NeuroAnatomy Toolbox for Analysis of 3D Image Data
Write data and metadata to NRRD file or create a detached NRRD (nhdr) ...
Write out a neuron in any of the file formats we know about
Write out a neuronlistfh object to an RDS file
Write neurons from a neuronlist object to individual files, or a zip a...
Write object to VTK file
Transform the 3D location of objects such as neurons
Write a 3D data object to an amiramesh format file
Write a suitable list to a CMTK TypedStream file on disk
Write out CMTK registration list to folder
Write Amira surface (aka HxSurface or HyperSurface) into .surf file.
Decompose homogeneous affine matrix to CMTK registration parameters
all.equal method tailored to dotprops objects
Check equality on data and key attributes of im3d objects
Check equality on key fields of neuron object
Read AmiraMesh data in binary or ascii format
Return the type of an amiramesh file on disk or a parsed header
Convert an object to a nat hxsurf object
Convert a suitable object to an im3d object.
Convert an object to an rgl mesh3d
convert neuronlistfh to a regular (in memory) neuronlist
Make a list of neurons that can be used for coordinate plotting/analys...
Get the bounding box of an im3d volume or other compatible object
Combine multiple neuronlists into a single list
Return function that finds maximum of its inputs within a clamping ran...
Return path to directory containing CMTK binaries
Utility function to create and run calls to CMTK commandline tools
Convert CMTK registration to homogeneous affine matrix with dof2mat
Extract affine registration from CMTK registration file or in-memory l...
Use CMTK mat2dof to convert homogeneous affine matrix into CMTK regist...
Reformat an image with a CMTK registration using the reformatx tool
Calculate image statistics for a nrrd or other CMTK compatible file
Defines a target volume for a CMTK reformatx operation
Return cmtk version or test for presence of at least a specific versio...
Compose homogeneous affine matrix from CMTK registration parameters
Create and test cmtkreg objects that specify path to a CMTK registrati...
Make in-memory CMTK registration list from affine matrix or CMTK param...
Find 1D indices into a 3D image given spatial coordinates
Arithmetic for dotprops objects
dotprops: Neurons as point clouds with tangent vectors (but no connect...
Set or return list of registered file formats that we can read
Find neurons within a 3D selection box (usually drawn in rgl window)
Find neurons with soma inside 3D selection box (usually drawn in rgl w...
Flip an array, matrix or vector about an axis
Get or set the attached data.frame of a neuronlist
Return root, end, or branchpoints of an igraph object
Interconvert pixel and physical coordinates
Read/Write calibrated 3D blocks of image data
Construct an im3d object representing 3D image data, densities etc
Method to plot spatially calibrated image arrays
Convert locations of im3d voxel grid into XYZ coordinates
Make a scalebar to accompany an image.im3d plot
Slice out a 3D subarray (or 2d matrix) from a 3D image array
Find XYZ coords corresponding to 1D indices into a 3D image
Find the intersection of two collections of objects
Check if file is amiramesh format
Check whether a file is in Fiji's simple neurite tracer format
Test if an object is of class im3d
Check whether a file is in NeuroML format
Test objects of neuronlist class to store multiple neurons
Check if a file is a NRRD file
Test if a file is an SWC format neuron
Check if a file is in the raw image format used by Hanchuan Peng's Vaa...
Mask an object, typically to produce a copy with some values zeroed ou...
Extract or set the materials for an object
Mirror 3D object about a given axis, optionally using a warping regist...
Analyse 3D biological image data especially neurons
Calculated normalised digest value for an object
Arithmetic for neuron coordinates
neuron: class to represent traced neurons
Arithmetic for neuron coordinates applied to neuronlists
Methods for working with the dataframe attached to a neuronlist
Create a neuronlist from zero or more neurons
neuronlistfh - List of neurons loaded on demand from disk or remote we...
ngraph: a graph to encode a neuron's connectivity
lapply and mapply for neuronlists (with optional parallelisation)
Scan through a set of neurons, individually plotting each one in 3D
Open customised rgl window
Normalise an SWC format block of neuron morphology data
Remove plotted neurons or other 3D objects
Return voxel dimensions (by default absolute voxel dimensions)
Find the number of vertices in an object (or each element of a neuronl...
Set the 3D viewpoint of an RGL window using anatomical terms
Return the space origin of a 3D image object
Some useful extensions / changes to rgl defaults
Plot a 2D projection of a neuron
2D plots of the elements in a neuronlist, optionally using a subset ex...
Plot a bounding box in 3D
Plot the domain of a CMTK registration
3D plots of dotprops objects using rgl package
Plot amira surface objects in 3D using rgl
Plot neurons in 3D using rgl library
3D plots of the elements in a neuronlist, optionally using a subset ex...
plot3d methods for different nat objects
Find which points of an object are inside a surface
Calculate number of potential synapses between two neurons
Make 2D (orthogonal) projection of 3D image data
prune an object by removing points near (or far) from a target object
Prune a neuron by removing segments with a given Strahler order
Prune selected vertices or edges from a neuron
Read CMTK TypedStream file to a list in memory
Read a CMTK format registration
Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf o...
Generic functions to read/write landmarks in any supported format
Return parsed XML or R list versions of a NeuroML file
Read a neuron saved by Fiji's Simple Neurite Tracer Plugin
Read one or more neurons from a NeuroML v1 file
Read a single neuron from a file
Read a neuron in swc file format
Read a local, or remote, neuronlistfh object saved to a file.
Read one or more neurons from file to a neuronlist in memory
Read nrrd file into an array in memory
Read Vaa3d format image data
A simple wrapper class for multiple transformations
Synchronise a remote object
Resample an object with a new spacing
Return the root or branch points of a neuron or graph
Scale and centre neuron 3D coordinates
Calculate length of all segments in neuron
Make/convert neuron connectivity information into a seglist object
Recalculate Neurons's SWCData using SegList and point information
Return a simplified segment graph for a neuron
Find the (asymmetric) difference between two collections of objects
Simplify a registration list
Smooth the 3D coordinates of a neuron skeleton
Compute the longest path (aka spine or backbone) of a neuron
Find the Strahler order of each point in a neuron
Extract from neuronlistfh object or its attached data.frame
Find 1D index given n-dimensional indices
Subset points in dotprops object that match given conditions
Subset hxsurf object to specified regions
Subset neuron by keeping only vertices that match given conditions
Subset neuronlist returning either new neuronlist or names of chosen n...
Subset methods for different nat objects
Summary statistics for neurons (e.g. cable length, number of nodes)
Threshold an object, typically to produce a mask
Find the union of two collections of objects
Make im3d image array containing values at locations defined by a mask
Return voxel dimensions of an object
Transform image files using a registration or affine matrix
Transform 3D points using a registration, affine matrix or function
Get and assign coordinates for classes containing 3D vertex data
NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Useful links