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).

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Description file content

Package
nat
Type
Package
Title
NeuroAnatomy Toolbox for Analysis of 3D Image Data
Version
1.8.11
URL
BugReports
https://github.com/jefferis/nat/issues
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 but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
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
License
GPL-3
LazyData
yes
Collate
'alphashape3d.R' 'amiralandmarks-io.R' 'amiramesh-io.R' 'cmtk-reformat.R' 'cmtk.R' 'cmtk_geometry.R' 'cmtk_io.R' 'cmtkreg.R' 'coordinates.R' 'dist3D_Segment_to_Segment.R' 'neuron.R' 'dotprops.R' 'graph-nodes.R' 'hxsurf.R' 'im3d.R' 'nat-data.R' 'nat-package.R' 'ndigest.R' 'neuron-io-amira.R' 'neuron-io-fiji.R' 'neuron-io-neuroml.R' 'neuron-io.R' 'neuron-plot.R' 'neuronlist.R' 'neuronlist_interactive_3d.R' 'neuronlist_sets.R' 'neuronlistfh.R' 'ngraph.R' 'nrrd-io.R' 'pop3d.R' 'potential_synapses.R' 'reglist.R' 'seglist.R' 'summary.R' 'utils.R' 'vaa3draw-io.R' 'vtk-io.R' 'xform.R' 'xformimage.R' 'xformpoints.R' 'zzz.R'
RoxygenNote
6.0.1
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2017-11-10 22:47:36 UTC; jefferis
Author
Gregory Jefferis [aut, cre], James Manton [aut]
Maintainer
Gregory Jefferis
Repository
CRAN
Date/Publication
2017-11-12 17:09:05 UTC

install.packages('nat')

1.8.11

a year ago

https://github.com/jefferis/nat

Gregory Jefferis

GPL-3

Depends on

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

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