>
    <submitter>Norbert Lindow</submitter>
    <author>Stefanie Redemann</author>
    <author>Florian Brünig</author>
    <author>Gunar Fabig</author>
    <author>Thomas Müller-Reichert</author>
    <author>Steffen Prohaska</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>7541</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2019-12-10</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms</title>
    <abstract language="eng">Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-75416</identifier>
    <identifier type="doi">10.1016/j.pacs.2019.100157</identifier>
    <enrichment key="SourceTitle">Photoacoustics 17:100157, 2020</enrichment>
    <author>Jens Buchmann</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Bernhard Kaplan</author>
    <author>Samuel Powell</author>
    <author>Steffen Prohaska</author>
    <author>Jan Laufer</author>
    <series>
      <title>ZIB-Report</title>
      <number>19-60</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>quantitative photoacoustic imaging</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>blood oxygen saturation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>inverse problem</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>model-based inversion</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>Monte Carlo</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>spectral unmixing</value>
    </subject>
    <collection role="ccs" number="J.">Computer Applications</collection>
    <collection role="pacs" number="80.00.00">INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY</collection>
    <collection role="msc" number="65-XX">NUMERICAL ANALYSIS</collection>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="dfg-photom">dfg-photom</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/7541/zibreport-19-60_v1.pdf</file>
  </doc>
  <doc>
    <id>7542</id>
    <completedYear/>
    <publishedYear>2020</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>100157</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>17</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2020-01-08</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantitative PA tomography of high resolution 3-D images: experimental validation in tissue phantoms</title>
    <abstract language="eng">Quantitative photoacoustic tomography aims recover the spatial distribution of absolute chromophore concentrations and their ratios from deep tissue, high-resolution images. In this study, a model-based inversion scheme based on a Monte-Carlo light transport model is experimentally validated on 3-D multispectral images of a tissue phantom acquired using an all-optical scanner with a planar detection geometry. A calibrated absorber allowed scaling of the measured data during the inversion, while an acoustic correction method was employed to compensate the effects of limited view detection. Chromophore- and fluence-dependent step sizes and Adam optimization were implemented to achieve rapid convergence. High resolution 3-D maps of absolute concentrations and their ratios were recovered with high accuracy. Potential applications of this method include quantitative functional and molecular photoacoustic tomography of deep tissue in preclinical and clinical studies.</abstract>
    <parentTitle language="eng">Photoacoustics</parentTitle>
    <identifier type="doi">10.1016/j.pacs.2019.100157</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2019-12-05</enrichment>
    <enrichment key="PreprintUrn">urn:nbn:de:0297-zib-75416</enrichment>
    <author>Jens Buchmann</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Bernhard Kaplan</author>
    <author>Samuel Powell</author>
    <author>Steffen Prohaska</author>
    <author>Jan Laufer</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="dfg-photom">dfg-photom</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>7792</id>
    <completedYear/>
    <publishedYear>2020</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>e50988</pageFirst>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume>9</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Sperm-specific meiotic chromosome segregation in C. elegans</title>
    <parentTitle language="eng">eLife</parentTitle>
    <identifier type="doi">10.7554/eLife.50988</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <enrichment key="AcceptedDate">2020-03-08</enrichment>
    <author>Gunar Fabig</author>
    <submitter>Steffen Prohaska</submitter>
    <author>Robert Kiewisz</author>
    <author>Norbert Lindow</author>
    <author>James A. Powers</author>
    <author>Vanessa Cota</author>
    <author>Luis J. Quintanilla</author>
    <author>Jan Brugués</author>
    <author>Steffen Prohaska</author>
    <author>Diana S. Chu</author>
    <author>Thomas Müller-Reichert</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>7952</id>
    <completedYear/>
    <publishedYear>2020</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2020-05-28</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography</title>
    <abstract language="eng">We present a software-assisted workflow for the alignment and matching of filamentous structures across a 3D stack of serial images. This is achieved by combining automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. Supported by a visual quality assessment of regions that have been already inspected, this allows a trade-off between quality and manual labor. The software tool was developed to investigate cell division by quantitative 3D analysis of microtubules (MTs) in both mitotic and meiotic spindles. For this, each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The serial tomograms are then stitched and non-rigidly aligned to allow tracing and connecting of MTs across tomogram boundaries. In practice, automatic stitching alone provides only an incomplete solution, because large physical distortions and a low signal-to-noise ratio often cause experimental difficulties. To derive 3D models of spindles despite the problems related to sample preparation and subsequent data collection, semi-automatic validation and correction is required to remove stitching mistakes. However, due to the large number of MTs in spindles (up to 30k) and their resulting dense spatial arrangement, a naive inspection of each MT is too time consuming. Furthermore, an interactive visualization of the full image stack is hampered by the size of the data (up to 100 GB). Here, we present a specialized, interactive, semi-automatic solution that considers all requirements for large-scale stitching of filamentous structures in serial-section image stacks. The key to our solution is a careful design of the visualization and interaction tools for each processing step to guarantee real-time response, and an optimized workflow that efficiently guides the user through datasets.</abstract>
    <parentTitle language="eng">bioRxiv</parentTitle>
    <identifier type="doi">10.1101/2020.05.28.120899</identifier>
    <enrichment key="PeerReviewed">no</enrichment>
    <enrichment key="SourceTitle">bioRxiv</enrichment>
    <enrichment key="AcceptedDate">2020-05-28</enrichment>
    <author>Norbert Lindow</author>
    <submitter>Daniel Baum</submitter>
    <author>Florian Brünig</author>
    <author>Vincent J. Dercksen</author>
    <author>Gunar Fabig</author>
    <author>Robert Kiewisz</author>
    <author>Stefanie Redemann</author>
    <author>Thomas Müller-Reichert</author>
    <author>Steffen Prohaska</author>
    <author>Daniel Baum</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="MODAL-MedLab">MODAL-MedLab</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="projects" number="MODAL-Gesamt">MODAL-Gesamt</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6796</id>
    <completedYear/>
    <publishedYear>2018</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>1027</pageFirst>
    <pageLast>1038.e4</pageLast>
    <pageNumber/>
    <edition/>
    <issue>7</issue>
    <volume>28</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>2018-03-15</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals</title>
    <abstract language="eng">Neurons are highly polarized cells that require continuous turnover of membrane proteins at axon terminals to develop, function, and survive. Yet, it is still unclear whether membrane protein degradation requires transport back to the cell body or whether degradation also occurs locally at the axon terminal, where live observation of sorting and degradation has remained a challenge. Here, we report direct observation of two cargo-specific membrane protein degradation mechanisms at axon terminals based on a live-imaging approach in intact Drosophila brains.&#13;
We show that different acidification-sensing cargo probes are sorted into distinct classes of degradative ‘‘hub’’ compartments for synaptic vesicle proteins and plasma membrane proteins at axon terminals. Sorting and degradation of the two cargoes in the separate hubs are molecularly distinct. Local sorting of synaptic vesicle proteins for degradation at the axon terminal is, surprisingly, Rab7 independent,&#13;
whereas sorting of plasma membrane proteins is Rab7 dependent. The cathepsin-like protease CP1 is specific to synaptic vesicle hubs, and its delivery requires the vesicle SNARE neuronal synaptobrevin. Cargo separation only occurs at the axon terminal, whereas degradative compartments at the cell body are mixed. These data show that at least two local, molecularly distinct pathways sort membrane cargo for degradation specifically at the axon terminal, whereas degradation can occur both at the terminal and en route to the cell body.</abstract>
    <parentTitle language="eng">Current Biology</parentTitle>
    <identifier type="doi">10.1016/j.cub.2018.02.032</identifier>
    <enrichment key="PeerReviewed">yes</enrichment>
    <author>Eugene Jennifer Jin</author>
    <submitter>Marc Osterland</submitter>
    <author>Ferdi Ridvan Kiral</author>
    <author>Mehmet Neset Ozel</author>
    <author>Lara Sophie Burchardt</author>
    <author>Marc Osterland</author>
    <author>Daniel Epstein</author>
    <author>Heike Wolfenberg</author>
    <author>Steffen Prohaska</author>
    <author>Peter Robin Hiesinger</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="FU-Images">FU-Images</collection>
    <collection role="projects" number="GC-Dynamics">GC-Dynamics</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6652</id>
    <completedYear/>
    <publishedYear>2017</publishedYear>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>researchdata</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Automated Segmentation of Complex Patterns in Biological Tissues: Lessons from Stingray Tessellated Cartilage (Supplementary Material)</title>
    <abstract language="eng">Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data. In particular, sections from hyomandibulae harvested from specimens of round stingray Urobatis halleri, donated from another study (DOI: 10.1002/etc.2564). Specimens were from sub-adults/adults collected by beach seine from collection sites in San Diego and Seal Beach, California, USA. The hyomandibulae were mounted in clay, sealed in ethanol-humidified plastic tubes and scanned with a Skyscan 1172 desktop μCT scanner (Bruker μCT, Kontich, Belgium) in association with another study (DOI: 10.1111/joa.12508). Scans for all samples were performed with voxel sizes of 4.89 μm at 59 kV source voltage and 167 μA source current, over 360◦ sample 120 rotation. For our segmentations, the datasets were resampled to a voxel size of 9.78 μm to reduce the size of the images and speed up processing. In addition, the processed data that was generated with the visualization software Amira with techniques described in the related publication based on the mentioned specimens.</abstract>
    <identifier type="doi">10.12752/4.DKN.1.0</identifier>
    <note>Supplementary data to reproduce and understand key results from the related publication, including original image data and processed data.</note>
    <enrichment key="ScientificResourceTypeGeneral">Dataset</enrichment>
    <enrichment key="ScientificGeolocation">San Diego and Seal Beach, California, USA</enrichment>
    <enrichment key="ScientificName">Urobatis halleri</enrichment>
    <enrichment key="ScientificDateCreated">2017</enrichment>
    <enrichment key="SoftwareDescription">The data was processed with the visualization software Amira. See http://www.zib.de/software/tesserae-segmentation for information about Amira and how to download the Amira extension package created for this publication. See https://github.com/zibamira/tesserae-segmentation.git for the source code of the Amira extension package.</enrichment>
    <enrichment key="zib_DownloadUrl">http://www.zib.de/ext-data/2017_Knoetel_PLOSONE-Supplementary-Material.zip</enrichment>
    <enrichment key="zib_relatedIdentifier">https://doi.org/10.1371/journal.pone.0188018</enrichment>
    <author>David Knötel</author>
    <submitter>David Knötel</submitter>
    <author>Ronald Seidel</author>
    <author>Paul Zaslansky</author>
    <author>Steffen Prohaska</author>
    <author>Mason N. Dean</author>
    <author>Daniel Baum</author>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="institutes" number="vissys">Image Analysis in Biology and Materials Science</collection>
    <collection role="persons" number="baum">Baum, Daniel</collection>
    <collection role="persons" number="knoetel">Knötel, David</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="TESSERAE">TESSERAE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
  </doc>
  <doc>
    <id>6656</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2018-02-01</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Quantification of Three-Dimensional Spindle Architecture</title>
    <abstract language="eng">Mitotic and meiotic spindles are microtubule-based structures to faithfully segregate chromosomes. Electron tomography is currently the method of choice to analyze the three-dimensional architecture of both types of spindles. Over the years, we have developed methods and software for automatic segmentation and stitching of microtubules in serial sections for large-scale reconstructions. Three-dimensional reconstruction of microtubules, however, is only the first step towards biological insight. The second step is the analysis of the structural data to derive measurable spindle properties. Here, we present a comprehensive set of techniques to quantify spindle parameters. These techniques provide quantitative analyses of specific microtubule classes and are applicable to a variety of tomographic reconstructions of spindles from different organisms.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-66562</identifier>
    <author>Norbert Lindow</author>
    <submitter>Norbert Lindow</submitter>
    <author>Stefanie Redemann</author>
    <author>Gunar Fabig</author>
    <author>Thomas Müller-Reichert</author>
    <author>Steffen Prohaska</author>
    <series>
      <title>ZIB-Report</title>
      <number>18-07</number>
    </series>
    <collection role="institutes" number="vis">Visual Data Analysis</collection>
    <collection role="persons" number="norbert.lindow">Lindow, Norbert</collection>
    <collection role="persons" number="prohaska">Prohaska, Steffen</collection>
    <collection role="projects" number="SPINDLE">SPINDLE</collection>
    <collection role="institutes" number="VDcC">Visual and Data-centric Computing</collection>
    <file>https://opus4.kobv.de/opus4-zib/files/6656/zib-report-final.pdf</file>
  </doc>
  <doc>
    <id>7439</id>
    <completedYear/>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber/>
    <edition/>
    <issue/>
    <volume/>
    <type>reportzib</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>0</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>2019-08-14</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Serial synapse formation through filopodial competition for synaptic seeding factors</title>
    <abstract language="eng">Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.</abstract>
    <identifier type="issn">1438-0064</identifier>
    <identifier type="urn">urn:nbn:de:0297-zib-74397</identifier>
    <identifier type="doi">10.1016/j.devcel.2019.06.014</identifier>
    <enrichment key="SourceTitle">Appeared in: Developmental Cell, 50(4), pp. 447-461, 2019</enrichment>
    <author>M. Neset Özel</author>
    <submitter>Josephine Brummer</submitter>
    <author>Abhishek Kulkarni</author>
    <author>Amr Hasan</author>
    <author>Josephine Brummer</author>
    <author>Marian Moldenhauer</author>
    <author>Ilsa-Maria Daumann</author>
    <author>Heike Wolfenberg</author>
    <author>Vincent J. Dercksen</author>
    <author>F. Ridvan Kiral</author>
    <author>Martin Weiser</author>
    <author>Steffen Prohaska</author>
    <author>Max von Kleist</author>
    <author>Peter Robin Hiesinger</author>
    <series>
      <title>ZIB-Report</title>
      <number>19-45</number>
    </series>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>filopodia</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>growth cone dynamics</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>brain wiring</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>2-photon microscopy</value>
    </subject>
    <subject>
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    <title language="eng">Semi-automatic Stitching of Serial Section Image Stacks with Filamentous Structures</title>
    <abstract language="eng">In this paper, we present a software-assisted workflow for the alignment and matching of filamentous structures across a stack of 3D serial image sections. This is achieved by a combination of automatic methods, visual validation, and interactive correction. After an initial alignment, the user can continuously improve the result by interactively correcting landmarks or matches of filaments. This is supported by a quality assessment that visualizes regions that have been already inspected and, thus, allows a trade-off between quality and manual labor.&#13;
The software tool was developed in collaboration with biologists who investigate microtubule-based spindles during cell division. To quantitatively understand the structural organization of such spindles, a 3D reconstruction of the numerous microtubules is essential. Each spindle is cut into a series of semi-thick physical sections, of which electron tomograms are acquired. The sections then need to be stitched, i.e. non-rigidly aligned; and the microtubules need to be traced in each section and connected across section boundaries. Experiments led to the conclusion that automatic methods for stitching alone provide only an incomplete solution to practical analysis needs. Automatic methods may fail due to large physical distortions, a low signal-to-noise ratio of the images, or other unexpected experimental difficulties. In such situations, semi-automatic validation and correction is required to rescue as much information as possible to derive biologically meaningful results despite of some errors related to data collection.&#13;
Since the correct stitching is visually not obvious due to the number of microtubules (up to 30k) and their dense spatial arrangement, these are difficult tasks. Furthermore, a naive inspection of each microtubule is too time consuming. In addition, interactive visualization is hampered by the size of the image data (up to 100 GB). Based on the requirements of our collaborators, we present a practical solution for the semi-automatic stitching of serial section image stacks with filamentous structures.</abstract>
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