nat: NeuroAnatomy Toolbox

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An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. See nat.examples and frulhns for sample code.

nat is a cleaned up version of code that has been used in a number of papers from our group including:

Cell 2007 Cover CB 2010 Cover Nature 2011 Cell 2013 Abstract

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 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("jefferis/nat")

Help

If you want some help using nat, then please use the following resources

Problems

If you think that you have found a bug

Thanks for your interest in nat!