nat.templatebrains (version 1.1)

nat.templatebrains-package: NeuroAnatomy Toolbox add-on package for handling template brains

Description

This package provides a class templatebrain that stores key information about reference brains along with helper functions to simplify transformation of data between template brains (a.k.a bridging) and mirroring of data within a template brain.

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

Helper functions

Easy-to-use functions for transforming data from one template brain to another, displaying slices alongside 3D data, etc. are provided.

For transforming between spaces, see especially xform_brain, mirror_brain. The regtemplate functions allow an R object containing neuroanatomical data to be tagged as in a particular template brain space.

plot3d.templatebrain provides a simple way to plot a surface object representing a given template brain.

Registrations

Functions such as xform_brain provided by nat.templatebrains are not very useful unless you tell the package about bridging/mirroring registrations that you have available. There are 4 supported ways to add registrations to the search list that will be considered:

• Install a package (e.g. nat.flybrains) that bundles registrations.

• download_reg_repo to download pre-packaged registration folders from github. This will automatically add the new folders to the registration search list both in the current session and on package startup.

• add_reg_folders to add additional local directories to the registration search list. You will need to do this each time your start an R session unless you add it to your Rprofile.

• add_reglist to add an in-memory reglist containing an arbitrary sequence of registrations. By default this will not persist across R sessions but this behaviour can be changed.

Note that the package implements a cache to avoid rescanning the directories in the registration search list all the time. The functions mentioned above will automatically ensure that the cache is reset whenever a new set of registrations are added to the search list.

Package options

• options('nat.templatebrains.regdirs') specifies a character vector of directories containing registrations i.e. a registration search list.

It is strongly recommended that you use the functions mentioned above rather than manipulating the registration search list directly.

Note that registration directories will be searched in the order that they are listed. It is therefore strongly recommended that individual registrations have globally unique names.

Author

Maintainer: Gregory Jefferis (ORCID)

Authors:

• James Manton (ORCID)

See Also

nat

Useful links:

• http://natverse.org/nat.templatebrains/

• https://github.com/natverse/nat.templatebrains

• Report bugs at https://github.com/natverse/nat.templatebrains/issues

Examples

if (FALSE) {
# Plot all known registrations
plot(bridging_graph(), vertex.size=25)

## manually add a new directory containing registrations to the search list
# Don't do this unless essential!
options(nat.templatebrains.regdirs=union(
  getOption('nat.templatebrains.regdirs'), "/my/new/path"))
# NB after mucking around with paths manually you must also manually update
# the cache so that new registrations are actually used.
nat.templatebrains:::reset_cache()

## same, but override any built-in registration by putting the new path
# at the first position in the search list
options(nat.templatebrains.regdirs=union("/my/new/path"),
  getOption('nat.templatebrains.regdirs'))
}