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Topological data analysis quantifies biological nano-structure from single molecule localization microscopy

View ORCID ProfileJeremy A. Pike, View ORCID ProfileAbdullah O. Khan, Chiara Pallini, Steven G. Thomas, View ORCID ProfileMarkus Mund, View ORCID ProfileJonas Ries, Natalie S. Poulter, View ORCID ProfileIain B. Styles
doi: https://doi.org/10.1101/400275
Jeremy A. Pike
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
2Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Abdullah O. Khan
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
2Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Chiara Pallini
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
2Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Steven G. Thomas
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
2Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Markus Mund
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
4Department of Biochemistry, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
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Jonas Ries
3Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Natalie S. Poulter
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
2Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Iain B. Styles
1Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
5School of Computer Science, University of Birmingham, Birmingham, B15 2TT, UK
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Abstract

The study of complex molecular organisation and nano-structure by localization based microscopy is limited by the available analysis tools. We present a segmentation protocol which, through the application of persistence based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components and endocytic proteins. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist based analysis and batch processing of localization microscopy data.

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Posted November 13, 2018.
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Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
Jeremy A. Pike, Abdullah O. Khan, Chiara Pallini, Steven G. Thomas, Markus Mund, Jonas Ries, Natalie S. Poulter, Iain B. Styles
bioRxiv 400275; doi: https://doi.org/10.1101/400275
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Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
Jeremy A. Pike, Abdullah O. Khan, Chiara Pallini, Steven G. Thomas, Markus Mund, Jonas Ries, Natalie S. Poulter, Iain B. Styles
bioRxiv 400275; doi: https://doi.org/10.1101/400275

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