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pyActigraphy: Open-source python package for actigraphy data visualization and analysis

Author

Listed:
  • Grégory Hammad
  • Mathilde Reyt
  • Nikita Beliy
  • Marion Baillet
  • Michele Deantoni
  • Alexia Lesoinne
  • Vincenzo Muto
  • Christina Schmidt
Abstract
Over the past 40 years, actigraphy has been used to study rest-activity patterns in circadian rhythm and sleep research. Furthermore, considering its simplicity of use, there is a growing interest in the analysis of large population-based samples, using actigraphy. Here, we introduce pyActigraphy, a comprehensive toolbox for data visualization and analysis including multiple sleep detection algorithms and rest-activity rhythm variables. This open-source python package implements methods to read multiple data formats, quantify various properties of rest-activity rhythms, visualize sleep agendas, automatically detect rest periods and perform more advanced signal processing analyses. The development of this package aims to pave the way towards the establishment of a comprehensive open-source software suite, supported by a community of both developers and researchers, that would provide all the necessary tools for in-depth and large scale actigraphy data analyses.Author summary: The possibility to continuously record locomotor movements using accelerometers (actigraphy) has allowed field studies of sleep and rest-activity patterns. It has also enabled large-scale data collections, opening new avenues for research. However, each brand of actigraph devices encodes recordings in its own format and closed-source proprietary softwares are typically used to read and analyse actigraphy data. In order to provide an alternative to these softwares, we developed a comprehensive open-source toolbox for actigraphy data analysis, pyActigraphy. It allows researchers to read actigraphy data from 7 different file formats and gives access to a variety of rest-activity rhythm variables, automatic sleep detection algorithms and more advanced signal processing techniques. Besides, in order to empower researchers and clinicians with respect to their analyses, we created a series of interactive tutorials that illustrate how to implement the key steps of typical actigraphy data analyses. As an open-source project, all kind of user’s contributions to our toolbox are welcome. As increasing evidence points to the predicting value of rest-activity patterns derived from actigraphy for brain integrity, we believe that the development of the pyActigraphy package will not only benefit the sleep and chronobiology research, but also the neuroscientific community at large.

Suggested Citation

  • Grégory Hammad & Mathilde Reyt & Nikita Beliy & Marion Baillet & Michele Deantoni & Alexia Lesoinne & Vincenzo Muto & Christina Schmidt, 2021. "pyActigraphy: Open-source python package for actigraphy data visualization and analysis," PLOS Computational Biology, Public Library of Science, vol. 17(10), pages 1-16, October.
    • Handle: RePEc:plo:pcbi00:1009514
    DOI: 10.1371/journal.pcbi.1009514
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    References listed on IDEAS

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    1. Aiden Doherty & Dan Jackson & Nils Hammerla & Thomas Plötz & Patrick Olivier & Malcolm H Granat & Tom White & Vincent T van Hees & Michael I Trenell & Christoper G Owen & Stephen J Preece & Rob Gillio, 2017. "Large Scale Population Assessment of Physical Activity Using Wrist Worn Accelerometers: The UK Biobank Study," PLOS ONE, Public Library of Science, vol. 12(2), pages 1-14, February.
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