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nat: NeuroAnatomy Toolbox

An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://natverse.github.io. nat (and its ancestors) have been used in a number of papers from our group including:

Quick Start

For the impatient ...

# install
install.packages("nat")
# use
library(nat)

# plot some test data (?kcs20 for details)
# Drosophila Kenyon cells processed from raw data at http://flycircuit.tw
head(kcs20)
open3d()
plot3d(kcs20, col=type)
# get help
?nat

Installation

A confirmed stable version of nat can be installed from CRAN.

install.packages("nat")

However, nat remains under quite active development, so if you will be using nat extensively, we generally recommend installing the latest development version directly from github using the devtools package.

# install devtools if required
if (!requireNamespace("devtools")) install.packages("devtools")
# then install nat
devtools::install_github("natverse/nat")

Learn

To get an idea of what nat can do:

When you're ready to learn more:

Help

If you want some help using nat:

  • For installation issues, see the Installation vignette
  • Contact nat-user Google group - we normally respond promptly and you will also be helping future users.

If you think that you have found a bug:

  • Install the development version of nat using devtools (see above) and see if that helps.
  • Check the github issues and

Thanks for your interest in nat!

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Version

Install

install.packages('nat')

Monthly Downloads

585

Version

1.8.24

License

GPL-3

Issues

Pull Requests

Stars

Forks

Last Published

February 5th, 2024

Functions in nat (1.8.24)

as.hxsurf

Convert an object to a nat hxsurf object
as.mesh3d

Convert an object to an rgl mesh3d
as.neuronlist.neuronlistfh

convert neuronlistfh to a regular (in memory) neuronlist
clampmax

Return function that finds maximum of its inputs within a clamping range
cmtk.extract_affine

Extract affine registration from CMTK registration file or in-memory list
c.neuronlist

Combine multiple neuronlists into a single list
cmtk.dof2mat

Convert CMTK registration to homogeneous affine matrix with dof2mat
cmtk.bindir

Return path to directory containing CMTK binaries
cmtk.call

Utility function to create and run calls to CMTK commandline tools
boundingbox

Get the bounding box of an im3d volume or other compatible object
as.neuronlist

Make a list of neurons that can be used for coordinate plotting/analysis
*.dotprops

Arithmetic for dotprops objects
cmtk.version

Return cmtk version or test for presence of at least a specific version
coord2ind

Find 1D indices into a 3D image given spatial coordinates
cmtk.mat2dof

Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration
cmtk.statistics

Calculate image statistics for a nrrd or other CMTK compatible file
cmtk.reformatx

Reformat an image with a CMTK registration using the reformatx tool
cmtkparams2affmat

Compose homogeneous affine matrix from CMTK registration parameters
flip

Flip an array, matrix or vector about an axis
as.data.frame.neuronlist

Get or set the attached data.frame of a neuronlist
im3d

Construct an im3d object representing 3D image data, densities etc
im3d-io

Read/Write calibrated 3D blocks of image data
find.soma

Find neurons with soma inside 3D selection box (usually drawn in rgl window)
is.amiramesh

Check if file is amiramesh format
cmtk.targetvolume

Defines a target volume for a CMTK reformatx operation
find.neuron

Find neurons within a 3D selection box (usually drawn in rgl window)
imscalebar

Make a scalebar to accompany an image.im3d plot
fileformats

Set or return list of registered file formats that we can read
dotprops

dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
imslice

Slice out a 3D subarray (or 2d matrix) from a 3D image array
cmtkreg

Create and test cmtkreg objects that specify path to a CMTK registration
is.fijitraces

Check whether a file is in Fiji's simple neurite tracer format
mask

Mask an object, typically to produce a copy with some values zeroed out
is.neuroml

Check whether a file is in NeuroML format
image.im3d

Method to plot spatially calibrated image arrays
imexpand.grid

Convert locations of im3d voxel grid into XYZ coordinates
materials

Extract or set the materials for an object
is.im3d

Test if an object is of class im3d
mirror

Mirror 3D object about a given axis, optionally using a warping registration
kcs20

List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects
nat-package

Analyse 3D biological image data especially neurons
cmtkreglist

Make in-memory CMTK registration list from affine matrix or CMTK parameters
ndigest

Calculated normalised digest value for an object
graph.nodes

Return root, end, or branchpoints of an igraph object
is.nrrd

Check if a file is a NRRD file
ngraph

ngraph: a graph to encode a neuron's connectivity
is.neuronlist

Test objects of neuronlist class to store multiple neurons
im3d-coords

Interconvert pixel and physical coordinates
is.vaa3draw

Check if a file is in the raw image format used by Hanchuan Peng's Vaa3D
is.swc

Test if a file is an SWC format neuron
ind2coord

Find XYZ coords corresponding to 1D indices into a 3D image
intersect

Find the intersection of two collections of objects
*.neuronlist

Arithmetic for neuron coordinates applied to neuronlists
neuronlist-dataframe-methods

Methods for working with the dataframe attached to a neuronlist
pan3d

Some useful extensions / changes to rgl defaults
nlapply

lapply and mapply for neuronlists (with optional parallelisation)
plot.neuron

Plot a 2D projection of a neuron
plot3d.boundingbox

Plot a bounding box in 3D
plot3d.cmtkreg

Plot the domain of a CMTK registration
*.neuron

Arithmetic for neuron coordinates
neuronlist

Create a neuronlist from zero or more neurons
nopen3d

Open customised rgl window
plot3d

plot3d methods for different nat objects
plot.neuronlist

2D plots of the elements in a neuronlist, optionally using a subset expression
nlscan

Scan through a set of neurons, individually plotting each one in 3D
plot3d.neuron

Plot neurons in 3D using rgl library
plot3d.neuronlist

3D plots of the elements in a neuronlist, optionally using a subset expression
plot3d.hxsurf

Plot amira surface objects in 3D using rgl
plot3d.dotprops

3D plots of dotprops objects using rgl package
read.morphml

Return parsed XML or R list versions of a NeuroML file
read.neuron

Read a single neuron from a file
prune_vertices

Prune selected vertices or edges from a neuron
npop3d

Remove plotted neurons or other 3D objects
prune_strahler

Prune a neuron by removing segments with a given Strahler order
normalise_swc

Normalise an SWC format block of neuron morphology data
prune

prune an object by removing points near (or far) from a target object
projection

Make 2D (orthogonal) projection of 3D image data
neuron

neuron: class to represent traced neurons
read.neuron.neuroml

Read one or more neurons from a NeuroML v1 file
read.neuron.fiji

Read a neuron saved by Fiji's Simple Neurite Tracer Plugin
read.hxsurf

Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object
read.landmarks

Generic functions to read/write landmarks in any supported format
read.cmtkreg

Read a CMTK format registration
pointsinside

Find which points of an object are inside a surface
setdiff

Find the (asymmetric) difference between two collections of objects
potential_synapses

Calculate number of potential synapses between two neurons
read.cmtk

Read CMTK TypedStream file to a list in memory
nview3d

Set the 3D viewpoint of an RGL window using anatomical terms
origin

Return the space origin of a 3D image object
read.neuron.swc

Read a neuron in swc file format
read.neuronlistfh

Read a local, or remote, neuronlistfh object saved to a file.
union

Find the union of two collections of objects
unmask

Make im3d image array containing values at locations defined by a mask
nrrd.voxdims

Return voxel dimensions (by default absolute voxel dimensions)
neuronlistfh

neuronlistfh - List of neurons loaded on demand from disk or remote website
nvertices

Find the number of vertices in an object (or each element of a neuronlist)
read.neurons

Read one or more neurons from file to a neuronlist in memory
seglengths

Calculate length of all segments in neuron
subset.neuron

Subset neuron by keeping only vertices that match given conditions
subset.neuronlist

Subset neuronlist returning either new neuronlist or names of chosen neurons
read.nrrd

Read nrrd file into an array in memory
seglist

Make/convert neuron connectivity information into a seglist object
simplify_reglist

Simplify a registration list
rootpoints

Return the root or branch points of a neuron or graph
read.vaa3draw

Read Vaa3d format image data
xform

Transform the 3D location of objects such as neurons
strahler_order

Find the Strahler order of each point in a neuron
reglist

A simple wrapper class for multiple transformations
[.neuronlistfh

Extract from neuronlistfh object or its attached data.frame
write.cmtk

Write a suitable list to a CMTK TypedStream file on disk
write.cmtkreg

Write out CMTK registration list to folder
xformimage

Transform image files using a registration or affine matrix
voxdims

Return voxel dimensions of an object
subset.dotprops

Subset points in dotprops object that match given conditions
write.amiramesh

Write a 3D data object to an amiramesh format file
write.hxsurf

Write Amira surface (aka HxSurface or HyperSurface) into .surf file.
seglist2swc

Recalculate Neurons's SWCData using SegList and point information
scale.neuron

Scale and centre neuron 3D coordinates
write.neuron

Write out a neuron in any of the file formats we know about
resample

Resample an object with a new spacing
subset

Subset methods for different nat objects
xformpoints

Transform 3D points using a registration, affine matrix or function
sub2ind

Find 1D index given n-dimensional indices
smooth_neuron

Smooth the 3D coordinates of a neuron skeleton
write.neurons

Write neurons from a neuronlist object to individual files, or a zip archive
spine

Compute the longest path (aka spine or backbone) of a neuron
write.neuronlistfh

Write out a neuronlistfh object to an RDS file
remotesync

Synchronise a remote object
write.nrrd

Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.
segmentgraph

Return a simplified segment graph for a neuron
write.vtk

Write object to VTK file
summary.neuronlist

Summary statistics for neurons (e.g. cable length, number of nodes)
subset.hxsurf

Subset hxsurf object to specified regions
threshold

Threshold an object, typically to produce a mask
xyzmatrix

Get and assign coordinates for classes containing 3D vertex data
read.amiramesh

Read AmiraMesh data in binary or ascii format
affmat2cmtkparams

Decompose homogeneous affine matrix to CMTK registration parameters
as.im3d

Convert a suitable object to an im3d object.
all.equal.dotprops

all.equal method tailored to dotprops objects
all.equal.im3d

Check equality on data and key attributes of im3d objects
amiratype

Return the type of an amiramesh file on disk or a parsed header
Cell07PNs

Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007
MBL.surf

Surface object (hxsurf) for the left mushroom body in FCWB template space
all.equal.neuron

Check equality on key fields of neuron object