jefferis/ NAT: Wrapper for informal neuroanatomy AnalysisSuite codebase

This package is a thin wrapper around the AnalysisSuite ( bundle of R code that I have been using for a number of years to analyse and visualise 3D biological image data, especially traced neurons. The idea is that this will immediately make it rather easier to install AnalysisSuite and that over time it should be possible to migrate many of the AnalysisSuite functions (currently in a loose bundle of R source code files and associated data) into formal R packages. AnalysisSuite provides functions to read/write a variety of 3D image formats including Amira, NRRD and Biorad PIC and can interact with the CMTK and IRTK image registration suites. There is read/write functionality for neuron tracings including SWC, Amiramesh (lineset and skeletonize), Neurolucida ASC. These data can then be visualised (including in 3D via rgl) or analysed including applying calculated registrations from image data to neuron tracings. There is also some recent functionality for representing image data for neurons that have been skeletonised but not formally traced. This representation also allows morphological comparison with neurons including searches/clustering.

Getting started

Package details

AuthorGreg Jefferis
MaintainerGreg Jefferis <>
LicenseGPL (>= 2)
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
jefferis/ documentation built on May 19, 2019, 3:06 a.m.