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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 (since v0.4.1), but since there are regular updates between CRAN releases we generally recommend that you install the development version from GitHub.

CRAN release

install.packages("nat.templatebrains")

Development version

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("remotes")) install.packages("remotes")
remotes::install_github("natverse/nat")
remotes::install_github("natverse/nat.templatebrains")

Note: Windows users may need Rtools as well as remotes to install this way.

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Version

Install

install.packages('nat.templatebrains')

Monthly Downloads

230

Version

1.1

License

GPL-3

Issues

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Last Published

June 14th, 2023

Functions in nat.templatebrains (1.1)

bridging_graph

Make or query connected graph of bridging registrations
templatebrain-meths

Template brain methods
plot3d.templatebrain

Plot 3D surface of a template brain
regtemplate

Get or set the registration template space in which an object lives
mirror_brain

Mirror 3D object around a given axis, optionally using a warping registration
update_reg_repos

Update local copy of git repository containing registrations
nat.templatebrains-package

NeuroAnatomy Toolbox add-on package for handling template brains
local_reg_dir_for_url

Standard local checkout location for extra registration directories
xform_brain

Transform 3D object between template brains
all_templatebrains

Find all template brains or those matching a given image volume
add_reglist

Add reglist object describing a bridging/mirroring registration
add_reg_folders

Set or list local folders containing registrations for nat.templatebrains
fit_xform_brain

Fit a single transform to a bridging registration between brains
FCWB.demo

Sample template brain: FlyCircuit Whole Brain
display_slice

Display an image slice in 3D
as.templatebrain

Use image file or other object to initialise template brain
fit_xform

Fit affine or thin plate spline transform to arbitrary transformation
bridging_sequence

Find sequence of one or more bridging registrations
allreg_dataframe

Make data.frame with details of all registrations
download_reg_repo

Download and register git repository containing registrations
templatebrain

Construct templatebrain object for an image registration template