NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

README.md

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. nat is the core package of a wider suite of neuroanatomy tools introduced at http://jefferislab.github.io. nat (and its ancestors) have been used in a number of papers from our group including:

Cell 2007 Cover CB 2010 Cover Nature 2011 Cell 2013 Abstract Neuron 2016

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("jefferis/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
    • file a bug report if this seems to be a new problem
    • comment on an existing bug report

Thanks for your interest in nat!