Convert an object to a nat hxsurf object
Convert an object to an rgl mesh3d
as.neuronlist.neuronlistfh
convert neuronlistfh to a regular (in memory) neuronlist
Return function that finds maximum of its inputs within a clamping range
Extract affine registration from CMTK registration file or in-memory list
Combine multiple neuronlists into a single list
Convert CMTK registration to homogeneous affine matrix with dof2mat
Return path to directory containing CMTK binaries
Utility function to create and run calls to CMTK commandline tools
Get the bounding box of an im3d volume or other compatible object
Make a list of neurons that can be used for coordinate plotting/analysis
Arithmetic for dotprops objects
Return cmtk version or test for presence of at least a specific version
Find 1D indices into a 3D image given spatial coordinates
Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration
Calculate image statistics for a nrrd or other CMTK compatible file
Reformat an image with a CMTK registration using the reformatx tool
Compose homogeneous affine matrix from CMTK registration parameters
Flip an array, matrix or vector about an axis
Get or set the attached data.frame of a neuronlist
Construct an im3d object representing 3D image data, densities etc
Read/Write calibrated 3D blocks of image data
Find neurons with soma inside 3D selection box (usually drawn in rgl window)
Check if file is amiramesh format
Defines a target volume for a CMTK reformatx operation
Find neurons within a 3D selection box (usually drawn in rgl window)
Make a scalebar to accompany an image.im3d plot
Set or return list of registered file formats that we can read
dotprops: Neurons as point clouds with tangent vectors (but no connectivity)
Slice out a 3D subarray (or 2d matrix) from a 3D image array
Create and test cmtkreg objects that specify path to a CMTK registration
Check whether a file is in Fiji's simple neurite tracer format
Mask an object, typically to produce a copy with some values zeroed out
Check whether a file is in NeuroML format
Method to plot spatially calibrated image arrays
Convert locations of im3d voxel grid into XYZ coordinates
Extract or set the materials for an object
Test if an object is of class im3d
Mirror 3D object about a given axis, optionally using a warping registration
List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects
Analyse 3D biological image data especially neurons
Make in-memory CMTK registration list from affine matrix or CMTK parameters
Calculated normalised digest value for an object
Return root, end, or branchpoints of an igraph object
Check if a file is a NRRD file
ngraph: a graph to encode a neuron's connectivity
Test objects of neuronlist class to store multiple neurons
Interconvert pixel and physical coordinates
Check if a file is in the raw image format used by Hanchuan Peng's Vaa3D
Test if a file is an SWC format neuron
Find XYZ coords corresponding to 1D indices into a 3D image
Find the intersection of two collections of objects
Arithmetic for neuron coordinates applied to neuronlists
neuronlist-dataframe-methods
Methods for working with the dataframe attached to a neuronlist
Some useful extensions / changes to rgl defaults
lapply and mapply for neuronlists (with optional parallelisation)
Plot a 2D projection of a neuron
Plot a bounding box in 3D
Plot the domain of a CMTK registration
Arithmetic for neuron coordinates
Create a neuronlist from zero or more neurons
Open customised rgl window
plot3d methods for different nat objects
2D plots of the elements in a neuronlist, optionally using a subset
expression
Scan through a set of neurons, individually plotting each one in 3D
Plot neurons in 3D using rgl library
3D plots of the elements in a neuronlist, optionally using a subset
expression
Plot amira surface objects in 3D using rgl
3D plots of dotprops objects using rgl package
Return parsed XML or R list versions of a NeuroML file
Read a single neuron from a file
Prune selected vertices or edges from a neuron
Remove plotted neurons or other 3D objects
Prune a neuron by removing segments with a given Strahler order
Normalise an SWC format block of neuron morphology data
prune an object by removing points near (or far) from a target object
Make 2D (orthogonal) projection of 3D image data
neuron: class to represent traced neurons
Read one or more neurons from a NeuroML v1 file
Read a neuron saved by Fiji's Simple Neurite Tracer Plugin
Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object
Generic functions to read/write landmarks in any supported format
Read a CMTK format registration
Find which points of an object are inside a surface
Find the (asymmetric) difference between two collections of objects
Calculate number of potential synapses between two neurons
Read CMTK TypedStream file to a list in memory
Set the 3D viewpoint of an RGL window using anatomical terms
Return the space origin of a 3D image object
Read a neuron in swc file format
Read a local, or remote, neuronlistfh object saved to a file.
Find the union of two collections of objects
Make im3d image array containing values at locations defined by a mask
Return voxel dimensions (by default absolute voxel dimensions)
neuronlistfh - List of neurons loaded on demand from disk or remote website
Find the number of vertices in an object (or each element of a neuronlist)
Read one or more neurons from file to a neuronlist in memory
Calculate length of all segments in neuron
Subset neuron by keeping only vertices that match given conditions
Subset neuronlist returning either new neuronlist or names of chosen neurons
Read nrrd file into an array in memory
Make/convert neuron connectivity information into a seglist object
Simplify a registration list
Return the root or branch points of a neuron or graph
Read Vaa3d format image data
Transform the 3D location of objects such as neurons
Find the Strahler order of each point in a neuron
A simple wrapper class for multiple transformations
Extract from neuronlistfh object or its attached data.frame
Write a suitable list to a CMTK TypedStream file on disk
Write out CMTK registration list to folder
Transform image files using a registration or affine matrix
Return voxel dimensions of an object
Subset points in dotprops object that match given conditions
Write a 3D data object to an amiramesh format file
Write Amira surface (aka HxSurface or HyperSurface) into .surf file.
Recalculate Neurons's SWCData using SegList and point information
Scale and centre neuron 3D coordinates
Write out a neuron in any of the file formats we know about
Resample an object with a new spacing
Subset methods for different nat objects
Transform 3D points using a registration, affine matrix or function
Find 1D index given n-dimensional indices
Smooth the 3D coordinates of a neuron skeleton
Write neurons from a neuronlist object to individual files, or a zip archive
Compute the longest path (aka spine or backbone) of a neuron
Write out a neuronlistfh object to an RDS file
Synchronise a remote object
Write data and metadata to NRRD file or create a detached NRRD (nhdr) file.
Return a simplified segment graph for a neuron
Write object to VTK file
Summary statistics for neurons (e.g. cable length, number of nodes)
Subset hxsurf object to specified regions
Threshold an object, typically to produce a mask
Get and assign coordinates for classes containing 3D vertex data
Read AmiraMesh data in binary or ascii format
Decompose homogeneous affine matrix to CMTK registration parameters
Convert a suitable object to an im3d object.
all.equal method tailored to dotprops objects
Check equality on data and key attributes of im3d objects
Return the type of an amiramesh file on disk or a parsed header
Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007
Surface object (hxsurf) for the left mushroom body in FCWB template space
Check equality on key fields of neuron object