The natverse is a collection of interoperable R packages to import, visualise, analyse, manipulate and export 3D neuroanatomical data, including neurons, brains and brain regions. It has been used to study brain and circuit organisation in species from flies to fish and mice. You can install quickly like this:
install.packages('natmanager') natmanager::install('core') # basic install natmanager::install('natverse') # or full install
See the install page for full details, especially if you are new to R.