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3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations

Leonid Andronov, Jonathan Michalon, Khalid Ouararhni, Igor Orlov, Ali Hamiche, Jean-Luc Vonesch, Bruno P. Klaholz
doi: https://doi.org/10.1101/146456
Leonid Andronov
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Jonathan Michalon
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Khalid Ouararhni
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Igor Orlov
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Ali Hamiche
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Jean-Luc Vonesch
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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Bruno P. Klaholz
1Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France;
2Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France;
3Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France;
4Université de Strasbourg, Strasbourg, France.
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  • For correspondence: klaholz@igbmc.fr
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Abstract

Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches for example at the interface of cryo electron microscopy (cryo-EM), X-ray crystallography, NMR and fluorescence imaging to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualisation of crystal or cryo-EM structures little exists for 3D SMLM data which can provide fascinating insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context. We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation & quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 07, 2017.
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3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations
Leonid Andronov, Jonathan Michalon, Khalid Ouararhni, Igor Orlov, Ali Hamiche, Jean-Luc Vonesch, Bruno P. Klaholz
bioRxiv 146456; doi: https://doi.org/10.1101/146456
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3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations
Leonid Andronov, Jonathan Michalon, Khalid Ouararhni, Igor Orlov, Ali Hamiche, Jean-Luc Vonesch, Bruno P. Klaholz
bioRxiv 146456; doi: https://doi.org/10.1101/146456

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