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Image analysis and interactive visualization techniques for electron microscopy tomograms

Svensson, Lennart (2014). Image analysis and interactive visualization techniques for electron microscopy tomograms. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2014:94
ISBN 978-91-576-8136-2
eISBN 978-91-576-8137-9
[Doctoral thesis]

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Abstract

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.

Authors/Creators:Svensson, Lennart
Title:Image analysis and interactive visualization techniques for electron microscopy tomograms
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2014
Volume:2014:94
Number of Pages:65
Papers/manuscripts:
NumberReferences
I.Lennart Svensson, Ingela Nyström, Stina Svensson, Ida-Maria Sintorn (2011). Investigating measures for transfer function generation for visualization of MET biomedical data. In Proceedings of the WSCG Conference of Computer Graphics 2011, pp. 113--120.
II.Lennart Svensson, Anders Brun, Ingela Nyström, Ida-Maria Sintorn (2011). Registration parameter spaces for molecular electron tomography images. In Proceedings of the International Conference on Image Analysis and Processing (ICIAP), Lecture Notes in Computer Science 6978, pp. 403--412.
III.Lennart Svensson, Johan Nysjö, Anders Brun, Ingela Nyström, Ida-Maria Sintorn (2012). Rigid template registration in MET images using CUDA. In Proceedings of the International Conference on Computer Vision Theory and Applications (VISAPP), SciTePress, pp. 418--422.
IV.Lennart Svensson, Ida-Maria Sintorn (2013). A probabilistic template model for finding macromolecules in MET volume images. In Proceedings of the 6th Iberian Conference on Pattern Recognition and Image Analysis (IbPRIA), Lecture Notes in Computer Science 7887, pp 855--862.
V.Lennart Svensson, Stina Svensson, Ingela Nyström, Fredrik Nysjö, Johan Nysjö, Aurelie Laloeuf, Lianne den Hollander, Anders Brun, Sergej Masish, Ida-Maria Sintorn. ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms. Submitted for journal publication, 2014.
Place of Publication:Uppsala
Publisher:Centrum för bildanalys, Sveriges lantbruksuniversitet
ISBN for printed version:978-91-576-8136-2
ISBN for electronic version:978-91-576-8137-9
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:U Auxiliary disciplines > U40 Surveying methods
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > Computer Vision and Robotics (Autonomous Systems)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > Other Computer and Information Science
Agrovoc terms:image analysis, imagery, tomography, computer software
Keywords:interdisciplinary image analysis and visualization, electron tomography, interactive software tools
URN:NBN:urn:nbn:se:slu:epsilon-e-2191
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2191
ID Code:11609
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
External funders:Invest in Sweden Agency and Knowledge Foundation and Swedish Foundation for Strategic Research and Swedish Agency for Innovation Systems and Vårdalstiftelsen
Deposited By: Lennart Svensson
Deposited On:30 Oct 2014 15:18
Metadata Last Modified:02 Dec 2014 11:09

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