nat.templatebrains v1.0
Monthly downloads
NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains
Extends package 'nat' (NeuroAnatomy Toolbox) by
providing objects and functions for handling template brains.
Readme
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.
Functions in nat.templatebrains
Name | Description | |
display_slice | Display an image slice in 3D | |
FCWB.demo | Sample template brain: FlyCircuit Whole Brain | |
all_templatebrains | Find all template brains or those matching a given image volume | |
add_reglist | Add reglist object describing a bridging/mirroring registration | |
as.templatebrain | Use image file or other object to initialise template brain | |
allreg_dataframe | Make data.frame with details of all registrations | |
bridging_sequence | Find sequence of one or more bridging registrations | |
templatebrain-meths | Template brain methods | |
update_reg_repos | Update local copy of git repository containing registrations | |
bridging_graph | Make or query connected graph of bridging registrations | |
templatebrain | Construct templatebrain object for an image registration template | |
plot3d.templatebrain | Plot 3D surface of a template brain | |
regtemplate | Get or set the registration template space in which an object lives | |
xform_brain | Transform 3D object between template brains | |
nat.templatebrains-package | NeuroAnatomy Toolbox add-on package for handling template brains | |
mirror_brain | Mirror 3D object around a given axis, optionally using a warping registration | |
add_reg_folders | Set or list local folders containing registrations for nat.templatebrains | |
download_reg_repo | Download and register git repository containing registrations | |
local_reg_dir_for_url | Standard local checkout location for extra registration directories | |
No Results! |
Last month downloads
Details
Type | Package |
License | GPL-3 |
URL | http://natverse.org/nat.templatebrains/, https://github.com/natverse/nat.templatebrains |
Encoding | UTF-8 |
RoxygenNote | 7.1.1 |
BugReports | https://github.com/natverse/nat.templatebrains/issues |
Language | en-GB |
NeedsCompilation | no |
Packaged | 2020-10-19 14:05:49 UTC; jefferis |
Repository | CRAN |
Date/Publication | 2020-10-19 14:20:02 UTC |
suggests | covr , git2r (>= 0.22.1) , nabor , spelling , testthat (>= 2.1.0) |
imports | digest , igraph , memoise , rappdirs |
depends | nat (>= 1.8.6) , R (>= 2.10) , rgl |
Contributors | James Manton |
Include our badge in your README
[](http://www.rdocumentation.org/packages/nat.templatebrains)