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https://github.com/natverse/nat

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

3d cran image-analysis neuroanatomy neuroanatomy-toolbox neuron neuron-morphology neuroscience r visualisation

Last synced: 2 months ago
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NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

Host: GitHub
URL: https://github.com/natverse/nat
Owner: natverse
Created: 2014-01-02T07:54:01.000Z (over 10 years ago)
Default Branch: master
Last Pushed: 2024-02-18T11:01:13.000Z (5 months ago)
Last Synced: 2024-05-06T00:03:12.439Z (2 months ago)
Topics: 3d, cran, image-analysis, neuroanatomy, neuroanatomy-toolbox, neuron, neuron-morphology, neuroscience, r, visualisation
Language: R
Homepage: https://natverse.github.io/nat/
Size: 60.6 MB
Stars: 60
Watchers: 17
Forks: 25
Open Issues: 61
Metadata Files:
- Readme: README.md
- Code of conduct: CODE_OF_CONDUCT.md

Lists

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

README

        # nat: NeuroAnatomy Toolbox 





[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.org/)

[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.10171-blue.svg)](http://dx.doi.org/10.5281/zenodo.10171) 

[![Release Version](https://img.shields.io/github/release/natverse/nat.svg)](https://github.com/natverse/nat/releases/latest) 

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/nat)](https://cran.r-project.org/package=nat) 

[![Build status](https://github.com/natverse/nat/workflows/R-CMD-check/badge.svg)](https://github.com/natverse/nat/actions)

[![Coverage Status](https://codecov.io/gh/natverse/nat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/natverse/nat)

[![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.org//nat/reference/)

[![Downloads](http://cranlogs.r-pkg.org/badges/nat?color=brightgreen)](https://www.r-pkg.org:443/pkg/nat)

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](https://github.com/jefferis/AnalysisSuite))

have been used in a number of papers from our group including:

[![Cell 2007 Cover](http://www.cell.com/cms/attachment/602399/4753939/cov200h.gif "Olfactory Projection Neuron Mapping")](http://dx.doi.org/10.1016/j.cell.2007.01.040)

[![CB 2010 Cover](http://www.cell.com/cms/attachment/612001/4900537/cov200h.gif "fruitless Circuit Mapping")](http://dx.doi.org/10.1016/j.cub.2010.07.045)

[](http://dx.doi.org/10.1038/nature10428)

[](http://dx.doi.org/10.1016/j.cell.2013.11.025)

[![Neuron 2016](http://www2.mrc-lmb.cam.ac.uk/wordpress/wp-content/uploads/P1Clustering_200_sq_crop-215x215.jpg "NBLAST")](http://dx.doi.org/10.1016/j.neuron.2016.06.012)

## Quick Start

For the impatient ...

```r

# 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. 

```r

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](https://rmarkdown.rstudio.com/) reports used 

  to generate the [figures for our NBLAST paper](http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/paper/).

When you're ready to learn more:

* Read the [overview package documentation](https://natverse.org//nat/reference/nat-package.html)

  (`?nat` in R)

* Read the [Introduction to neurons](https://natverse.org//nat/articles/neurons-intro.html) article

* Check out the thematically organised [function reference documentation](https://natverse.org//nat/reference/). 

  * Most help pages include examples.

* Try out sample code:

  - [nat.examples](https://github.com/natverse/nat.examples) has detailed 

    examples for data sets from a range of model organisms and techniques

  - [frulhns](https://github.com/jefferis/frulhns) analysis of sexually dimorphic circuits

  - [NBLAST figures](https://github.com/jefferislab/NBLAST_figures/)

## Help

If you want some help using **nat**:

* For installation issues, see the [Installation vignette](https://natverse.org//nat/articles/Installation.html)

* Contact [nat-user](https://groups.google.com/forum/#!forum/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](https://github.com/natverse/nat/issues?q=is%3Aissue) and 

  - [file a  bug report](https://github.com/natverse/nat/issues/new) if this seems to be a new problem

  - comment on an existing bug report 

Thanks for your interest in **nat**!