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 06 Mar. 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

openxlsx  
Read, Write and Edit xlsx Files
Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, stylin ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
solitude  
An Implementation of Isolation Forest
Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detecti ...
Download / Learn more Package Citations See dependency  
EMVS  
The Expectation-Maximization Approach to Bayesian Variable Selection
An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization p ...
Download / Learn more Package Citations See dependency  
mlr3viz  
Visualizations for 'mlr3'
Visualization package of the 'mlr3' ecosystem. It features plots for mlr3 objects such as tasks, le ...
Download / Learn more Package Citations See dependency  
lbfgs  
Limited-memory BFGS Optimization
A wrapper built around the libLBFGS optimization library by Naoaki Okazaki. The lbfgs package implem ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,244

Author Associations

26,265

Publication Badges

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