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An open-source platform for analyzing and sharing worm-behavior data

Nature Methods volume 15, pages 645–646 (2018)Cite this article

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To the Editor — Animal behavior is increasingly being recorded in systematic imaging studies that generate large datasets. To maximize the usefulness of these data, there is a need for improved resources for analyzing and sharing behavioral data that will encourage reanalysis and methodological developments1. However, for behavioral data, unlike genomic or protein structural data, there are no widely used standards. It is therefore desirable to make data available in a relatively raw form to enable flexibility in data analysis. For computational ethology to approach the level of maturity of other areas of bioinformatics, at least three challenges must be addressed: storing and accessing video files; defining flexible data formats to facilitate data sharing; and developing software to read, write, browse, and analyze the data. We have generated an open resource to begin addressing these challenges for Caenorhabditis elegans behavioral data.

Second, we have defined an interchange format named Worm tracker Commons Object Notation (WCON), to facilitate data sharing and software reuse among groups working on worm behavior. WCON uses the widely supported JSON format to store tracking data as text that is readable by both humans and machines. It is compatible with single and multiworm3 tracking data at any resolution, from a single point representing worm position over time4 to many points representing the high-resolution skeleton of a moving worm2. It also supports custom feature additions so that individual laboratories can store their own specific datasets alongside the existing set of basic worm data. WCON readers are available for Python, MATLAB, Scala, and C. Detailed documentation for the file formats and software is available on the project page (https://github.com/openworm/tracker-commons/).

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Fig. 1: Schematic of the searchable database and Tierpsy analysis pipeline.

References

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Acknowledgements

This work was supported by the MRC through grant MC-A658-5TY30 to A.E.X.B. Q.C. is supported by an ERC Starting Grant (NeuroAge 242666), a Research Councils UK Fellowship, and the University of London Central Research Fund. Some strains were provided by the CGC, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440).

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Authors and Affiliations

  1. MRC London Institute of Medical Sciences, London, UK

    Avelino Javer, Kezhi Li & André E. X. Brown

  2. Institute of Clinical Sciences, Imperial College London, London, UK

    Avelino Javer, Kezhi Li & André E. X. Brown

  3. OpenWorm Foundation, San Diego, CA, USA

    Michael Currie, Chee Wai Lee & Jim Hokanson

  4. Department of Biomedical Engineering, Duke University, Durham, NC, USA

    Jim Hokanson

  5. European Research Institute for the Biology of Ageing, University of Groningen, Groningen, the Netherlands

    Céline N. Martineau & Ellen A. A. Nollen

  6. Department of Biological Sciences, Columbia University, New York, NY, USA

    Eviatar Yemini

  7. MRC Laboratory of Molecular Biology, Cambridge, UK

    Laura J. Grundy & William R. Schafer

  8. Department of Biology, City College of the City University of New York, New York, NY, USA

    Chris Li

  9. Centre for Developmental Neurobiology, King’s College London, London, UK

    QueeLim Ch’ng

  10. Calico Life Sciences LLC, South San Francisco, CA, USA

    Rex Kerr

Authors
  1. Avelino Javer
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  14. André E. X. Brown
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Contributions

A.J. wrote Tierpsy Tracker and analyzed data; M.C. wrote WCON viewer, the database, and OpenWorm Analysis Toolbox; C.W.L. wrote the database, web interface, and WCON viewer; J.H. wrote the MATLAB WCON viewer and OpenWorm Analysis Toolbox; K.L. wrote stage-alignment code; C.N.M. collected data; E.Y. wrote the skeletonization algorithm and stage-alignment code; L.J.G. collected data; C.L. contributed strains and planned experiments; Q.C. contributed strains and planned experiments; W.R.S. planned the study; E.A.A.N. contributed strains and planned experiments; R.K. designed WCON and wrote several readers; A.E.X.B. planned the study and wrote the manuscript.

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Correspondence to André E. X. Brown.

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The authors declare no competing interests.

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Supplementary Software

Source code and documentation for Tierpsy Tracker software

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Javer, A., Currie, M., Lee, C.W. et al. An open-source platform for analyzing and sharing worm-behavior data. Nat Methods 15, 645–646 (2018). https://doi.org/10.1038/s41592-018-0112-1

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