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

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 natvers...

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Bibliographic Details
Published inbioRxiv
Main Authors Bates, Alexander S, Manton, James D, Jagannathan, Sridhar R, Costa, Marta, Schlegel, Philipp, Rohlfing, Torsten, Gregory S X E Jefferis
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 07.11.2019
Subjects
Anatomy
Brain
Brain architecture
Brain mapping
Cerebral hemispheres
Data banks
Genomes
Insects
Invertebrates
Nomenclature
Species
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Summary: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
DOI:10.1101/006353