NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains

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


CRAN_Status_Badge Release Version Build Status Coverage Status Docs

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("devtools")) install.packages("devtools")
devtools::install_github("jefferislab/nat")
devtools::install_github("jefferislab/nat.templatebrains")

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

News

nat.templatebrains 0.9

  • shortest_bridging_seq complains if template brain does not exist in graph (#34)
  • xform_brain does not transform when sample and reference are identical (#33)
  • templatebrain constructor does not need all boundingbox/origin etc fields to be specified (#24)
  • as.templatebrain.im3d should not need an im3d made from a file (#25)
  • Fix unstated dependencies in 'tests' error noted by CRAN r-devel for 0.8.2

nat.templatebrains 0.8

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.

  • xform_brain should tag objects with their space (#16)
  • add regtemplate function as part of this
  • fix xform_brain should give better error when sample unknown (#29)
  • fix: teach plot3d.templatebrain to work with regtemplate (#32)
  • fix: add_reglist should not return anything (visibly) (#30)

nat.templatebrains 0.7

This is the first public release since 0.6.2 and there are some significant changes under the hood, hence the major version bump.

  • fix inversion of reglist objects read from disk (so that xform_brain calls depending on reglist objects work in both directions).
  • add support for memoisation of shortest_bridging_seq so that we do not need to rescan registration directories / reload on disk reglist objects.

nat.templatebrains 0.6.4

  • Add regtemplate function and integrate it with xform_brain and mirror_brain. It will often no longer be necessary to specify the initial space of objects to be transformed - you'll still need to specify your target space though!

nat.templatebrains 0.6.3

  • add support for reglist objects containing one or more arbitrary transforms as bridging or mirroring registrations. A function add_reglist makes it easy to add new in memory reglist objects to those that can be used for bridging / mirroing between template brains (#21).

nat.templatebrains 0.6.2

  • fix issues with git repository cloning on Windows

nat.templatebrains 0.6.1

  • fix bug in mirror_brain for non-zero origin (#14)

nat.templatebrains 0.6

  • add functions to download new registrations from git repositories: add_reg_folder, download_reg_repo, local_reg_dir_for_url, update_reg_repos.
  • add tests and documentation for new git functionality.
  • downloaded registrations are automatically made available on package load.

nat.templatebrains 0.5

  • xform_brain can now find the best available path from one template to another automatically.
  • this uses new functions bridging_graph, shortest_bridging_seq and allreg_dataframe
  • xform_brain now has an imagedata argument (to set sensible defaults for handling of inverse registrations, which are very slow for image data)
  • add doi field to templatebrain object
  • fix: mirror_brain passes on transform argument
  • dev: now imports igraph
  • dev: requires nat >=1.7.0

nat.templatebrains 0.4.1

  • fix handling of regName in templatebrain
  • fix as.templatebrain.im3d (completely broken due to variable name error)
  • better defaults in as.templatebrain.im3d / as.templatebrain.character (both name and short name will be take from file name)
  • print.templatebrain now includes short name

nat.templatebrains 0.4

  • prepare for CRAN release
  • fix export of is.templatebrain
  • give mirror_brain explicit transform argument
  • full examples in mirror_brain and xform_brain functions and templatebrain-meths.
  • add FCWB.demo as data object that can be loaded
  • dev: integrate with nat.flybrains build on travis

nat.templatebrains 0.3

  • add bridging_sequence function to return a bridging registrations sequence that may span more than 2 template brains.
  • xform_brain can apply compound registrations in one streamxform call (but depends on nat >=1.5.9 and CMTK >= 3.2.2)
  • add is.templatebrain and as.character.templatebrain utility functions.
  • switch to single option regdirs for all paths
  • no longer suggests nat.flybrains but includes basic tests with internal data.

nat.templatebrains 0.2

  • move all generic functionality from nat.flybrains (which is now a data only package).
  • give xform_brain a via option
  • add options for directories containing bridging and mirroring registrations nb these can accept multiple dirs, but registration names must be globally unique.
  • suggest nat.flybrains for tests
  • package docs and tests

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("nat.templatebrains")

0.9 by Gregory Jefferis, 9 months ago


https://github.com/jefferislab/nat.templatebrains


Browse source code at https://github.com/cran/nat.templatebrains


Authors: Gregory Jefferis [aut, cre] , James Manton [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports igraph, digest, rappdirs, memoise

Depends on rgl, nat

Suggests testthat, git2r, nabor


See at CRAN