James Manton

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).

This package is a port of the MATLAB colourmap functions accompanying the paper M. Geissbuehler and T. Lasser, "How to display data by color schemes compatible with red-green color perception deficiencies," Opt. Express 21, 9862-9874 (2013) to R.

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' 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. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).

Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.