natverse
The R toolchain — nat and its companion packages for importing, transforming, comparing and plotting neurons.
The natverse is a collection of interoperable R packages for working with 3D neuroanatomical data. It covers much the same ground as navis and its ecosystem does in Python, so which you reach for is usually decided by what the rest of your analysis is written in rather than by capability.
The pieces you are most likely to want:
nat is the core — reading, manipulating and plotting neurons and surfaces.
nat.templatebrains and nat.flybrains provide the template spaces and the bridging and
mirroring registrations between them, the R counterpart to
flybrains. nat.nblast implements
NBLAST. neuprintr queries neuPrint, and
elmr supports EM–light-microscopy comparison.
Install
install.packages('natmanager')
natmanager::install('core') # nat and the essentials
natmanager::install('natverse') # everything
Transforms need CMTK
The VFB and Jefferis lab registrations that nat.flybrains uses are CMTK transforms, so
applying them needs CMTK installed and its tools on your PATH. nat
locates them with cmtk.bindir(); if that returns nothing, CMTK is either not installed or not
where R can find it.
VFB publishes the same transform set to both ecosystems, so a route computed here and one computed in Python agree — see bridging registrations for what those routes are and what chaining them costs in accuracy.
Where next
Full documentation: natverse.org, which links the reference manuals for each constituent package. The natverse paper is Bates et al. (2020).