{"id":13716510,"url":"https://github.com/natverse/nat","last_synced_at":"2025-10-22T06:20:10.904Z","repository":{"id":2423580,"uuid":"15578625","full_name":"natverse/nat","owner":"natverse","description":"NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single 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nat: NeuroAnatomy Toolbox \n\n\u003cimg src=\"man/figures/logo.svg\" align=\"right\" width=\"120px\" /\u003e\n\u003cimg src=\"man/figures/hex-natverse_logo.png\" align=\"right\" width=\"120px\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.org/)\n[![DOI](https://img.shields.io/badge/doi-10.5281%2Fzenodo.10171-blue.svg)](http://dx.doi.org/10.5281/zenodo.10171) \n[![Release Version](https://img.shields.io/github/release/natverse/nat.svg)](https://github.com/natverse/nat/releases/latest) \n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/nat)](https://cran.r-project.org/package=nat) \n[![R-CMD-check](https://github.com/natverse/nat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/natverse/nat/actions/workflows/R-CMD-check.yaml)\n[![Coverage Status](https://codecov.io/gh/natverse/nat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/natverse/nat)\n[![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.org//nat/reference/)\n[![Downloads](http://cranlogs.r-pkg.org/badges/nat?color=brightgreen)](https://www.r-pkg.org:443/pkg/nat)\n\u003c!-- badges: end --\u003e\n\nAn R package for the (3D) visualisation and analysis of biological image data, especially tracings of\nsingle neurons. **nat** is the core package of a wider suite of neuroanatomy \ntools introduced at http://natverse.github.io. **nat** (and its [ancestors](https://github.com/jefferis/AnalysisSuite))\nhave been used in a number of papers from our group including:\n\n[![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)\n[![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)\n[\u003cimg src=\"https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fnature10428/MediaObjects/41586_2011_Article_BFnature10428_Fig4_HTML.jpg\" alt=\"Food and Pheromone Integration\" style=\"height: 200px;\"/\u003e](http://dx.doi.org/10.1038/nature10428)\n[\u003cimg src=\"http://www2.mrc-lmb.cam.ac.uk/wordpress/wp-content/uploads/Switch-altered_jefferis.jpg\" alt=\"Cell 2013 Abstract\" style=\"height: 200px;\"/\u003e](http://dx.doi.org/10.1016/j.cell.2013.11.025)\n[![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)\n\n\n## Quick Start\n\nFor the impatient ...\n\n```r\n# install\ninstall.packages(\"nat\")\n# use\nlibrary(nat)\n\n# plot some test data (?kcs20 for details)\n# Drosophila Kenyon cells processed from raw data formerly available at\n# flycircuit.tw\nhead(kcs20)\nopen3d()\nplot3d(kcs20, col=type)\n# get help\n?nat\n```\n\n## Installation\n\nA confirmed stable version of **nat** can be installed from CRAN. \n\n```r\ninstall.packages(\"nat\")\n````\n\nHowever, **nat** remains under quite active development, so if you will be \nusing **nat** extensively, we generally\nrecommend installing the latest development version directly from github using\nthe [devtools](https://cran.r-project.org/package=devtools) package.\n\n```r\n# install devtools if required\nif (!requireNamespace(\"devtools\")) install.packages(\"devtools\")\n# then install nat\ndevtools::install_github(\"natverse/nat\")\n\n```\n## Learn\n\nTo get an idea of what **nat** can do:\n\n* Skim through the Articles listed at https://natverse.org//nat/\n* Take a look at the [R Markdown](https://rmarkdown.rstudio.com/) reports used \n  to generate the [figures for our NBLAST paper](https://flybrain.mrc-lmb.cam.ac.uk/si/nblast/www/paper/).\n\nWhen you're ready to learn more:\n\n* Read the [overview package documentation](https://natverse.org//nat/reference/nat-package.html)\n  (`?nat` in R)\n* Read the [Introduction to neurons](https://natverse.org//nat/articles/neurons-intro.html) article\n* Check out the thematically organised [function reference documentation](https://natverse.org//nat/reference/). \n  * Most help pages include examples.\n* Try out sample code:\n  - [nat.examples](https://github.com/natverse/nat.examples) has detailed \n    examples for data sets from a range of model organisms and techniques\n  - [frulhns](https://github.com/jefferis/frulhns) analysis of sexually dimorphic circuits\n  - [NBLAST figures](https://github.com/jefferislab/NBLAST_figures/)\n\n## Help\nIf you want some help using **nat**:\n\n* For installation issues, see the [Installation vignette](https://natverse.org//nat/articles/Installation.html)\n* Contact [nat-user](https://groups.google.com/forum/#!forum/nat-user) Google group - \n  we normally respond promptly and you will also be helping future users.\n\nIf you think that you have found a bug:\n\n* Install the development version of nat using devtools (see above) and see if \n  that helps.\n* Check the [github issues](https://github.com/natverse/nat/issues?q=is%3Aissue) and \n  - [file a  bug report](https://github.com/natverse/nat/issues/new) if this seems to be a new problem\n  - comment on an existing bug report \n\nThanks for your interest in **nat**!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnatverse%2Fnat","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnatverse%2Fnat","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnatverse%2Fnat/lists"}