*.dotprops              Arithmetic for dotprops objects
*.neuron                Arithmetic for neuron coordinates
*.neuronlist            Arithmetic for neuron coordinates applied to
                        neuronlists
Cell07PNs               Cell07PNs: 40 Sample Projection Neurons from
                        Jefferis, Potter et al 2007
[.neuronlistfh          extract a sublist from a neuronlistfh,
                        converting to regular in memory list
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.im3d                 Convert a suitable object to an im3d object.
as.neuronlist           Make a list of neurons that can be used for
                        coordinate plotting/analysis
as.neuronlist.neuronlistfh
                        convert neuronlistfh to a regular (in memory)
                        neuronlist
boundingbox             Get the bounding box of an im3d volume or other
                        compatible object
clampmax                Return function that finds maximum of its
                        inputs within a clamping range
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.mat2dof            Use CMTK mat2dof to convert homogeneous affine
                        matrix into CMTK registration
cmtk.targetvolume       Defines a target volume for a CMTK reformatx
                        operation
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
fileformats             Set or return list of registered file formats
                        that we can read
find.neuron             Find names of neurons within a 3d selection box
                        (usually drawn in rgl window)
flip                    Flip an array, matrix or vector about an axis
graph.nodes             Return root, end, or branchpoints of an igraph
                        object
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
is.amiramesh            Check if file is amiramesh format
is.dotprops             dotprops: Neurons as point clouds with tangent
                        vectors (but no connectivity)
is.neuronlist           Test objects of neuronlist class to store
                        multiple neurons
is.nrrd                 Check if a file is a NRRD file
kcs20                   List of 20 Kenyon Cells from Chiang et al 2011
                        converted to dotprops objects
materials               Extract or set the materials for an object
mirror                  Mirror 3d object about a given axis, optionally
                        using a warping registration
nat-package             Analyse 3D biological image data especially
                        neurons
ndigest                 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
nopen3d                 Open customised rgl window
nrrd.voxdims            Return voxel dimensions (by default absolute
                        voxel dimensions)
origin                  Return the space origin of a 3d image object
pan3d                   Some useful extensions / changes to rgl
                        defaults
plot.neuron             Plot a 2D project of a neuron
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
projection              Make 2D (orthogonal) projection of 3d image
                        data
prune                   prune an object by removing points near (or
                        far) from a target object
read.amiralandmarks     Read and Write Amira Landmarks files
read.amiramesh          Read AmiraMesh data in binary or ascii format
read.cmtk               Read CMTK TypedStream file to a list in memory
read.cmtklandmarks      Read and Write CMTK landmarks
read.cmtkreg            Read a CMTK format registration
read.hxsurf             Read Amira surface (aka HxSurface or
                        HyperSurface) files into hxsurf object
read.neuron             Read a single neuron from a 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 3d array in memory
remotesync              Synchronise a remote object
rootpoints              Return the root or branch points of a neuron or
                        graph
scale.dotprops          Scale and Centre dotprops coords
scale.neuron            Divide neuron coords by a factor (and
                        optionally center)
seglist                 Make/convert neuron connectivity information
                        into a seglist object
seglist2swc             Recalculate Neurons's SWCData using SegList and
                        point information
spine                   Compute the longest path (aka spine or
                        backbone) of a neuron
sub2ind                 Find 1D index given n-dimensional indices
subset.dotprops         Subset points in dotprops object that match
                        given conditions
subset.neuronlist       Subset neuronlist returning either new
                        neuronlist or names of chosen neurons
threshold               Threshold an object, typically to produce a
                        mask
trim                    nat package internal functions
unmask                  Make im3d image array containing values at
                        locations defined by a mask
voxdims                 Return voxel dimensions of an object
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.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
write.nrrd              Write a 3d array to a NRRD file
xform                   Transform the 3d location of objects such as
                        neurons
xformpoints             Transform 3d points using a registration,
                        affine matrix or function
xyzmatrix               Get and assign coordinates for classes
                        containing 3d vertex data
