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  • 1. den Hollander, Lianne
    et al.
    Han, HongMei
    de Winter, Matthijs
    Svensson, Lennart
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Masich, Sergej
    Daneholt, Bertil
    Norlén, Lars
    Skin lamellar bodies are not discrete vesicles but part of a tubuloreticular network2016In: Acta Dermato-Venereologica, ISSN 0001-5555, E-ISSN 1651-2057, Vol. 96, no 3, p. 303-309Article in journal (Refereed)
  • 2.
    Svensson, Lennart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Brun, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sintorn, Ida-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Registration Parameter Spaces for Molecular Electron Tomography Images2011In: Image Analysis and Processing – ICIAP 2011: Part I / [ed] Maino, Giuseppe; Foresti, Gian Luca, Berlin: Springer-Verlag , 2011, p. 403-412Conference paper (Refereed)
  • 3.
    Svensson, Lennart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nysjö, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Brun, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sintorn, Ida-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Rigid registration for MET image exploration using CUDA2012In: Proceedings SSBA 2012, 2012Conference paper (Other academic)
  • 4.
    Svensson, Lennart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Svensson, Stina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sintorn, Ida-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Investigating measures for transfer function generation for visualization of MET biomedical data2011In: WSCG '2011: Communication Papers Proceedings / [ed] Baranoski, Gladimir; Skala, Vaclav, Plzen, Czech Republic: Union Agency , 2011, p. 113-120Conference paper (Refereed)
    Abstract [en]

    In this paper, the question of automatically setting transfer functions for volume images is further explored. Morespecifically, the focus is automatic visualization of Molecular Electron Tomography (MET) volume images usingone-dimensional transfer functions. We investigate how well a few general measures based on density, gradient,curvature and connected component information are suited for generating these transfer functions. To assessthis, an expert has set suitable transfer function levels manually and we have studied how these levels relate todifferent characteristics of the selected measures for 29 data sets. We have found that the measures can be used toautomatically generate a transfer function used to visualize MET data, to give the user an approximate view of thecomponents in the image.

  • 5.
    Svensson, Lennart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Sintorn, Ida-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    A probabilistic template model for finding macromolecules in MET volume images2013In: Pattern Recognition and Image Analysis, Springer Berlin/Heidelberg, 2013, p. 855-862Conference paper (Refereed)
    Abstract [en]

    We introduce and investigate probabilistic templates with particular focus on the application of protein identification in electron tomography volumes. We suggest to create templates with a weighted averaging operation of several object instances after alignment of an identified subpart. The subpart to be aligned should, ideally, correspond to a rigid and easily identifiable part of the object. The proposed templates enable common rigid template matching methods to also find different shape variations without increasing time complexity in the actual search procedure, since a static template is still used. We present general ideas on how to perform the object instance alignment and look specifically at how to do it for the antibody macromolecule IgG.

  • 6.
    Svensson, Lennart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Svensson, Stina
    RaySearch Labs, Stockholm, Sweden.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Nysjö, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nysjö, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Laloeuf, Aurelie
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden.
    den Hollander, Lianne
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden.
    Brun, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Masich, Sergej
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden.
    Sandblad, Linda
    Umea Univ, Dept Mol Biol, Umea, Sweden.
    Sani, Musa
    Vironova AB, Stockholm, Sweden.
    Sintorn, Ida-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Vironova AB, Stockholm, Sweden.
    ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms2017In: COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, ISSN 2168-1163, Vol. 5, no 6, p. 446-454Article in journal (Refereed)
    Abstract [en]

    Visual understanding is a key aspect when studying electron tomography data-sets, aside quantitative assessments such as registration of high-resolution structures. We here present the free software tool ProViz (Protein Visualization) for visualisation and templatematching in electron tomograms of biological samples. The ProViz software contains methods and tools which we have developed, adapted and computationally optimised for easy and intuitive visualisation and analysis of electron tomograms with low signal-to-noise ratio. ProViz complements existing software in the application field and serves as an easy and convenient tool for a first assessment and screening of the tomograms. It provides enhancements in three areas: (1) improved visualisation that makes connections as well as intensity differences between and within objects or structures easier to see and interpret, (2) interactive transfer function editing with direct visual result feedback using both piecewise linear functions and Gaussian function elements, (3) computationally optimised template matching and tools to visually assess and interactively explore the correlation results. The visualisation capabilities and features of ProViz are demonstrated on various biological volume data-sets: bacterial filament structures in vitro, a desmosome and the transmembrane cadherin connections therein in situ, and liposomes filled with doxorubicin in solution. The explorative template matching is demonstrated on a synthetic IgG data-set.

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