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The natverse: a versatile computational toolbox to combine and analyse neuroanatomical data

View ORCID ProfileAlexander S. Bates, View ORCID ProfileJames D. Manton, View ORCID ProfileSridhar R. Jagannathan, View ORCID ProfileMarta Costa, View ORCID ProfilePhilipp Schlegel, View ORCID ProfileTorsten Rohlfing, View ORCID ProfileGregory S. X. E. Jefferis
doi: https://doi.org/10.1101/006353
Alexander S. Bates
1MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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James D. Manton
1MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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Sridhar R. Jagannathan
2Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
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Marta Costa
1MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
2Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
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Philipp Schlegel
2Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
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Torsten Rohlfing
3SRI International, Neuroscience Program, Center for Health Sciences, Menlo Park, CA, USA
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Gregory S. X. E. Jefferis
1MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
2Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
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  • For correspondence: jefferis@mrc-lmb.cam.ac.uk
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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, clustering and graph-theoretic analysis of neuronal branching. Unlike most tools, the natverse enables comparison of morphology and connectivity across many neurons 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.

Footnotes

  • The paper has been extended from the 2014 version 1) to cover multimodal bridging registrations between light and electron microscopy data, 2) additional support for analysis of connectomics data 3) description of the full suite of computational neuroscience tools that we offer (aka the natverse) 4) additional examples from a range of species including diverse insects, fish and mice 5) in tandem with this, there have been many updates to the tools and documentation now available at natverse.org 6) examples of bridging registrations across different Drosophilid species have been removed from this revision.

  • https://natverse.github.io

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 07, 2019.
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The natverse: a versatile computational toolbox to combine and analyse neuroanatomical data
Alexander S. Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory S. X. E. Jefferis
bioRxiv 006353; doi: https://doi.org/10.1101/006353
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The natverse: a versatile computational toolbox to combine and analyse neuroanatomical data
Alexander S. Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory S. X. E. Jefferis
bioRxiv 006353; doi: https://doi.org/10.1101/006353

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