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Doctoral thesis2014Open access

Image analysis and interactive visualization techniques for electron microscopy tomograms

Svensson, Lennart


Images are an important data source in modern science and engineering. A continued challenge is to perform measurements on and extract useful information from the image data, i.e., to perform image analysis. Additionally, the image analysis results need to be visualized for best comprehension and to enable correct assessments. In this thesis, research is presented about digital image analysis and three-dimensional (3-D) visualization techniques for use with transmission electron microscopy (TEM) image data and in particular electron tomography, which provides 3-D reconstructions of the nano-structures. The electron tomograms are difficult to interpret because of, e.g., low signal-to-noise ratio, artefacts that stem from sample preparation and insufficient reconstruction information. Analysis is often performed by visual inspection or by registration, i.e., fitting, of molecular models to the image data. Setting up a visualization can however be tedious, and there may be large intra- and inter-user variation in how visualization parameters are set. Therefore, one topic studied in this thesis concerns automatic setup of the transfer function used in direct volume rendering of these tomograms. Results indicate that histogram and gradient based measures are useful in producing automatic and coherent visualizations. Furthermore, research has been conducted concerning registration of templates built using molecular models. Explorative visualization techniques are presented that can provide means of visualizing and navigating model parameter spaces. This gives a new type of visualization feedback to the biologist interpretating the TEM data. The introduced probabilistic template has an improved coverage of the molecular flexibility, by incorporating several conformations into a static model. Evaluation by cross-validation shows that the probabilistic template gives a higher correlation response than using a Protein Databank (PDB) devised model. The software ProViz (for Protein Visualization) is also introduced, where selected developed techniques have been incorporated and are demonstrated in practice.


interdisciplinary image analysis and visualization; electron tomography; interactive software tools

Published in

Acta Universitatis Agriculturae Sueciae
2014, number: 2014:94
ISBN: 978-91-576-8136-2, eISBN: 978-91-576-8137-9
Publisher: Centre for Image Analysis, Swedish University of Agricultural Sciences

      SLU Authors

    • Svensson, Lennart

      • Centre for Image Analysis, Swedish University of Agricultural Sciences

    UKÄ Subject classification

    Other Computer and Information Science
    Bioinformatics (Computational Biology)
    Computer Vision and Robotics (Autonomous Systems)

    Permanent link to this page (URI)