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