Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
For the impatient ...
# installinstall.packages("nat.templatebrains")# uselibrary(nat.templatebrains)# basic examples for templatebrain classexample("as.templatebrain")example("templatebrain-meths")# run examples for mirroringexample("mirror_brain")# ... and bridging# NB you need to install nat.flybrains package to run some examples which are# not run by defaultexample("xform_brain")# get overview help for package?nat.templatebrains# help for main functions?mirror_brain?xform_brain# if you want to construct your own templatebrains?templatebrain# run testslibrary(testthat)test_package("nat.templatebrains")
nat.templatebrains provides additional functions for use with the NeuroAnatomy Toolbox (nat). In particular, it defines the notion of a template brain, as used in image registration of 3D data, along with bridging registrations between template brains (see https://github.com/jefferislab/BridgingRegistrations) and mirroring registrations from one brain hemisphere to the other.
This is a generic package, usable with data from any species. For Drosophila specific functions and data, see our nat.flybrains package. Installing/loading nat.flybrains will automatically install/load nat.templatebrains.
This package has now been released to CRAN (since v0.4.1), but since there are regular updates between CRAN releases we generally recommend that you install the development version from GitHub.
If you want to install the development version of nat.templatebrains, you can do this using devtools. You will probably also wish to install the development version of the nat package if you do this.
if (!require("devtools")) install.packages("devtools")devtools::install_github("jefferislab/nat")devtools::install_github("jefferislab/nat.templatebrains")
This is another major version bump since there is significant new/changed behaviour in xform_brain brain and friends which will now tag transformed objects with a registration template space. This means that nat functions will typically not be need to told the space of an object such as a neuron list in many cases, but some objects will have a new regtemplate attribute.
This is the first public release since 0.6.2 and there are some significant changes under the hood, hence the major version bump.