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

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.

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.

Metrics

  • 4,962
    views
  • 649
    downloads
  • 177
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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
(2020)
The natverse, a versatile toolbox for combining and analysing neuroanatomical data
eLife 9:e53350.
https://doi.org/10.7554/eLife.53350

Share this article

https://doi.org/10.7554/eLife.53350

Further reading

    1. Computational and Systems Biology
    2. Neuroscience
    Cesare V Parise, Marc O Ernst
    Research Article

    Audiovisual information reaches the brain via both sustained and transient input channels, representing signals’ intensity over time or changes thereof, respectively. To date, it is unclear to what extent transient and sustained input channels contribute to the combined percept obtained through multisensory integration. Based on the results of two novel psychophysical experiments, here we demonstrate the importance of the transient (instead of the sustained) channel for the integration of audiovisual signals. To account for the present results, we developed a biologically inspired, general-purpose model for multisensory integration, the multisensory correlation detectors, which combines correlated input from unimodal transient channels. Besides accounting for the results of our psychophysical experiments, this model could quantitatively replicate several recent findings in multisensory research, as tested against a large collection of published datasets. In particular, the model could simultaneously account for the perceived timing of audiovisual events, multisensory facilitation in detection tasks, causality judgments, and optimal integration. This study demonstrates that several phenomena in multisensory research that were previously considered unrelated, all stem from the integration of correlated input from unimodal transient channels.

    1. Computational and Systems Biology
    Franck Simon, Maria Colomba Comes ... Herve Isambert
    Tools and Resources

    Live-cell microscopy routinely provides massive amounts of time-lapse images of complex cellular systems under various physiological or therapeutic conditions. However, this wealth of data remains difficult to interpret in terms of causal effects. Here, we describe CausalXtract, a flexible computational pipeline that discovers causal and possibly time-lagged effects from morphodynamic features and cell–cell interactions in live-cell imaging data. CausalXtract methodology combines network-based and information-based frameworks, which is shown to discover causal effects overlooked by classical Granger and Schreiber causality approaches. We showcase the use of CausalXtract to uncover novel causal effects in a tumor-on-chip cellular ecosystem under therapeutically relevant conditions. In particular, we find that cancer-associated fibroblasts directly inhibit cancer cell apoptosis, independently from anticancer treatment. CausalXtract uncovers also multiple antagonistic effects at different time delays. Hence, CausalXtract provides a unique computational tool to interpret live-cell imaging data for a range of fundamental and translational research applications.