*.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
MBL.surf                Surface object (hxsurf) for the left mushroom
                        body in FCWB template space
[.neuronlistfh          Extract from neuronlistfh object or its
                        attached data.frame
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.data.frame.neuronlist
                        Get or set the attached data.frame of a
                        neuronlist
as.hxsurf               Convert an object to a nat hxsurf object
as.im3d                 Convert a suitable object to an im3d object.
as.mesh3d               Convert an object to an rgl mesh3d
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
c.neuronlist            Combine multiple neuronlists into a single list
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 and run calls to
                        CMTK commandline tools
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.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
dotprops                dotprops: Neurons as point clouds with tangent
                        vectors (but no connectivity)
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
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
intersect               Find the intersection of two collections of
                        objects
is.amiramesh            Check if file is amiramesh format
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.neuronlist           Test objects of neuronlist class to store
                        multiple neurons
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
kcs20                   List of 20 Kenyon Cells from Chiang et al 2011
                        converted to dotprops objects
mask                    Mask an object, typically to produce a copy
                        with some values zeroed out
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 (with
                        optional parallelisation)
nlscan                  Scan through a set of neurons, individually
                        plotting each one in 3D
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)
nvertices               Find the number of vertices in an object (or
                        each element of a neuronlist)
nview3d                 Set the 3D viewpoint of an RGL window using
                        anatomical terms
origin                  Return the space origin of a 3D image object
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.cmtkreg          Plot the domain of a CMTK registration
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
potential_synapses      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_strahler          Prune a neuron by removing segments with a
                        given Strahler order
prune_vertices          Prune selected vertices or edges from a neuron
read.amiramesh          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.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.vaa3draw           Read Vaa3d format image data
reglist                 A simple wrapper class for multiple
                        transformations
remotesync              Synchronise a remote object
resample                Resample an object with a new spacing
rootpoints              Return the root or branch points of a neuron or
                        graph
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
simplify_reglist        Simplify a registration list
smooth_neuron           Smooth the 3D coordinates of a neuron skeleton
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.neuronlist      Summary statistics for neurons (e.g. cable
                        length, number of nodes)
threshold               Threshold an object, typically to produce a
                        mask
union                   Find the union of two collections of objects
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, or a zip archive
write.nrrd              Write data and metadata to NRRD file or create
                        a detached NRRD (nhdr) file.
write.vtk               Write object to VTK file
xform                   Transform the 3D location of objects such as
                        neurons
xformimage              Transform image files using a registration or
                        affine matrix
xformpoints             Transform 3D points using a registration,
                        affine matrix or function
xyzmatrix               Get and assign coordinates for classes
                        containing 3D vertex data
