1. Computational and Systems Biology
  2. Neuroscience
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The natverse, a versatile toolbox for combining and analysing neuroanatomical data

  1. Alexander S Bates
  2. James D Manton
  3. Sridhar R Jagannathan
  4. Marta Costa
  5. Philipp Schlegel
  6. Torsten Rohlfing
  7. Gregory SXE Jefferis  Is a corresponding author
  1. MRC Laboratory of Molecular Biology, United Kingdom
  2. University of Cambridge, United Kingdom
  3. SRI International, Neuroscience Program, United States
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Cite this article as: eLife 2020;9:e53350 doi: 10.7554/eLife.53350

Abstract

To analyse neuron data at scale, neuroscientists expend substantial effort reading documentation, installing dependencies and moving between analysis and visualisation environments. To facilitate this, we have developed a suite of interoperable open-source R packages called the natverse. The natverse allows users to read local and remote data, perform popular analyses including visualisation and clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison across many neurons of morphology and connectivity after imaging or co-registration within a common template space. The natverse also enables transformations between different template spaces and imaging modalities. We demonstrate tools that integrate the vast majority of Drosophila neuroanatomical light microscopy and electron microscopy connectomic datasets. The natverse is an easy-to-use environment for neuroscientists to solve complex, large-scale analysis challenges as well as an open platform to create new code and packages to share with the community.

Data availability

All code is described at natverse.org which links to individual git repositories at github.com/natverse.

Article and author information

Author details

  1. Alexander S Bates

    Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1195-0445
  2. James D Manton

    Neurobiology Divison, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9260-3156
  3. Sridhar R Jagannathan

    Department of Zoology, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Marta Costa

    Department of Zoology, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5948-3092
  5. Philipp Schlegel

    Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5633-1314
  6. Torsten Rohlfing

    SRI International, Neuroscience Program, Menlo Park, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Gregory SXE Jefferis

    Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
    For correspondence
    jefferis@mrc-lmb.cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0587-9355

Funding

Medical Research Council (MC-U105188491)

  • Alexander S Bates
  • James D Manton
  • Gregory SXE Jefferis

H2020 European Research Council (649111)

  • Alexander S Bates
  • James D Manton
  • Marta Costa
  • Gregory SXE Jefferis

Wellcome (203261/Z/16/Z)

  • Sridhar R Jagannathan
  • Marta Costa
  • Philipp Schlegel
  • Gregory SXE Jefferis

Boehringer Ingelheim Fonds

  • Alexander S Bates

Herchel Smith Fund

  • Alexander S Bates

Fitzwilliam College

  • James D Manton

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. K VijayRaghavan, National Centre for Biological Sciences, Tata Institute of Fundamental Research, India

Publication history

  1. Received: November 5, 2019
  2. Accepted: April 11, 2020
  3. Accepted Manuscript published: April 14, 2020 (version 1)
  4. Version of Record published: May 21, 2020 (version 2)

Copyright

© 2020, Bates et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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