Reference

Package Help

Provides an overview of key functions and classes

nat.templatebrains-package nat.templatebrains

NeuroAnatomy Toolbox add-on package for handling template brains

Template Brains

Functions that handle defining template brain spaces and setting the space for objects.

templatebrain()

Construct templatebrain object for an image registration template

is.templatebrain() as.character(<templatebrain>) print(<templatebrain>) as.im3d(<templatebrain>) origin(<templatebrain>) dim(<templatebrain>) voxdims(<templatebrain>) boundingbox(<templatebrain>)

Template brain methods

regtemplate() `regtemplate<-`()

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

as.templatebrain()

Use image file or other object to initialise template brain

plot3d(<templatebrain>)

Plot 3D surface of a template brain

display_slice()

Display an image slice in 3D

Transformations

Functions that handle transformations of objects between different template brain spaces

xform_brain()

Transform 3D object between template brains

mirror_brain()

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

fit_xform()

Fit affine or thin plate spline transform to arbitrary transformation

fit_xform_brain()

Fit a single transform to a bridging registration between brains

Registration Sequences

Functions that list available registrations or return registration sequences between different template brains (used by xform_brain and friends but may be useful in their own right).

bridging_sequence()

Find sequence of one or more bridging registrations

bridging_graph() shortest_bridging_seq()

Make or query connected graph of bridging registrations

allreg_dataframe()

Make data.frame with details of all registrations

Finding Template Brains

Functions that help you find available template brain objects

all_templatebrains() guess_templatebrain()

Find all template brains or those matching a given image volume

Managing Registrations

Functions that inform the package of available bridging registrations or download / update registrations from remote sources.

add_reg_folders() extra_reg_folders()

Set or list local folders containing registrations for nat.templatebrains

add_reglist()

Add reglist object describing a bridging/mirroring registration

download_reg_repo()

Download and register git repository containing registrations

update_reg_repos()

Update local copy of git repository containing registrations

local_reg_dir_for_url()

Standard local checkout location for extra registration directories

Sample data

Sample template brain (see nat.flybrains package for more examples)

FCWB.demo

Sample template brain: FlyCircuit Whole Brain