Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite
(see https://github.com/jefferis/nat.as) bundle of R code that we have
image data, especially traced neurons. The nat package is considerably
cleaner, properly documented and provides all of the core functionality of
nat.as / 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
Imports: nabor, igraph, methods, filehash, digest, nat.utils (>=

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
neurons including searches and clustering (via the 'nat.nblast' extension

'dotprops.R' 'graph-nodes.R' 'hxsurf.R' 'im3d.R' 'nat-data.R'

person("Gregory", "Jefferis", , "jefferis@gmail.com", role = c("aut", "cre")),
person("James", "Manton", role = c("aut"))
Imports: nabor, igraph (>= 0.7.1), methods, filehash, digest, nat.utils
Suggests: Rvcg (>= 0.17), testthat, httr, XML, knitr, rmarkdown, MASS,
'neuron.R' 'dotprops.R' 'graph-nodes.R' 'hxsurf.R' 'im3d.R'
'summary.R' 'utils.R' 'vaa3draw-io.R' 'vtk-io.R' 'xform.R'