README.md

In natverse/nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

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](https://cran.r-project.org/package=devtools) package.

```r
# 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:

• Skim through the Articles listed at https://natverse.org//nat/
• Take a look at the R Markdown reports used to generate the figures for our NBLAST paper.

When you're ready to learn more:

• Read the overview package documentation (?nat in R)
• Read the Introduction to neurons article
• Check out the thematically organised function reference documentation.
• Most help pages include examples.
• Try out sample code:
• nat.examples has detailed examples for data sets from a range of model organisms and techniques
• frulhns analysis of sexually dimorphic circuits
• NBLAST figures

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!

natverse/nat documentation built on Feb. 19, 2024, 7:19 a.m.