Other packages > Find by keyword >

nat  

NeuroAnatomy Toolbox for Analysis of 3D Image Data
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", "1.8.25")



Attach the package and use:
library("nat")
Maintained by
Gregory Jefferis
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-02-04
Latest Update: 2025-09-03
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 1.8.25, https://cran.r-project.org/web/packages/nat. Accessed 04 Jun. 2026.
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), 1.8.24 (2024-02-05 19:30)
Other packages that cited nat R package
View nat citation profile
Other R packages that nat depends, imports, suggests or enhances
Complete documentation for nat
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

phers  
Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and ...
Download / Learn more Package Citations See dependency  
murphydiagram  
Murphy Diagrams for Forecast Comparisons
Data and code for the paper by Ehm, Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Con ...
Download / Learn more Package Citations See dependency  
AMPLE  
Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. ...
Download / Learn more Package Citations See dependency  
shinybusy  
Busy Indicators and Notifications for 'Shiny' Applications
Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the ...
Download / Learn more Package Citations See dependency  
crplyr  
A 'dplyr' Interface for Crunch
In order to facilitate analysis of datasets hosted on the Crunch data platform ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA