nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite (see bundle of R code that we have been using for a number of years to analyse and visualise 3D biological image data, especially traced neurons. The nat package is considerably cleaner, properly documented and provides all of the core functionality of / AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats and read surfaces in Amira's 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. The package also has a simple representation for neurons that have been subjected to a 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the nat.nblast extension package).

Version: 1.6.4
Depends: R (≥ 2.15.1), rgl
Imports: nabor, igraph, methods, filehash, digest, nat.utils (≥ 0.4.2), plyr, yaml
Suggests: Rvcg, testthat, httr, XML
Published: 2015-02-10
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis at>
License: GPL-3
NeedsCompilation: no
Citation: nat citation info
Materials: README NEWS
CRAN checks: nat results


Reference manual: nat.pdf
Package source: nat_1.6.4.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X Snow Leopard binaries: r-release: not available, r-oldrel: nat_1.4.10.tgz
OS X Mavericks binaries: r-release: nat_1.6.4.tgz
Old sources: nat archive

Reverse dependencies:

Reverse depends: nat.nblast, nat.templatebrains