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: 1.8.11
Depends: R (≥ 2.15.1), rgl (≥ 0.98.1)
Imports: nabor, igraph (≥ 0.7.1), methods, filehash, digest, nat.utils (≥ 0.4.2), plyr, yaml
Suggests: Rvcg (≥ 0.17), testthat, httr, XML, knitr, rmarkdown, MASS, alphashape3d
Published: 2017-11-12
Author: Gregory Jefferis [aut, cre], James Manton [aut]
Maintainer: Gregory Jefferis <jefferis at>
License: GPL-3
NeedsCompilation: no
Citation: nat citation info
Materials: README NEWS
CRAN checks: nat results


Reference manual: nat.pdf
Vignettes: Installation Details
Introduction to neurons and neuronlists
Package source: nat_1.8.11.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X binaries: r-release: nat_1.8.11.tgz, r-oldrel: nat_1.8.11.tgz
Old sources: nat archive

Reverse dependencies:

Reverse depends: nat.nblast, nat.templatebrains
Reverse imports: RIA, tcie


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