Package: nat
Type: Package
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Version: 1.11.0
Authors@R: c(
    person("Gregory","Jefferis", email="jefferis@gmail.com", 
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0587-9355")),
    person("James", "Manton", role = c("aut"), comment = c(ORCID = "0000-0001-9260-3156")),
    person("Sridhar", "Jagannathan", role = c("aut"), comment = c(ORCID = "0000-0002-2078-1145")),
    person("Dominik", "Krzeminski", role = c("ctb"), comment = c(ORCID = "0000-0003-4568-0583")),
    person("Philipp", "Schlegel", role = c("ctb"), comment = c(ORCID = "0000-0002-5633-1314")),
    person("Duncan", "Murdoch", role = c("ctb"), email = 'murdoch.duncan@gmail.com')
    )
URL: https://github.com/natverse/nat, https://natverse.org/
BugReports: https://github.com/natverse/nat/issues
Description: NeuroAnatomy Toolbox (nat) enables analysis and
        visualisation of 3D biological image data, especially traced
        neurons. Reads and writes 3D images in NRRD and 'Amira'
        AmiraMesh formats and reads surfaces in 'Amira' hxsurf format.
        Traced neurons can be imported from and written to SWC and
        'Amira' LineSet and SkeletonGraph formats. These data can then
        be visualised in 3D via 'rgl', manipulated including applying
        calculated registrations, e.g. using the 'CMTK' registration
        suite, and analysed. There is also a simple representation for
        neurons that have been subjected to 3D skeletonisation but not
        formally traced; this allows morphological comparison between
        neurons including searches and clustering (via the 'nat.nblast'
        extension package).
Depends: R (>= 2.15.1), rgl (>= 0.98.1)
Imports: nabor, igraph (>= 1.0), methods, filehash (>= 2.3), digest,
        nat.utils (>= 0.4.2), plyr, yaml, progress, checkmate, stringr,
        pbapply, zip
Suggests: spelling, Rvcg (>= 0.17), testthat, foreach, httr, XML,
        knitr, rmarkdown, MASS, alphashape3d, Morpho, plotly, readobj,
        brotli, jsonlite
Enhances: natcpp
License: GPL-3
LazyData: yes
Collate: 'alphashape3d.R' 'amiralandmarks-io.R' 'amiramesh-io.R'
        'brotli.R' 'cmtk-reformat.R' 'cmtk.R' 'cmtk_geometry.R'
        'cmtk_io.R' 'cmtkreg.R' 'coordinates.R'
        'dist3D_Segment_to_Segment.R' 'neuron.R' 'dotprops.R'
        'geometry.R' 'graph-nodes.R' 'hxsurf.R' 'im3d.R'
        'interactive.R' 'morphometry.R' 'nat-data.R' 'nat-package.R'
        'ndigest.R' 'neuron-io-amira.R' 'neuron-io-fiji.R'
        'neuron-io-neuroml.R' 'neuron-io.R' 'neuron-mesh.R'
        'neuron-plot.R' 'neuronlist.R' 'neuronlist_interactive_3d.R'
        'neuronlist_sets.R' 'neuronlistfh.R' 'neuronlistz.R' 'ngraph.R'
        'nrrd-io.R' 'pop3d.R' 'potential_synapses.R' 'reglist.R'
        'seglist.R' 'summary.R' 'utils.R' 'vaa3draw-io.R' 'vtk-io.R'
        'wire3d.R' 'xform.R' 'xformimage.R' 'xformpoints.R'
        'xyzmatrix.R' 'zzz.R'
RoxygenNote: 7.3.3
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-GB
Config/pak/sysreqs: cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev
        make texlive libicu-dev libpng-dev libuv1-dev libxml2-dev
        libgl1-mesa-dev zlib1g-dev
Repository: https://natverse.r-universe.dev
Date/Publication: 2026-06-12 06:04:15 UTC
RemoteUrl: https://github.com/natverse/nat
RemoteRef: HEAD
RemoteSha: ccf69b118f3475130748bafb1b087c8aca30a6ce
NeedsCompilation: no
Packaged: 2026-06-12 08:11:06 UTC; root
Author: Gregory Jefferis [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0587-9355>),
  James Manton [aut] (ORCID: <https://orcid.org/0000-0001-9260-3156>),
  Sridhar Jagannathan [aut] (ORCID:
    <https://orcid.org/0000-0002-2078-1145>),
  Dominik Krzeminski [ctb] (ORCID:
    <https://orcid.org/0000-0003-4568-0583>),
  Philipp Schlegel [ctb] (ORCID: <https://orcid.org/0000-0002-5633-1314>),
  Duncan Murdoch [ctb]
Maintainer: Gregory Jefferis <jefferis@gmail.com>