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nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

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).

Version: 1.8.24
Depends: R (≥ 2.15.1), rgl (≥ 0.98.1)
Imports: nabor, igraph (≥ 1.3.0), methods, filehash (≥ 2.3), digest, nat.utils (≥ 0.4.2), plyr, yaml
Suggests: Rvcg (≥ 0.17), testthat, httr, XML, knitr, rmarkdown, markdown, MASS, alphashape3d, webshot2
Published: 2024-02-05
DOI: 10.32614/CRAN.package.nat
Author: Gregory Jefferis ORCID iD [aut, cre], James Manton ORCID iD [aut], Dominik Krzeminski ORCID iD [ctb]
Maintainer: Gregory Jefferis <jefferis at gmail.com>
BugReports: https://github.com/natverse/nat/issues
License: GPL-3
URL: https://github.com/natverse/nat, https://natverse.org/
NeedsCompilation: no
Citation: nat citation info
Materials: README NEWS
CRAN checks: nat results

Documentation:

Reference manual: nat.pdf
Vignettes: Installation Details
Introduction to neurons and neuronlists

Downloads:

Package source: nat_1.8.24.tar.gz
Windows binaries: r-devel: nat_1.8.24.zip, r-release: nat_1.8.24.zip, r-oldrel: nat_1.8.24.zip
macOS binaries: r-release (arm64): nat_1.8.24.tgz, r-oldrel (arm64): nat_1.8.24.tgz, r-release (x86_64): nat_1.8.24.tgz, r-oldrel (x86_64): nat_1.8.24.tgz
Old sources: nat archive

Reverse dependencies:

Reverse depends: nat.nblast, nat.templatebrains
Reverse suggests: BloodCancerMultiOmics2017, RIA

Linking:

Please use the canonical form https://CRAN.R-project.org/package=nat to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.