nat.templatebrains

Quick Start

For the impatient ...

# install
install.packages("nat.templatebrains")

# use
library(nat.templatebrains)

# basic examples for templatebrain class
example("as.templatebrain")
example("templatebrain-meths")

# run examples for mirroring
example("mirror_brain")
# ... and bridging
# NB you need to install nat.flybrains package to run some examples which are
# not run by default
example("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 tests
library(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.

Installation

This package has now been released to CRAN (v0.4.1), but since this is the first official release you may wish to install the development version from GitHub.

CRAN release

install.packages("nat.templatebrains")

Bleeding Edge

You can install the development version by downloading the tar ball, and running R CMD INSTALL on it, or (recommended) using the devtools package:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("nat.templatebrains", "jefferislab")

Note: Windows users need Rtools and devtools to install this way.