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: | 1.8.14 |
Depends: | R (≥ 2.15.1), rgl (≥ 0.98.1) |
Imports: | nabor, igraph (≥ 0.7.1), methods, filehash (≥ 2.3), digest, nat.utils (≥ 0.4.2), plyr, yaml |
Suggests: | Rvcg (≥ 0.17), testthat, httr, XML, knitr, rmarkdown, MASS, alphashape3d |
Published: | 2020-02-07 |
Author: | Gregory Jefferis [aut, cre], James Manton [aut] |
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.github.io |
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_1.8.14.tar.gz |
Windows binaries: | r-devel: nat_1.8.14.zip, r-release: nat_1.8.14.zip, r-oldrel: nat_1.8.14.zip |
macOS binaries: | r-release: nat_1.8.14.tgz, r-oldrel: nat_1.8.14.tgz |
Old sources: | nat archive |
Reverse depends: | nat.nblast, nat.templatebrains |
Reverse imports: | hmgm, RIA |
Reverse suggests: | BloodCancerMultiOmics2017 |
Please use the canonical form https://CRAN.R-project.org/package=nat to link to this page.