NeuroAnatomy Toolbox for Analysis of 3D Image Data

[Up] [Top]

Documentation for package ‘nat’ version 1.8.1

Help Pages

A B C D E F G H I K M N O P R S T U V W X misc

nat-package Analyse 3D biological image data especially neurons

-- A --

affmat2cmtkparams Decompose homogeneous affine matrix to CMTK registration parameters
all.equal.dotprops all.equal method tailored to dotprops objects
all.equal.im3d Check equality on data and key attributes of im3d objects
all.equal.neuron Check equality on key fields of neuron object
amiratype Return the type of an amiramesh file on disk or a parsed header
as.cmtkreg Create and test cmtkreg objects that specify path to a CMTK registration
as.data.frame.neuronlist Get or set the attached data.frame of a neuronlist
as.dotprops dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
as.im3d Convert a suitable object to an im3d object.
as.im3d.im3d Convert a suitable object to an im3d object.
as.im3d.matrix Convert a suitable object to an im3d object.
as.mesh3d Convert an object to an rgl mesh3d
as.mesh3d.hxsurf Convert an object to an rgl mesh3d
as.neuron neuron: class to represent traced neurons
as.neuron.data.frame neuron: class to represent traced neurons
as.neuron.default neuron: class to represent traced neurons
as.neuron.ngraph neuron: class to represent traced neurons
as.neuronlist Make a list of neurons that can be used for coordinate plotting/analysis
as.neuronlist.default Make a list of neurons that can be used for coordinate plotting/analysis
as.neuronlist.neuronlistfh convert neuronlistfh to a regular (in memory) neuronlist
as.neuronlistfh neuronlistfh - List of neurons loaded on demand from disk or remote website
as.neuronlistfh.neuronlist neuronlistfh - List of neurons loaded on demand from disk or remote website
as.ngraph ngraph: a graph to encode a neuron's connectivity
as.ngraph.data.frame ngraph: a graph to encode a neuron's connectivity
as.ngraph.neuron ngraph: a graph to encode a neuron's connectivity
as.seglist Make/convert neuron connectivity information into a seglist object
as.seglist.igraph Make/convert neuron connectivity information into a seglist object
as.seglist.neuron Make/convert neuron connectivity information into a seglist object

-- B --

boundingbox Get the bounding box of an im3d volume or other compatible object
boundingbox.character Get the bounding box of an im3d volume or other compatible object
boundingbox.default Get the bounding box of an im3d volume or other compatible object
boundingbox.im3d Get the bounding box of an im3d volume or other compatible object
boundingbox.list Get the bounding box of an im3d volume or other compatible object
boundingbox.shape3d Get the bounding box of an im3d volume or other compatible object
boundingbox<- Get the bounding box of an im3d volume or other compatible object
branchpoints Return the root or branch points of a neuron or graph
branchpoints.default Return the root or branch points of a neuron or graph
branchpoints.igraph Return the root or branch points of a neuron or graph
branchpoints.neuron Return the root or branch points of a neuron or graph

-- C --

c.neuronlist Combine multiple neuronlists into a single list
Cell07PNs Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007
clampmax Return function that finds maximum of its inputs within a clamping range
cmtk Return path to directory containing CMTK binaries
cmtk.bindir Return path to directory containing CMTK binaries
cmtk.call Utility function to create a call to a cmtk commandline tool
cmtk.dof2mat Convert CMTK registration to homogeneous affine matrix with dof2mat
cmtk.extract_affine Extract affine registration from CMTK registration file or in-memory list
cmtk.mat2dof Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration
cmtk.reformatx Reformat an image with a CMTK registration using the reformatx tool
cmtk.statistics Calculate image statistics for a nrrd or other CMTK compatible file
cmtk.targetvolume Defines a target volume for a CMTK reformatx operation
cmtk.targetvolume.default Defines a target volume for a CMTK reformatx operation
cmtk.targetvolume.im3d Defines a target volume for a CMTK reformatx operation
cmtk.targetvolume.list Defines a target volume for a CMTK reformatx operation
cmtk.version Return cmtk version or test for presence of at least a specific version
cmtkparams2affmat Compose homogeneous affine matrix from CMTK registration parameters
cmtkreg Create and test cmtkreg objects that specify path to a CMTK registration
cmtkreglist Make in-memory CMTK registration list from affine matrix or CMTK parameters
coord2ind Find 1D indices into a 3D image given spatial coordinates
coord2ind.default Find 1D indices into a 3D image given spatial coordinates

-- D --

data.frame<- Get or set the attached data.frame of a neuronlist
data.frame<-.neuronlist Get or set the attached data.frame of a neuronlist
dotprops dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.character dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.default dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.dotprops dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.im3d dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.neuron dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
dotprops.neuronlist dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
droplevels Methods for working with the dataframe attached to a neuronlist
droplevels.neuronlist Methods for working with the dataframe attached to a neuronlist

-- E --

endpoints Return the root or branch points of a neuron or graph
endpoints.default Return the root or branch points of a neuron or graph
endpoints.igraph Return the root or branch points of a neuron or graph
endpoints.neuron Return the root or branch points of a neuron or graph

-- F --

fileformats Set or return list of registered file formats that we can read
find.neuron Find neurons within a 3D selection box (usually drawn in rgl window)
find.soma Find neurons with soma inside 3D selection box (usually drawn in rgl window)
flip Flip an array, matrix or vector about an axis
flip.array Flip an array, matrix or vector about an axis

-- G --

getformatreader Set or return list of registered file formats that we can read
getformatwriter Set or return list of registered file formats that we can read
graph.nodes Return root, end, or branchpoints of an igraph object

-- H --

head Methods for working with the dataframe attached to a neuronlist
head.neuronlist Methods for working with the dataframe attached to a neuronlist
hxsurf Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object

-- I --

ijkpos Interconvert pixel and physical coordinates
im3d Construct an im3d object representing 3D image data, densities etc
im3d-coords Interconvert pixel and physical coordinates
im3d-io Read/Write calibrated 3D blocks of image data
image.im3d Method to plot spatially calibrated image arrays
imexpand.grid Convert locations of im3d voxel grid into XYZ coordinates
imscalebar Make a scalebar to accompany an image.im3d plot
imslice Slice out a 3D subarray (or 2d matrix) from a 3D image array
ind2coord Find XYZ coords corresponding to 1D indices into a 3D image
ind2coord.array Find XYZ coords corresponding to 1D indices into a 3D image
ind2coord.default Find XYZ coords corresponding to 1D indices into a 3D image
ind2coord.im3d Find XYZ coords corresponding to 1D indices into a 3D image
intersect Find the intersection of two collections of objects
intersect.default Find the intersection of two collections of objects
intersect.neuronlist Find the intersection of two collections of objects
is.amiramesh Check if file is amiramesh format
is.cmtkreg Create and test cmtkreg objects that specify path to a CMTK registration
is.dotprops dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
is.fijitraces Check whether a file is in Fiji's simple neurite tracer format
is.im3d Test if an object is of class im3d
is.neuroml Check whether a file is in NeuroML format
is.neuron neuron: class to represent traced neurons
is.neuronlist Test objects of neuronlist class to store multiple neurons
is.neuronlistfh neuronlistfh - List of neurons loaded on demand from disk or remote website
is.nrrd Check if a file is a NRRD file
is.swc Test if a file is an SWC format neuron
is.vaa3draw Check if a file is in the raw image format used by Hanchuan Peng's Vaa3D

-- K --

kcs20 List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects

-- M --

materials Extract or set the materials for an object
materials.character Extract or set the materials for an object
materials.default Extract or set the materials for an object
materials.hxsurf Extract or set the materials for an object
MBL.surf Surface object (hxsurf) for the left mushroom body in FCWB template space
mirror Mirror 3D object about a given axis, optionally using a warping registration
mirror.character Mirror 3D object about a given axis, optionally using a warping registration
mirror.default Mirror 3D object about a given axis, optionally using a warping registration
mirror.neuronlist Mirror 3D object about a given axis, optionally using a warping registration

-- N --

nat Analyse 3D biological image data especially neurons
ndigest Calculated normalised digest value for an object
ndigest.dotprops Calculated normalised digest value for an object
ndigest.neuron Calculated normalised digest value for an object
ndigest.neuronlistfh Calculated normalised digest value for an object
neuron neuron: class to represent traced neurons
neuronlist Create a neuronlist from zero or more neurons
neuronlist-dataframe-methods Methods for working with the dataframe attached to a neuronlist
neuronlistfh neuronlistfh - List of neurons loaded on demand from disk or remote website
ngraph ngraph: a graph to encode a neuron's connectivity
nlapply lapply and mapply for neuronlists (with optional parallelisation)
nlscan Scan through a set of neurons, individually plotting each one in 3D
nmapply lapply and mapply for neuronlists (with optional parallelisation)
nopen3d Open customised rgl window
normalise_swc Normalise an SWC format block of neuron morphology data
npop3d Remove plotted neurons or other 3D objects
nrrd.voxdims Return voxel dimensions (by default absolute voxel dimensions)

-- O --

origin Return the space origin of a 3D image object

-- P --

pan3d Some useful extensions / changes to rgl defaults
plot.neuron Plot a 2D projection of a neuron
plot.neuronlist 2D plots of the elements in a neuronlist, optionally using a subset expression
plot3d plot3d methods for different nat objects
plot3d.boundingbox Plot a bounding box in 3D
plot3d.character 3D plots of the elements in a neuronlist, optionally using a subset expression
plot3d.dotprops 3D plots of dotprops objects using rgl package
plot3d.hxsurf Plot amira surface objects in 3D using rgl
plot3d.neuron Plot neurons in 3D using rgl library
plot3d.neuronlist 3D plots of the elements in a neuronlist, optionally using a subset expression
pointsinside Find which points of an object are inside a surface
pointsinside.default Find which points of an object are inside a surface
potential_synapses Calculate number of potential synapses between two neurons
potential_synapses.dotprops Calculate number of potential synapses between two neurons
potential_synapses.neuron Calculate number of potential synapses between two neurons
potential_synapses.neuronlist Calculate number of potential synapses between two neurons
projection Make 2D (orthogonal) projection of 3D image data
prune prune an object by removing points near (or far) from a target object
prune.default prune an object by removing points near (or far) from a target object
prune.dotprops prune an object by removing points near (or far) from a target object
prune.neuron prune an object by removing points near (or far) from a target object
prune.neuronlist prune an object by removing points near (or far) from a target object
prune_strahler Prune a neuron by removing segments with a given Strahler order
prune_vertices Prune selected vertices from a neuron

-- R --

read.amiramesh Read AmiraMesh data in binary or ascii format
read.amiramesh.header Read AmiraMesh data in binary or ascii format
read.cmtk Read CMTK TypedStream file to a list in memory
read.cmtkreg Read a CMTK format registration
read.hxsurf Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object
read.im3d Read/Write calibrated 3D blocks of image data
read.landmarks Generic functions to read/write landmarks in any supported format
read.morphml Return parsed XML or R list versions of a NeuroML file
read.neuron Read a single neuron from a file
read.neuron.fiji Read a neuron saved by Fiji's Simple Neurite Tracer Plugin
read.neuron.neuroml Read one or more neurons from a NeuroML v1 file
read.neuron.swc Read a neuron in swc file format
read.neuronlistfh Read a local, or remote, neuronlistfh object saved to a file.
read.neurons Read one or more neurons from file to a neuronlist in memory
read.nrrd Read nrrd file into an array in memory
read.nrrd.header Read nrrd file into an array in memory
read.vaa3draw Read Vaa3d format image data
registerformat Set or return list of registered file formats that we can read
remotesync Synchronise a remote object
remotesync.neuronlistfh Synchronise a remote object
resample Resample an object with a new spacing
resample.neuron Resample an object with a new spacing
rootpoints Return the root or branch points of a neuron or graph
rootpoints.default Return the root or branch points of a neuron or graph
rootpoints.igraph Return the root or branch points of a neuron or graph
rootpoints.neuron Return the root or branch points of a neuron or graph

-- S --

scale Scale and centre neuron 3D coordinates
scale.dotprops Scale and centre neuron 3D coordinates
scale.neuron Scale and centre neuron 3D coordinates
seglengths Calculate length of all segments in neuron
seglist Make/convert neuron connectivity information into a seglist object
seglist2swc Recalculate Neurons's SWCData using SegList and point information
segmentgraph Return a simplified segment graph for a neuron
setdiff Find the (asymmetric) difference between two collections of objects
setdiff.default Find the (asymmetric) difference between two collections of objects
setdiff.neuronlist Find the (asymmetric) difference between two collections of objects
spine Compute the longest path (aka spine or backbone) of a neuron
strahler_order Find the Strahler order of each point in a neuron
sub2ind Find 1D index given n-dimensional indices
subset Subset methods for different nat objects
subset.dotprops Subset points in dotprops object that match given conditions
subset.hxsurf Subset hxsurf object to specified regions
subset.neuron Subset neuron by keeping only vertices that match given conditions
subset.neuronlist Subset neuronlist returning either new neuronlist or names of chosen neurons
summary.dotprops Summary statistics for neurons (e.g. cable length, number of nodes)
summary.neuron Summary statistics for neurons (e.g. cable length, number of nodes)
summary.neuronlist Summary statistics for neurons (e.g. cable length, number of nodes)

-- T --

tail Methods for working with the dataframe attached to a neuronlist
tail.neuronlist Methods for working with the dataframe attached to a neuronlist
threshold Threshold an object, typically to produce a mask
threshold.im3d Threshold an object, typically to produce a mask
trim nat package internal functions

-- U --

union Find the union of two collections of objects
union.default Find the union of two collections of objects
union.neuronlist Find the union of two collections of objects
unmask Make im3d image array containing values at locations defined by a mask

-- V --

voxdims Return voxel dimensions of an object
voxdims.default Return voxel dimensions of an object

-- W --

with Methods for working with the dataframe attached to a neuronlist
with.neuronlist Methods for working with the dataframe attached to a neuronlist
write.amiramesh Write a 3D data object to an amiramesh format file
write.cmtk Write a suitable list to a CMTK TypedStream file on disk
write.cmtkreg Write out CMTK registration list to folder
write.hxsurf Write Amira surface (aka HxSurface or HyperSurface) into .surf file.
write.im3d Read/Write calibrated 3D blocks of image data
write.landmarks Generic functions to read/write landmarks in any supported format
write.neuron Write out a neuron in any of the file formats we know about
write.neuronlistfh Write out a neuronlistfh object to an RDS file
write.neurons Write neurons from a neuronlist object to individual files, or a zip archive
write.nrrd Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.
write.nrrd.header Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.
write.nrrd.header.for.file Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.

-- X --

xform Transform the 3D location of objects such as neurons
xform.character Transform the 3D location of objects such as neurons
xform.default Transform the 3D location of objects such as neurons
xform.dotprops Transform the 3D location of objects such as neurons
xform.list Transform the 3D location of objects such as neurons
xform.neuronlist Transform the 3D location of objects such as neurons
xform.shape3d Transform the 3D location of objects such as neurons
xformimage Transform image files using a registration or affine matrix
xformimage.character Transform image files using a registration or affine matrix
xformimage.cmtkreg Transform image files using a registration or affine matrix
xformimage.default Transform image files using a registration or affine matrix
xformpoints Transform 3D points using a registration, affine matrix or function
xformpoints.character Transform 3D points using a registration, affine matrix or function
xformpoints.cmtkreg Transform 3D points using a registration, affine matrix or function
xformpoints.default Transform 3D points using a registration, affine matrix or function
xyzmatrix Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.default Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.dotprops Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.hxsurf Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.igraph Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.mesh3d Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.neuron Get and assign coordinates for classes containing 3D vertex data
xyzmatrix.neuronlist Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<- Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<-.dotprops Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<-.hxsurf Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<-.igraph Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<-.neuron Get and assign coordinates for classes containing 3D vertex data
xyzmatrix<-.shape3d Get and assign coordinates for classes containing 3D vertex data
xyzpos Interconvert pixel and physical coordinates

-- misc --

*.dotprops Arithmetic for dotprops objects
*.neuron Arithmetic for neuron coordinates
*.neuronlist Arithmetic for neuron coordinates applied to neuronlists
+.dotprops Arithmetic for dotprops objects
+.neuron Arithmetic for neuron coordinates
+.neuronlist Arithmetic for neuron coordinates applied to neuronlists
-.dotprops Arithmetic for dotprops objects
-.neuron Arithmetic for neuron coordinates
-.neuronlist Arithmetic for neuron coordinates applied to neuronlists
/.dotprops Arithmetic for dotprops objects
/.neuron Arithmetic for neuron coordinates
/.neuronlist Arithmetic for neuron coordinates applied to neuronlists
[.neuronlist Methods for working with the dataframe attached to a neuronlist
[.neuronlistfh Extract from neuronlistfh object or its attached data.frame
[<-.neuronlist Methods for working with the dataframe attached to a neuronlist