nat: nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

This package is a reboot of the AnalysisSuite (https://github.com/jefferis/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. AnalysisSuite is most easily installed using the nat.as package presently available at https://github.com/jefferis/nat.as. The nat package is considerably cleaner but currently provides only a subset of the full functionality of nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira formats and read surfaces in Amira's hxsurf format. Traced neurons can be imported from and written to SWC and Amira LineSet and SkeletonGraph formats. These data can then be visualised in 3D via rgl, manipulated including applying calculated registrations, e.g. using the CMTK registration suite, and analysed. The package also has a simple representation for neurons that have been subjected to a 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering.

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