| 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 im3d volume or other compatible... |
| 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 commandline... |
| 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 indices into a 3D image given spatial coordinates |
| dotprops | dotprops: Neurons as point clouds with tangent vectors (but... |
| dotprops-arithmetic | Arithmetic for dotprops 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 |
| 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... |
| 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 |
| 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 |
| pan3d | Some useful extensions / changes to rgl defaults |
| 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 |
| plot3d.neuronlist | 3D plots of the elements in a neuronlist, optionally using a... |
| 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_strahler | Prune a neuron by removing segments with a given Strahler... |
| 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 file into an array in 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 or branch 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 |
| setdiff | Find the (asymmetric) difference between two collections of... |
| 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 |
| 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 |
| 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 |
| 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... |
