NeuroAnatomy Toolbox for Analysis of 3D Image Data

affmat2cmtkparams | Decompose homogeneous affine matrix to CMTK registration... |

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 |

amiramesh-io | Read AmiraMesh data in binary or ascii format |

amiratype | Return the type of an AmiraMesh file on disk or a parsed... |

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... |

as.neuronlist.neuronlistfh | convert neuronlistfh to a regular (in memory) neuronlist |

boundingbox | Get the bounding box of an image volume or object containing... |

Cell07PNs | Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter... |

clampmax | Return function that finds maximum of its inputs within a... |

cmtk.bindir | Return path to directory containing CMTK binaries |

cmtk.call | Utility function to create and run calls to CMTK command line... |

cmtk.dof2mat | Convert CMTK registration to homogeneous affine matrix with... |

cmtk.extract_affine | Extract affine registration from CMTK registration file or... |

cmtk.mat2dof | Use CMTK mat2dof to convert homogeneous affine matrix into... |

cmtkparams2affmat | Compose homogeneous affine matrix from CMTK registration... |

cmtk.reformatx | Reformat an image with a CMTK registration using the... |

cmtkreg | Create and test cmtkreg objects that specify path to a CMTK... |

cmtkreglist | Make in-memory CMTK registration list from affine matrix or... |

cmtk.statistics | Calculate image statistics for a nrrd or other CMTK... |

cmtk.targetvolume | Defines a target volume for a CMTK reformatx operation |

cmtk.version | Return cmtk version or test for presence of at least a... |

c.neuronlist | Combine multiple neuronlists into a single list |

coord2ind | Find 1D or 3D voxel indices into a 3D image given spatial... |

correct_root | Interactively re-root neurons (usually to their soma) |

distal_to | Return indices of points in a neuron distal to a given node |

dl1neuron | Olfactory Projection Neuron reconstructed from EM data |

dotprops | dotprops: Neurons as point clouds with tangent vectors (but... |

dotprops-arithmetic | Arithmetic for nat dotprops and surface objects |

fileformats | Set or return list of registered file formats that we can... |

find.neuron | Find neurons within a 3D selection box (usually drawn in rgl... |

find.soma | Find neurons with soma inside 3D selection box (usually drawn... |

flip | Flip an array, matrix or vector about an axis |

get-set-neuronlist-data.frame | Get or set the attached data.frame of a neuronlist |

graph.nodes | Return root, end, or branchpoints of an igraph object |

im3d | Construct an im3d object representing 3D image data,... |

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 |

intersect_plane | Find the points on a plane that are intersected by an object |

is.amiramesh | Check if file is AmiraMesh format |

is.fijitraces | Check whether a file is in Fiji's simple neurite tracer... |

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... |

kcs20 | List of 20 Kenyon Cells from Chiang et al 2011 converted to... |

makeboundingbox | Construct a 3D bounding box object |

make_model | Generate a 3D model from connector and/or tree node data |

mask | Mask an object, typically to produce a copy with some values... |

materials | Extract or set the materials for an object |

MBL.surf | Surface object (hxsurf) for the left mushroom body in FCWB... |

mirror | Mirror 3D object about a given axis, optionally using a... |

nat-package | Analyse 3D biological image data especially neurons |

nclear3d | Clear the rgl or plotly 3D scene |

ndigest | Calculated normalised digest value for an object |

neuron | neuron: class to represent traced neurons |

neuron-arithmetic | Arithmetic for neuron coordinates |

neuronlist | Create a neuronlist from zero or more neurons |

neuronlist-arithmetic | Arithmetic for neuron coordinates applied to neuronlists |

neuronlist-dataframe-methods | Methods for working with the dataframe attached to a... |

neuronlistfh | neuronlistfh - List of neurons loaded on demand from disk or... |

ngraph | ngraph: a graph to encode a neuron's connectivity |

nlapply | lapply and mapply for neuronlists (with optional... |

nlscan | Scan through a set of neurons, individually plotting each one... |

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... |

nvertices | Find the number of vertices in an object (or each element of... |

nview3d | Set the 3D viewpoint of an RGL window using anatomical terms |

origin | Return the space origin of a 3D image object |

overlap_score | Generate a connectivity matrix based on euclidean distance... |

pan3d | Some useful extensions / changes to rgl defaults |

plane_coefficients | Find the coefficients of the plane equation |

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 or plotly module |

plot3d.neuronlist | 3D plots of the elements in a neuronlist, optionally using a... |

plot3d.ngraph | Plot 3d representation of neuron (ngraph) with directed edges |

plot.neuron | Plot a 2D projection of a neuron |

plot.neuronlist | 2D plots of the elements in a neuronlist, optionally using a... |

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... |

prune_in_volume | Prune neuron(s) within a volume defined by a 3D mesh |

prune_online | Prune a neuron interactively in an rgl window |

prune_strahler | Prune a neuron by removing segments with a given Strahler... |

prune_twigs | Remove all twigs less than a certain path length from a... |

prune_vertices | Prune selected vertices or edges from a neuron |

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... |

read.landmarks | Generic functions to read/write landmarks in any supported... |

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.neuronlistfh | Read a local, or remote, neuronlistfh object saved to a file. |

read.neuron.neuroml | Read one or more neurons from a NeuroML v1 file |

read.neurons | Read one or more neurons from file to a neuronlist in memory |

read.neuron.swc | Read a neuron in swc file format |

read.nrrd | Read NRRD files/headers into 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, branch, or end 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... |

seglist2swc | Recalculate Neurons's SWCData using SegList and point... |

segmentgraph | Return a simplified segment graph for a neuron |

select_points | Interactively select 3D points in space |

setdiff | Find the (asymmetric) difference between two collections of... |

sholl_analysis | Perform a Sholl analysis on neuron skeletons |

simplify_neuron | Simplify a neuron to the longest tree with n branch points |

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 |

stitch_neuron | Stitch two neurons together at their closest endpoint |

stitch_neurons | Stitch multiple fragments into single neuron using nearest... |

stitch_neurons_mst | Stitch multiple fragments into single neuron using minimum... |

strahler_order | Find the Strahler order of each point in a neuron |

sub2ind | Find 1D index given n-dimensional indices |

sub-.neuronlistfh | Extract from neuronlistfh object or its attached data.frame |

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... |

subset.neuronlist | Subset neuronlist returning either new neuronlist or names of... |

summary.neuron | Summary statistics for neurons (e.g. cable length, number of... |

threshold | Threshold an object, typically to produce a mask |

tpsreg | Thin plate spline registrations via xform and friends |

union | Find the union of two collections of objects |

unmask | Make im3d image array containing values at locations defined... |

voxdims | Return voxel dimensions of an object |

wire3d | Wire frame plots |

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... |

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,... |

write.nrrd | Write data and metadata to NRRD file or create a detached... |

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... |

xyzmatrix | Get and assign coordinates for classes containing 3D vertex... |

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