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", "1.8.24")



Attach the package and use:
library("nat")
Maintained by
Gregory Jefferis
[Scholar Profile | Author Map]
First Published: 2014-02-04
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. Accessed 23 Feb. 2025.
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
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
01/2401/2501/2601/2701/2801/2901/3001/3102/0102/0202/0302/0402/0502/0602/0702/0802/0902/1002/1102/1202/1302/1402/1502/1602/1702/1802/1902/2002/21Downloads for nat0102030405060708090TrendBars

Today's Hot Picks in Authors and Packages

seqest  
Sequential Method for Classification and Generalized Estimating Equations Problem
Sequential method to solve the the binary classification problem by Wang (2019) ...
Download / Learn more Package Citations See dependency  
mlma  
Multilevel Mediation Analysis
Do multilevel mediation analysis with generalized additive multilevel models. The analysis method is ...
Download / Learn more Package Citations See dependency  
SSNbayes  
Bayesian Spatio-Temporal Analysis in Stream Networks
Fits Bayesian spatio-temporal models and makes predictions on stream networks using the approach by ...
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  
imdbapi  
Get Movie, Television Data from the 'imdb' Database
Provides API access to the which maintains metadata about movies, games and te ...
Download / Learn more Package Citations See dependency  

23,712

R Packages

205,795

Dependencies

64,332

Author Associations

23,713

Publication Badges

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