| Analyse 3D biological image data especially neurons | nat-package nat |
| Extract from neuronlistfh object or its attached data.frame | [.neuronlistfh |
| Arithmetic for neuron coordinates applied to neuronlists | *.neuronlist +.neuronlist -.neuronlist /.neuronlist |
| Decompose homogeneous affine matrix to CMTK registration parameters | affmat2cmtkparams |
| all.equal method tailored to dotprops objects | all.equal.dotprops |
| Check equality on data and key attributes of im3d objects | all.equal.im3d |
| Check equality on key fields of neuron object | all.equal.neuron |
| Return the type of an AmiraMesh file on disk or a parsed header | amiratype |
| Get or set the attached data.frame of a neuronlist | as.data.frame.neuronlist data.frame<- data.frame<-.neuronlist |
| Convert an object to a nat hxsurf object | as.hxsurf as.hxsurf.mesh3d |
| Convert a suitable object to an im3d object. | as.im3d as.im3d.im3d as.im3d.matrix |
| Convert an object to an rgl mesh3d | as.mesh3d as.mesh3d.ashape3d as.mesh3d.boundingbox as.mesh3d.hxsurf |
| Make a list of neurons that can be used for coordinate plotting/analysis | as.neuronlist as.neuronlist.default |
| convert neuronlistfh to a regular (in memory) neuronlist | as.neuronlist.neuronlistfh |
| Get the bounding box of an image volume or object containing 3D vertices | boundingbox boundingbox.character boundingbox.default boundingbox.im3d boundingbox<- |
| Concatenate HyperSurface objects | c.hxsurf |
| Combine multiple neuronlists into a single list | c.neuronlist |
| Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007 | Cell07PNs |
| Return function that finds maximum of its inputs within a clamping range | clampmax |
| Return path to directory containing CMTK binaries | cmtk cmtk.bindir |
| Utility function to create and run calls to CMTK command line tools | cmtk.call cmtk.system2 |
| Convert CMTK registration to homogeneous affine matrix with dof2mat | cmtk.dof2mat |
| Extract affine registration from CMTK registration file or in-memory list | cmtk.extract_affine |
| Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration | cmtk.mat2dof |
| Reformat an image with a CMTK registration using the reformatx tool | cmtk.reformatx |
| Calculate image statistics for a nrrd or other CMTK compatible file | cmtk.statistics |
| Defines a target volume for a CMTK reformatx operation | cmtk.targetvolume cmtk.targetvolume.default cmtk.targetvolume.im3d cmtk.targetvolume.list |
| Return cmtk version or test for presence of at least a specific version | cmtk.version |
| Compose homogeneous affine matrix from CMTK registration parameters | cmtkparams2affmat |
| Create and test cmtkreg objects that specify path to a CMTK registration | as.cmtkreg as.cmtkreg.default as.cmtkreg.matrix as.cmtkreg.reglist cmtkreg is.cmtkreg |
| Make in-memory CMTK registration list from affine matrix or CMTK parameters | cmtkreglist |
| Find 1D or 3D voxel indices into a 3D image given spatial coordinates | coord2ind coord2ind.default |
| Interactively re-root neurons (usually to their soma) | correct_root |
| Return indices of points in a neuron distal to a given node | distal_to |
| Olfactory Projection Neuron reconstructed from EM data | dl1neuron |
| dotprops: Neurons as point clouds with tangent vectors (but no connectivity) | as.dotprops dotprops dotprops.character dotprops.default dotprops.dotprops dotprops.im3d dotprops.neuron dotprops.neuronlist is.dotprops |
| Set or return list of registered file formats that we can read | fileformats getformatreader getformatwriter registerformat |
| Find neurons within a 3D selection box (usually drawn in rgl window) | find.neuron |
| Find neurons with soma inside 3D selection box (usually drawn in rgl window) | find.soma |
| Flip an array, matrix or vector about an axis | flip flip.array |
| Get topological features per each node | get_distance_to_soma get_topo_features |
| Return root, end, or branchpoints of an igraph object | graph.nodes |
| Construct an im3d object representing 3D image data, densities etc | im3d |
| Interconvert pixel and physical coordinates | ijkpos im3d-coords xyzpos |
| Read/Write calibrated 3D blocks of image data | im3d-io read.im3d write.im3d |
| Method to plot spatially calibrated image arrays | image.im3d |
| Convert locations of im3d voxel grid into XYZ coordinates | imexpand.grid |
| Make a scalebar to accompany an image.im3d plot | imscalebar |
| Slice out a 3D subarray (or 2d matrix) from a 3D image array | imslice |
| Find XYZ coords corresponding to 1D indices into a 3D image | ind2coord ind2coord.array ind2coord.default ind2coord.im3d |
| Find the intersection of two collections of objects | intersect intersect.default intersect.neuronlist |
| Find the points on a plane that are intersected by an object | intersect_plane intersect_plane.default intersect_plane.neuron |
| Check if file is AmiraMesh format | is.amiramesh |
| Check whether a file is in Fiji's simple neurite tracer format | is.fijitraces |
| Test if an object is of class im3d | is.im3d |
| Check whether a file is in NeuroML format | is.neuroml |
| Test objects of neuronlist class to store multiple neurons | is.neuronlist |
| Check if a file is a NRRD file | is.nrrd |
| Test if a file is an SWC format neuron | is.swc |
| Check if a file is in the raw image format used by Hanchuan Peng's Vaa3D | is.vaa3draw |
| List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects | kcs20 |
| Generate a 3D model from connector and/or tree node data | make_model |
| Construct a 3D bounding box object | makeboundingbox |
| Mask an object, typically to produce a copy with some values zeroed out | mask mask.im3d |
| Extract or set the materials for an object | materials materials.character materials.default materials.hxsurf |
| Surface object (hxsurf) for the left mushroom body in FCWB template space | MBL.surf |
| Mirror 3D object about a given axis, optionally using a warping registration | mirror mirror.character mirror.default mirror.neuronlist |
| Clear the rgl or plotly 3D scene | nclear3d |
| Calculated normalised digest value for an object | ndigest ndigest.dotprops ndigest.neuron ndigest.neuronlistfh |
| neuron: class to represent traced neurons | as.neuron as.neuron.data.frame as.neuron.default as.neuron.igraph as.neuron.ngraph is.neuron neuron |
| Create a neuronlist from zero or more neurons | neuronlist |
| Methods for working with the dataframe attached to a neuronlist | droplevels droplevels.neuronlist head head.neuronlist neuronlist-dataframe-methods tail tail.neuronlist with with.neuronlist [.neuronlist [<-.neuronlist |
| neuronlistfh - List of neurons loaded on demand from disk or remote website | as.neuronlistfh as.neuronlistfh.neuronlist c.neuronlistfh is.neuronlistfh neuronlistfh |
| A neuronlist object that will read neurons from a zip file on demand | as.neuronlist.neuronlistz neuronlistz |
| ngraph: a graph to encode a neuron's connectivity | as.ngraph as.ngraph.data.frame as.ngraph.neuron ngraph |
| lapply and mapply for neuronlists (with optional parallelisation) | nlapply nmapply progress_natprogress |
| Scan through a set of neurons, individually plotting each one in 3D | nlscan |
| Open customised rgl window | nopen3d |
| Normalise an SWC format block of neuron morphology data | normalise_swc |
| Remove plotted neurons or other 3D objects | npop3d |
| Return voxel dimensions (by default absolute voxel dimensions) | nrrd.voxdims |
| Find the number of vertices in an object (or each element of a neuronlist) | nvertices nvertices.default nvertices.neuronlist nvertices.shapelist3d |
| Set the 3D viewpoint of an RGL window using anatomical terms | nview3d |
| Arithmetic for nat dotprops and surface objects | Ops.dotprops Ops.hxsurf Ops.mesh3d |
| Arithmetic for neuron coordinates | Ops.neuron |
| Return the space origin of a 3D image object | origin |
| Generate a connectivity matrix based on euclidean distance between points | overlap_score |
| Some useful extensions / changes to rgl defaults | pan3d |
| Find the coefficients of the plane equation | plane_coefficients |
| Plot a 2D projection of a neuron | plot.dotprops plot.neuron |
| 2D plots of the elements in a neuronlist, optionally using a subset expression | plot.neuronlist |
| plot3d methods for different nat objects | plot3d |
| Plot a bounding box in 3D | plot3d.boundingbox |
| Plot the domain of a CMTK registration | plot3d.cmtkreg |
| 3D plots of dotprops objects using rgl package | plot3d.dotprops |
| Plot amira surface objects in 3D using rgl | plot3d.hxsurf |
| Plot neurons in 3D using rgl library or plotly module | plot3d.neuron |
| 3D plots of the elements in a neuronlist, optionally using a subset expression | plot3d.character plot3d.neuronlist |
| Plot 3d representation of neuron (ngraph) with directed edges | plot3d.ngraph |
| Find which points of an object are inside a surface | pointsinside pointsinside.default |
| Calculate number of potential synapses between two neurons | potential_synapses potential_synapses.dotprops potential_synapses.neuron potential_synapses.neuronlist |
| Make 2D (orthogonal) projection of 3D image data | projection |
| prune an object by removing points near (or far) from a target object | prune prune.default prune.dotprops prune.neuron prune.neuronlist |
| Prune neuron(s) within a volume defined by a 3D mesh | prune_in_volume prune_in_volume.neuron prune_in_volume.neuronlist |
| Prune a neuron interactively in an rgl window | prune_online prune_online.neuron prune_online.neuronlist |
| Prune a neuron by removing segments with a given Strahler order | prune_strahler |
| Remove all twigs less than a certain path length from a neuron | prune_twigs prune_twigs.neuron prune_twigs.neuronlist |
| Prune selected vertices or edges from a neuron | prune_edges prune_vertices |
| Read AmiraMesh data in binary or ascii format | read.amiramesh read.amiramesh.header |
| Read CMTK TypedStream file to a list in memory | read.cmtk |
| Read a CMTK format registration | read.cmtkreg |
| Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object | hxsurf read.hxsurf |
| Generic functions to read/write landmarks in any supported format | read.landmarks write.landmarks |
| Return parsed XML or R list versions of a NeuroML file | read.morphml |
| Read a single neuron from a file | read.neuron |
| Read a neuron saved by Fiji's Simple Neurite Tracer Plugin | read.neuron.fiji |
| Read one or more neurons from a NeuroML v1 file | read.neuron.neuroml |
| Read a neuron in swc file format | read.neuron.swc read.ngraph.swc |
| Read a local, or remote, neuronlistfh object saved to a file. | read.neuronlistfh |
| Read one or more neurons from file to a neuronlist in memory | read.neurons |
| Read NRRD files/headers into memory | nrrd.datafiles read.nrrd read.nrrd.header |
| Read Vaa3d format image data | read.vaa3draw |
| A simple wrapper class for multiple transformations | c.reglist invert_reglist reglist |
| Synchronise a remote object | remotesync remotesync.neuronlistfh |
| Reroot neurons | reroot reroot.neuron reroot.neuronlist |
| Resample an object with a new spacing | resample resample.neuron resample.neuronlist |
| Return the root, branch, or end points of a neuron or graph | branchpoints branchpoints.default branchpoints.igraph branchpoints.neuron endpoints endpoints.default endpoints.igraph endpoints.neuron rootpoints rootpoints.default rootpoints.igraph rootpoints.neuron |
| Scale and centre neuron 3D coordinates | scale scale.dotprops scale.neuron |
| Calculate length of all segments in neuron | seglengths |
| Make/convert neuron connectivity information into a seglist object | as.seglist as.seglist.igraph as.seglist.neuron seglist |
| Recalculate Neurons's SWCData using SegList and point information | seglist2swc |
| Return a simplified segment graph for a neuron | segmentgraph |
| Interactively select 3D points in space | select_points |
| Find the (asymmetric) difference between two collections of objects | setdiff setdiff.default setdiff.neuronlist |
| Perform a Sholl analysis on neuron skeletons | sholl_analysis sholl_analysis.neuron sholl_analysis.neuronlist |
| Simplify a neuron to the longest tree with n branch points | simplify_neuron |
| Simplify a registration list | simplify_reglist |
| Smooth the 3D coordinates of a neuron skeleton | smooth_neuron smooth_segment_gauss |
| Compute the longest path (aka spine or backbone) of a neuron | spine |
| Stitch two neurons together at their closest endpoint | stitch_neuron |
| Stitch multiple fragments into single neuron using nearest endpoints | stitch_neurons |
| Stitch multiple fragments into single neuron using minimum spanning tree | stitch_neurons_mst |
| Find the Strahler order of each point in a neuron | strahler_order |
| Find 1D index given n-dimensional indices | sub2ind |
| Subset methods for different nat objects | subset |
| Subset points in dotprops object that match given conditions | subset.dotprops |
| Subset hxsurf object to specified regions | subset.hxsurf |
| Subset neuron by keeping only vertices that match given conditions | subset.neuron |
| Subset neuronlist returning either new neuronlist or names of chosen neurons | subset.neuronlist |
| Summary statistics for neurons (e.g. cable length, number of nodes) | summary summary.dotprops summary.mesh3d summary.neuron summary.neuronlist |
| Threshold an object, typically to produce a mask | threshold threshold.im3d |
| Thin plate spline registrations via xform and friends | tpsreg xformpoints.tpsreg |
| Find the union of two collections of objects | union union.default union.neuronlist |
| Make im3d image array containing values at locations defined by a mask | unmask |
| Return voxel dimensions of an object | voxdims voxdims.character voxdims.default voxdims.im3d |
| Wire frame plots | wire3d wire3d.hxsurf wire3d.mesh3d wire3d.shapelist3d |
| Write a 3D data object to an AmiraMesh format file | write.amiramesh |
| Write a suitable list to a CMTK TypedStream file on disk | write.cmtk |
| Write out CMTK registration list to folder | write.cmtkreg |
| Write Amira surface (aka HxSurface or HyperSurface) into .surf file. | write.hxsurf |
| Write out a neuron skeleton or mesh in any of the file formats we know about | write.neuron |
| Write out a neuronlistfh object to an RDS file | write.neuronlistfh |
| Write neurons from a neuronlist object to individual files, or a zip archive | write.neurons |
| Write data and metadata to NRRD file or create a detached NRRD (nhdr) file. | write.nrrd write.nrrd.header write.nrrd.header.for.file |
| Write object to VTK file | write.vtk write.vtk.neuron |
| Transform the 3D location of objects such as neurons | xform xform.character xform.data.frame xform.default xform.dotprops xform.list xform.mesh3d xform.neuron xform.neuronlist xform.shape3d |
| Transform image files using a registration or affine matrix | xformimage xformimage.character xformimage.cmtkreg xformimage.default xformimage.reglist |
| Transform 3D points using a registration, affine matrix or function | xformpoints xformpoints.character xformpoints.cmtkreg xformpoints.default xformpoints.reglist |
| Get and assign coordinates for classes containing 3D vertex data | xyzmatrix xyzmatrix.character xyzmatrix.default xyzmatrix.dotprops xyzmatrix.hxsurf xyzmatrix.igraph xyzmatrix.list xyzmatrix.mesh3d xyzmatrix.neuron xyzmatrix.neuronlist xyzmatrix.shapelist3d xyzmatrix2list xyzmatrix2str xyzmatrix<- xyzmatrix<-.character xyzmatrix<-.dotprops xyzmatrix<-.hxsurf xyzmatrix<-.igraph xyzmatrix<-.mesh3d xyzmatrix<-.neuron xyzmatrix<-.neuronlist xyzmatrix<-.shape3d xyzmatrix<-.shapelist3d |
