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Svensson, Lennart
Publications (6 of 6) Show all publications
Svensson, L., Svensson, S., Nyström, I., Nysjö, F., Nysjö, J., Laloeuf, A., . . . Sintorn, I.-M. (2017). ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, 5(6), 446-454
Open this publication in new window or tab >>ProViz: a tool for explorative 3-D visualization and template matching in electron tomograms
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2017 (English)In: COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING-IMAGING AND VISUALIZATION, ISSN 2168-1163, Vol. 5, no 6, p. 446-454Article in journal (Refereed) Published
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.

Keywords
Electron tomography, direct volume rendering, image registration, connected component filtering, visualisation and analysis software
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-359635 (URN)10.1080/21681163.2016.1154483 (DOI)000428130400009 ()
Funder
Swedish Foundation for Strategic Research VINNOVA
Available from: 2018-09-05 Created: 2018-09-05 Last updated: 2018-09-05Bibliographically approved
den Hollander, L., Han, H., de Winter, M., Svensson, L., Masich, S., Daneholt, B. & Norlén, L. (2016). Skin lamellar bodies are not discrete vesicles but part of a tubuloreticular network. Acta Dermato-Venereologica, 96(3), 303-309
Open this publication in new window or tab >>Skin lamellar bodies are not discrete vesicles but part of a tubuloreticular network
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2016 (English)In: Acta Dermato-Venereologica, ISSN 0001-5555, E-ISSN 1651-2057, Vol. 96, no 3, p. 303-309Article in journal (Refereed) Published
National Category
Dermatology and Venereal Diseases Medical Image Processing
Research subject
Computerized Image Processing
Identifiers
urn:nbn:se:uu:diva-296791 (URN)10.2340/00015555-2249 (DOI)000373314500005 ()26439096 (PubMedID)
Available from: 2015-10-06 Created: 2016-06-20 Last updated: 2017-11-28Bibliographically approved
Svensson, L. & Sintorn, I.-M. (2013). A probabilistic template model for finding macromolecules in MET volume images. In: Pattern Recognition and Image Analysis: . Paper presented at IbPRIA 2013, June 5-7, Funchal, Madeira, Portugal (pp. 855-862). Springer Berlin/Heidelberg
Open this publication in new window or tab >>A probabilistic template model for finding macromolecules in MET volume images
2013 (English)In: Pattern Recognition and Image Analysis, Springer Berlin/Heidelberg, 2013, p. 855-862Conference paper, Poster (with or without abstract) (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.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2013
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 7887
National Category
Medical Image Processing
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-209645 (URN)10.1007/978-3-642-38628-2_101 (DOI)978-3-642-38627-5 (ISBN)
Conference
IbPRIA 2013, June 5-7, Funchal, Madeira, Portugal
Available from: 2013-10-23 Created: 2013-10-23 Last updated: 2013-10-30Bibliographically approved
Svensson, L., Nysjö, J., Brun, A., Nyström, I. & Sintorn, I.-M. (2012). Rigid registration for MET image exploration using CUDA. In: Proceedings SSBA 2012. Paper presented at SSBA 2012.
Open this publication in new window or tab >>Rigid registration for MET image exploration using CUDA
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2012 (English)In: Proceedings SSBA 2012, 2012Conference paper, Published paper (Other academic)
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-190025 (URN)
Conference
SSBA 2012
Available from: 2013-01-07 Created: 2013-01-07 Last updated: 2018-01-11
Svensson, L., Nyström, I., Svensson, S. & Sintorn, I.-M. (2011). Investigating measures for transfer function generation for visualization of MET biomedical data. In: Baranoski, Gladimir; Skala, Vaclav (Ed.), WSCG '2011: Communication Papers Proceedings. Paper presented at 19th International Conference on Computer Graphics, Visualization and Computer Vision 2011, January 31 – February 3, Plzen, Czech Republic (pp. 113-120). Plzen, Czech Republic: Union Agency
Open this publication in new window or tab >>Investigating measures for transfer function generation for visualization of MET biomedical data
2011 (English)In: WSCG '2011: Communication Papers Proceedings / [ed] Baranoski, Gladimir; Skala, Vaclav, Plzen, Czech Republic: Union Agency , 2011, p. 113-120Conference paper, Published 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.

Place, publisher, year, edition, pages
Plzen, Czech Republic: Union Agency, 2011
Keywords
Volume visualization, direct volume rendering, transfer functions, automatic visualization, molecular electron tomography
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-147167 (URN)978-80-86943-82-4 (ISBN)
Conference
19th International Conference on Computer Graphics, Visualization and Computer Vision 2011, January 31 – February 3, Plzen, Czech Republic
Projects
ProViz
Available from: 2011-10-31 Created: 2011-02-24 Last updated: 2018-01-12Bibliographically approved
Svensson, L., Brun, A., Nyström, I. & Sintorn, I.-M. (2011). Registration Parameter Spaces for Molecular Electron Tomography Images. In: Maino, Giuseppe; Foresti, Gian Luca (Ed.), Image Analysis and Processing – ICIAP 2011: Part I. Paper presented at 16th International Conference on Image Analysis and Processing, Ravenna, Italy, September 14-16, 2011 (pp. 403-412). Berlin: Springer-Verlag
Open this publication in new window or tab >>Registration Parameter Spaces for Molecular Electron Tomography Images
2011 (English)In: Image Analysis and Processing – ICIAP 2011: Part I / [ed] Maino, Giuseppe; Foresti, Gian Luca, Berlin: Springer-Verlag , 2011, p. 403-412Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Berlin: Springer-Verlag, 2011
Series
Lecture Notes in Computer Science ; 6978
National Category
Medical Image Processing
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-160677 (URN)10.1007/978-3-642-24085-0_42 (DOI)978-3-642-24084-3 (ISBN)
Conference
16th International Conference on Image Analysis and Processing, Ravenna, Italy, September 14-16, 2011
Projects
ProViz
Available from: 2011-10-31 Created: 2011-10-29 Last updated: 2016-04-22Bibliographically approved
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