nat: NeuroAnatomy Toolbox

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:

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("natverse/nat")

Help

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

• For installation issues, see the Installation vignette
• Start with the overview package documentation (?nat in R)
• Thematically organised function reference documentation
• nat.examples sample code
• nat-user Google group - we normally respond promptly and you will also be helping future users.

Problems

If you think that you have found a bug

• Install the development version of nat using devtools (see above)
• Check the github issues and
  • file a bug report if this seems to be a new problem
  • comment on an existing bug report
• Write to the nat-user list for help.

Thanks for your interest in nat!