Function reference • nat

Package Help Provides an overview of key functions and classes
`nat-package`	Analyse 3D biological image data especially neurons
Neurons (traced) Functions for working with traced neurons (fully connected tree structures)
`neuron()` `is.neuron()` `as.neuron()`	neuron: class to represent traced neurons
`read.neuron()`	Read a single neuron from a file
`write.neuron()`	Write out a neuron skeleton or mesh in any of the file formats we know about
`plot(<dotprops>)` `plot(<neuron>)`	Plot a 2D projection of a neuron
`subset(<neuron>)`	Subset neuron by keeping only vertices that match given conditions
`prune()`	prune an object by removing points near (or far) from a target object
`prune_vertices()` `prune_edges()`	Prune selected vertices or edges from a neuron
`prune_in_volume()`	Prune neuron(s) within a volume defined by a 3D mesh
`Ops(<neuron>)`	Arithmetic for neuron coordinates
`scale(<neuron>)` `scale(<dotprops>)`	Scale and centre neuron 3D coordinates
`resample()`	Resample an object with a new spacing
`seglist()` `as.seglist()`	Make/convert neuron connectivity information into a seglist object
`seglist2swc()`	Recalculate Neurons's SWCData using SegList and point information
`seglengths()`	Calculate length of all segments in neuron
`smooth_neuron()` `smooth_segment_gauss()`	Smooth the 3D coordinates of a neuron skeleton
`normalise_swc()`	Normalise an SWC format block of neuron morphology data
Neurons (as graphs) Functions for working with the graph structure of neurons
`ngraph()` `as.ngraph()`	ngraph: a graph to encode a neuron's connectivity
`graph.nodes()`	Return root, end, or branchpoints of an igraph object
`rootpoints()` `branchpoints()` `endpoints()`	Return the root, branch, or end points of a neuron or graph
`segmentgraph()`	Return a simplified segment graph for a neuron
`distal_to()`	Return indices of points in a neuron distal to a given node
`spine()`	Compute the longest path (aka spine or backbone) of a neuron
`strahler_order()`	Find the Strahler order of each point in a neuron
`prune_strahler()`	Prune a neuron by removing segments with a given Strahler order
`get_topo_features()` `get_distance_to_soma()`	Get topological features per each node
`prune_twigs()`	Remove all twigs less than a certain path length from a neuron
`simplify_neuron()`	Simplify a neuron to the longest tree with n branch points
`stitch_neuron()`	Stitch two neurons together at their closest endpoint
`stitch_neurons()`	Stitch multiple fragments into single neuron using nearest endpoints
`stitch_neurons_mst()`	Stitch multiple fragments into single neuron using minimum spanning tree
`reroot()`	Reroot neurons
Skeletonised Neurons (dotprops aka vector cloud) Functions for working with skeletonised neurons consisting of unconnected vectors rather than a fully connected tree.
`is.dotprops()` `as.dotprops()` `dotprops()`	dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
`subset(<dotprops>)`	Subset points in dotprops object that match given conditions
`Ops(<dotprops>)` `Ops(<mesh3d>)` `Ops(<hxsurf>)`	Arithmetic for nat dotprops and surface objects
Collections of Neurons (neuronlists) Functions for working with collections of neurons, which are packaged as neuronlist objects with an attached data.frame containing metadata.
`neuronlist()`	Create a neuronlist from zero or more neurons
`read.neurons()`	Read one or more neurons from file to a neuronlist in memory
`write.neurons()`	Write neurons from a neuronlist object to individual files, or a zip archive
`neuronlistz()` `as.neuronlist(<neuronlistz>)`	A neuronlist object that will read neurons from a zip file on demand
`nlapply()` `progress_natprogress()` `nmapply()`	lapply and mapply for neuronlists (with optional parallelisation)
`plot(<neuronlist>)`	2D plots of the elements in a neuronlist, optionally using a subset expression
`plot3d(<neuronlist>)` `plot3d(<character>)`	3D plots of the elements in a neuronlist, optionally using a subset expression
`subset(<neuronlist>)`	Subset neuronlist returning either new neuronlist or names of chosen neurons
`summary(<neuronlist>)` `summary(<neuron>)` `summary(<mesh3d>)` `summary(<dotprops>)`	Summary statistics for neurons (e.g. cable length, number of nodes)
`as.neuronlist()`	Make a list of neurons that can be used for coordinate plotting/analysis
`c(<neuronlist>)`	Combine multiple neuronlists into a single list
`as.data.frame(<neuronlist>)` `data.frame<-`()	Get or set the attached data.frame of a neuronlist
`is.neuronlist()`	Test objects of neuronlist class to store multiple neurons
`*`(<neuronlist>) `+`(<neuronlist>) `-`(<neuronlist>) `/`(<neuronlist>)	Arithmetic for neuron coordinates applied to neuronlists
`[`(<neuronlist>) `[<-`(<neuronlist>) `droplevels(<neuronlist>)` `with(<neuronlist>)` `head(<neuronlist>)` `tail(<neuronlist>)`	Methods for working with the dataframe attached to a neuronlist
Collections of Neurons with Remote Data (neuronlistfh) Functions for working with collections of neurons where the data will be dynamically loaded into memory from disk and/or downloaded from a remote site.
`neuronlistfh()` `is.neuronlistfh()` `as.neuronlistfh()` `c(<neuronlistfh>)`	neuronlistfh - List of neurons loaded on demand from disk or remote website
`read.neuronlistfh()`	Read a local, or remote, neuronlistfh object saved to a file.
`write.neuronlistfh()`	Write out a neuronlistfh object to an RDS file
`remotesync()`	Synchronise a remote object
`as.neuronlist(<neuronlistfh>)`	convert neuronlistfh to a regular (in memory) neuronlist
`[`(<neuronlistfh>)	Extract from neuronlistfh object or its attached data.frame
Surfaces and Landmarks (hxsurf, mesh3d) Functions for working with surface data, either in a class hxsurf modeled on Amira’s representation of surfaces or the rgl::mesh3d class.
`read.hxsurf()`	Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object
`write.hxsurf()`	Write Amira surface (aka HxSurface or HyperSurface) into .surf file.
`read.landmarks()` `write.landmarks()`	Generic functions to read/write landmarks in any supported format
`plot3d(<hxsurf>)`	Plot amira surface objects in 3D using rgl
`subset(<hxsurf>)`	Subset hxsurf object to specified regions
`as.hxsurf()`	Convert an object to a nat hxsurf object
`c(<hxsurf>)`	Concatenate HyperSurface objects
`as.mesh3d(<ashape3d>)` `as.mesh3d(<hxsurf>)` `as.mesh3d(<boundingbox>)`	Convert an object to an rgl mesh3d
`pointsinside()`	Find which points of an object are inside a surface
3D Plotting of Objects Functions to help plot neurons, surfaces and other 3D objects via RGL.
`plot3d`	plot3d methods for different nat objects
`nopen3d()`	Open customised rgl window
`nclear3d()`	Clear the rgl or plotly 3D scene
`nview3d()`	Set the 3D viewpoint of an RGL window using anatomical terms
`npop3d()`	Remove plotted neurons or other 3D objects
`pan3d()`	Some useful extensions / changes to rgl defaults
`wire3d()`	Wire frame plots
`nlscan()`	Scan through a set of neurons, individually plotting each one in 3D
`plot3d(<boundingbox>)`	Plot a bounding box in 3D
`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 or plotly module
`plot3d(<cmtkreg>)`	Plot the domain of a CMTK registration
`plot3d(<ngraph>)`	Plot 3d representation of neuron (ngraph) with directed edges
3D Interaction with Objects Functions to review, identify, and modify objects by interactive selection in RGL windows.
`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)
`select_points()`	Interactively select 3D points in space
`correct_root()`	Interactively re-root neurons (usually to their soma)
`prune_online()`	Prune a neuron interactively in an rgl window
`make_model()`	Generate a 3D model from connector and/or tree node data
3D Geometry Functions for analysing 3D geometry of neurons and other objects
`nvertices()`	Find the number of vertices in an object (or each element of a neuronlist)
`xyzmatrix()` `xyzmatrix<-`() `xyzmatrix2str()` `xyzmatrix2list()`	Get and assign coordinates for classes containing 3D vertex data
`potential_synapses()`	Calculate number of potential synapses between two neurons
`overlap_score()`	Generate a connectivity matrix based on euclidean distance between points
`sholl_analysis()`	Perform a Sholl analysis on neuron skeletons
`plane_coefficients()`	Find the coefficients of the plane equation
`intersect_plane()`	Find the points on a plane that are intersected by an object
Object transformation Generic strategies for transforming 3D objects/images and registration
`xform()`	Transform the 3D location of objects such as neurons
`mirror()`	Mirror 3D object about a given axis, optionally using a warping registration
`reglist()` `invert_reglist()` `c(<reglist>)`	A simple wrapper class for multiple transformations
`xformimage()`	Transform image files using a registration or affine matrix
`xformpoints()`	Transform 3D points using a registration, affine matrix or function
`simplify_reglist()`	Simplify a registration list
`tpsreg()` `xformpoints(<tpsreg>)`	Thin plate spline registrations via xform and friends
Images (im3d) Functions for working with 3d image volumes
`im3d()`	Construct an im3d object representing 3D image data, densities etc
`read.im3d()` `write.im3d()`	Read/Write calibrated 3D blocks of image data
`as.im3d()`	Convert a suitable object to an im3d object.
`is.im3d()`	Test if an object is of class im3d
`imslice()`	Slice out a 3D subarray (or 2d matrix) from a 3D image array
`image(<im3d>)`	Method to plot spatially calibrated image arrays
`imscalebar()`	Make a scalebar to accompany an image.im3d plot
`flip()`	Flip an array, matrix or vector about an axis
`projection()`	Make 2D (orthogonal) projection of 3D image data
`threshold()`	Threshold an object, typically to produce a mask
`mask()`	Mask an object, typically to produce a copy with some values zeroed out
`unmask()`	Make im3d image array containing values at locations defined by a mask
`clampmax()`	Return function that finds maximum of its inputs within a clamping range
`boundingbox()` `boundingbox<-`()	Get the bounding box of an image volume or object containing 3D vertices
`makeboundingbox()`	Construct a 3D bounding box object
`origin()`	Return the space origin of a 3D image object
`voxdims()`	Return voxel dimensions of an object
`nrrd.voxdims()`	Return voxel dimensions (by default absolute voxel dimensions)
`xyzpos()` `ijkpos()`	Interconvert pixel and physical coordinates
`coord2ind()`	Find 1D or 3D voxel indices into a 3D image given spatial coordinates
`ind2coord()`	Find XYZ coords corresponding to 1D indices into a 3D image
`sub2ind()`	Find 1D index given n-dimensional indices
`imexpand.grid()`	Convert locations of im3d voxel grid into XYZ coordinates
`materials()`	Extract or set the materials for an object
CMTK Registration Functions to interface to the CMTK image registration suite
`cmtk.bindir()`	Return path to directory containing CMTK binaries
`cmtk.version()`	Return cmtk version or test for presence of at least a specific version
`cmtkparams2affmat()`	Compose homogeneous affine matrix from CMTK registration parameters
`affmat2cmtkparams()`	Decompose homogeneous affine matrix to CMTK registration parameters
`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.extract_affine()`	Extract affine registration from CMTK registration file or in-memory list
`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
`cmtkreg()` `as.cmtkreg()` `is.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
`cmtk.call()` `cmtk.system2()`	Utility function to create and run calls to CMTK command line tools
Sample Data Sample data objects (neurons, surfaces)
`Cell07PNs`	Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007
`kcs20`	List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects
`dl1neuron`	Olfactory Projection Neuron reconstructed from EM data
`MBL.surf`	Surface object (hxsurf) for the left mushroom body in FCWB template space
Generic Functions Generic versions of base functions for which we provide specialised methods for nat objects.
`intersect()`	Find the intersection of two collections of objects
`setdiff()`	Find the (asymmetric) difference between two collections of objects
`subset`	Subset methods for different nat objects
`union()`	Find the union of two collections of objects
Utility Functions Functions primarily intended for developer use
`ndigest()`	Calculated normalised digest value for an object
`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
File formats Support for different formats. It is generally recommended to use more generic functions such as read.neuron(s) rather than these functions.
`fileformats()` `registerformat()` `getformatreader()` `getformatwriter()`	Set or return list of registered file formats that we can read
`read.cmtk()`	Read CMTK TypedStream file to a list in memory
`read.cmtkreg()`	Read a CMTK format registration
`read.morphml()`	Return parsed XML or R list versions of a NeuroML 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.ngraph.swc()`	Read a neuron in swc file format
`read.nrrd()` `read.nrrd.header()` `nrrd.datafiles()`	Read NRRD files/headers into memory
`read.vaa3draw()`	Read Vaa3d format image data
`read.amiramesh()` `read.amiramesh.header()`	Read AmiraMesh data in binary or ascii format
`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.nrrd()` `write.nrrd.header()` `write.nrrd.header.for.file()`	Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.
`write.vtk()`	Write object to VTK file
`amiratype()`	Return the type of an AmiraMesh file on disk or a parsed header
`is.amiramesh()`	Check if file is AmiraMesh format
`is.fijitraces()`	Check whether a file is in Fiji's simple neurite tracer format
`is.neuroml()`	Check whether a file is in NeuroML format
`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

Reference

Package Help

Neurons (traced)

Neurons (as graphs)

Skeletonised Neurons (dotprops aka vector cloud)

Collections of Neurons (neuronlists)

Collections of Neurons with Remote Data (neuronlistfh)

Surfaces and Landmarks (hxsurf, mesh3d)

3D Plotting of Objects

3D Interaction with Objects

3D Geometry

Object transformation

Images (im3d)

CMTK Registration

Sample Data

Generic Functions

Utility Functions

File formats