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nat
View on CRAN: Click
here
Download and install nat package within the R console
Install from CRAN:
install.packages("nat")
Install from Github:
library("remotes")
install_github("cran/nat")
Install by package version:
library("remotes")
install_version("nat", "1.8.24")
Attach the package and use:
library("nat")
Maintained by
Gregory Jefferis
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-02-07
Latest Update: 2023-08-25
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).
How to cite:
Gregory Jefferis (2014). nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data. R package version 1.8.24, https://cran.r-project.org/web/packages/nat
Previous versions and publish date:
1.0.1 (2014-02-07 13:56), 1.0 (2014-02-04 10:35), 1.4.5 (2014-03-28 16:12), 1.4.6 (2014-03-30 17:39), 1.4.10 (2014-04-30 07:49), 1.5.12 (2014-08-21 19:06), 1.6.4 (2015-02-10 00:24), 1.6.6 (2015-05-28 01:55), 1.7.0 (2015-07-01 14:41), 1.8.1 (2015-12-30 23:24), 1.8.4 (2016-07-18 16:15), 1.8.7 (2016-11-10 08:19), 1.8.9 (2017-05-08 16:00), 1.8.11 (2017-11-12 18:09), 1.8.13 (2019-08-22 17:30), 1.8.14 (2020-02-07 07:30), 1.8.16 (2020-09-22 18:40), 1.8.17 (2021-09-03 18:00), 1.8.18 (2021-09-06 15:40), 1.8.19 (2022-04-06 13:50), 1.8.21 (2023-01-29 00:50), 1.8.22 (2023-06-07 16:50), 1.8.23 (2023-08-25 17:40)
Other packages that cited nat R package
View nat citation profile
Other R packages that nat depends,
imports, suggests or enhances
Functions, R codes and Examples using
the nat R package
Some associated functions: Cell07PNs . MBL.surf . affmat2cmtkparams . all.equal.dotprops . all.equal.im3d . all.equal.neuron . amiramesh-io . amiratype . as.hxsurf . as.im3d . as.mesh3d . as.neuronlist.neuronlistfh . as.neuronlist . boundingbox . c.neuronlist . clampmax . cmtk.bindir . cmtk.call . cmtk.dof2mat . cmtk.extract_affine . cmtk.mat2dof . cmtk.reformatx . cmtk.statistics . cmtk.targetvolume . cmtk.version . cmtkparams2affmat . cmtkreg . cmtkreglist . coord2ind . dotprops-arithmetic . dotprops . fileformats . find.neuron . find.soma . flip . get-set-neuronlist-data.frame . graph.nodes . im3d-coords . im3d-io . im3d . image.im3d . imexpand.grid . imscalebar . imslice . ind2coord . intersect . is.amiramesh . is.fijitraces . is.im3d . is.neuroml . is.neuronlist . is.nrrd . is.swc . is.vaa3draw . kcs20 . mask . materials . mirror . nat-package . ndigest . neuron-arithmetic . neuron . neuronlist-arithmetic . neuronlist-dataframe-methods . neuronlist . neuronlistfh . ngraph . nlapply . nlscan . nopen3d . normalise_swc . npop3d . nrrd.voxdims . nvertices . nview3d . origin . pan3d . plot.neuron . plot.neuronlist . plot3d.boundingbox . plot3d.cmtkreg . plot3d.dotprops . plot3d.hxsurf . plot3d.neuron . plot3d.neuronlist . plot3d . pointsinside . potential_synapses . projection . prune . prune_strahler . prune_vertices . read.cmtk . read.cmtkreg . read.hxsurf . read.landmarks . read.morphml . read.neuron.fiji . read.neuron.neuroml . read.neuron . read.neuron.swc . read.neuronlistfh . read.neurons . read.nrrd . read.vaa3draw . reglist . remotesync . resample . rootpoints . scale.neuron . seglengths . seglist . seglist2swc . segmentgraph . setdiff . simplify_reglist . smooth_neuron . spine . strahler_order . sub-.neuronlistfh . sub2ind . subset.dotprops . subset.hxsurf . subset.neuron . subset.neuronlist . subset . summary.neuron . threshold . union . unmask . voxdims . write.amiramesh . write.cmtk . write.cmtkreg . write.hxsurf . write.neuron . write.neuronlistfh . write.neurons . write.nrrd . write.vtk . xform . xformimage . xformpoints . xyzmatrix .
Some associated R codes: 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 . 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 . neuron.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 . Full nat package functions and examples
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