NeuroAnatomy Toolbox for Analysis of 3D Image Data
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Documentation for package ‘nat’ version 1.8.24
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A B C D E F G H I K M N O P R S T U V W X misc
| nat-package | Analyse 3D biological image data especially neurons |
-- A --
| affmat2cmtkparams | Decompose homogeneous affine matrix to CMTK registration parameters |
| 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 |
| amiratype | Return the type of an amiramesh file on disk or a parsed header |
| as.cmtkreg | Create and test cmtkreg objects that specify path to a CMTK registration |
| as.cmtkreg.default | Create and test cmtkreg objects that specify path to a CMTK registration |
| as.cmtkreg.matrix | Create and test cmtkreg objects that specify path to a CMTK registration |
| as.cmtkreg.reglist | Create and test cmtkreg objects that specify path to a CMTK registration |
| as.data.frame.neuronlist | Get or set the attached data.frame of a neuronlist |
| as.dotprops | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| as.hxsurf | Convert an object to a nat hxsurf object |
| as.hxsurf.mesh3d | Convert an object to a nat hxsurf object |
| as.im3d | Convert a suitable object to an im3d object. |
| as.im3d.im3d | Convert a suitable object to an im3d object. |
| as.im3d.matrix | Convert a suitable object to an im3d object. |
| as.mesh3d | Convert an object to an rgl mesh3d |
| as.mesh3d.ashape3d | Convert an object to an rgl mesh3d |
| as.mesh3d.hxsurf | Convert an object to an rgl mesh3d |
| as.neuron | neuron: class to represent traced neurons |
| as.neuron.data.frame | neuron: class to represent traced neurons |
| as.neuron.default | neuron: class to represent traced neurons |
| as.neuron.igraph | neuron: class to represent traced neurons |
| as.neuron.ngraph | neuron: class to represent traced neurons |
| as.neuronlist | Make a list of neurons that can be used for coordinate plotting/analysis |
| as.neuronlist.default | Make a list of neurons that can be used for coordinate plotting/analysis |
| as.neuronlist.neuronlistfh | convert neuronlistfh to a regular (in memory) neuronlist |
| as.neuronlistfh | neuronlistfh - List of neurons loaded on demand from disk or remote website |
| as.neuronlistfh.neuronlist | neuronlistfh - List of neurons loaded on demand from disk or remote website |
| as.ngraph | ngraph: a graph to encode a neuron's connectivity |
| as.ngraph.data.frame | ngraph: a graph to encode a neuron's connectivity |
| as.ngraph.neuron | ngraph: a graph to encode a neuron's connectivity |
| as.seglist | Make/convert neuron connectivity information into a seglist object |
| as.seglist.igraph | Make/convert neuron connectivity information into a seglist object |
| as.seglist.neuron | Make/convert neuron connectivity information into a seglist object |
-- B --
| boundingbox | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.character | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.default | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.im3d | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.list | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.neuron | Get the bounding box of an im3d volume or other compatible object |
| boundingbox.shape3d | Get the bounding box of an im3d volume or other compatible object |
| boundingbox<- | Get the bounding box of an im3d volume or other compatible object |
| branchpoints | Return the root or branch points of a neuron or graph |
| branchpoints.default | Return the root or branch points of a neuron or graph |
| branchpoints.igraph | Return the root or branch points of a neuron or graph |
| branchpoints.neuron | Return the root or branch points of a neuron or graph |
-- C --
| c.neuronlist | Combine multiple neuronlists into a single list |
| c.reglist | A simple wrapper class for multiple transformations |
| Cell07PNs | Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007 |
| clampmax | Return function that finds maximum of its inputs within a clamping range |
| cmtk | Return path to directory containing CMTK binaries |
| cmtk.bindir | Return path to directory containing CMTK binaries |
| cmtk.call | Utility function to create and run calls to CMTK commandline tools |
| cmtk.dof2mat | Convert CMTK registration to homogeneous affine matrix with dof2mat |
| cmtk.extract_affine | Extract affine registration from CMTK registration file or in-memory list |
| cmtk.mat2dof | Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration |
| cmtk.reformatx | Reformat an image with a CMTK registration using the reformatx tool |
| cmtk.statistics | Calculate image statistics for a nrrd or other CMTK compatible file |
| cmtk.system2 | Utility function to create and run calls to CMTK commandline tools |
| cmtk.targetvolume | Defines a target volume for a CMTK reformatx operation |
| cmtk.targetvolume.default | Defines a target volume for a CMTK reformatx operation |
| cmtk.targetvolume.im3d | Defines a target volume for a CMTK reformatx operation |
| cmtk.targetvolume.list | Defines a target volume for a CMTK reformatx operation |
| cmtk.version | Return cmtk version or test for presence of at least a specific version |
| cmtkparams2affmat | Compose homogeneous affine matrix from CMTK registration parameters |
| cmtkreg | Create and test cmtkreg objects that specify path to a CMTK registration |
| cmtkreglist | Make in-memory CMTK registration list from affine matrix or CMTK parameters |
| coord2ind | Find 1D indices into a 3D image given spatial coordinates |
| coord2ind.default | Find 1D indices into a 3D image given spatial coordinates |
-- D --
| data.frame<- | Get or set the attached data.frame of a neuronlist |
| data.frame<-.neuronlist | Get or set the attached data.frame of a neuronlist |
| dotprops | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.character | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.default | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.dotprops | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.im3d | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.neuron | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| dotprops.neuronlist | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| droplevels | Methods for working with the dataframe attached to a neuronlist |
| droplevels.neuronlist | Methods for working with the dataframe attached to a neuronlist |
-- E --
| endpoints | Return the root or branch points of a neuron or graph |
| endpoints.default | Return the root or branch points of a neuron or graph |
| endpoints.igraph | Return the root or branch points of a neuron or graph |
| endpoints.neuron | Return the root or branch points of a neuron or graph |
-- F --
| fileformats | Set or return list of registered file formats that we can read |
| find.neuron | Find neurons within a 3D selection box (usually drawn in rgl window) |
| find.soma | Find neurons with soma inside 3D selection box (usually drawn in rgl window) |
| flip | Flip an array, matrix or vector about an axis |
| flip.array | Flip an array, matrix or vector about an axis |
-- G --
| getformatreader | Set or return list of registered file formats that we can read |
| getformatwriter | Set or return list of registered file formats that we can read |
| graph.nodes | Return root, end, or branchpoints of an igraph object |
-- H --
| head | Methods for working with the dataframe attached to a neuronlist |
| head.neuronlist | Methods for working with the dataframe attached to a neuronlist |
| hxsurf | Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object |
-- I --
| ijkpos | Interconvert pixel and physical coordinates |
| im3d | Construct an im3d object representing 3D image data, densities etc |
| 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 |
| ind2coord.array | Find XYZ coords corresponding to 1D indices into a 3D image |
| ind2coord.default | Find XYZ coords corresponding to 1D indices into a 3D image |
| ind2coord.im3d | Find XYZ coords corresponding to 1D indices into a 3D image |
| intersect | Find the intersection of two collections of objects |
| intersect.default | Find the intersection of two collections of objects |
| intersect.neuronlist | Find the intersection of two collections of objects |
| invert_reglist | A simple wrapper class for multiple transformations |
| is.amiramesh | Check if file is amiramesh format |
| is.cmtkreg | Create and test cmtkreg objects that specify path to a CMTK registration |
| is.dotprops | dotprops: Neurons as point clouds with tangent vectors (but no connectivity) |
| is.fijitraces | Check whether a file is in Fiji's simple neurite tracer format |
| is.im3d | Test if an object is of class im3d |
| is.neuroml | Check whether a file is in NeuroML format |
| is.neuron | neuron: class to represent traced neurons |
| is.neuronlist | Test objects of neuronlist class to store multiple neurons |
| is.neuronlistfh | neuronlistfh - List of neurons loaded on demand from disk or remote website |
| 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 Peng's Vaa3D |
-- K --
| kcs20 | List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects |
-- M --
| mask | Mask an object, typically to produce a copy with some values zeroed out |
| mask.im3d | Mask an object, typically to produce a copy with some values zeroed out |
| materials | Extract or set the materials for an object |
| materials.character | Extract or set the materials for an object |
| materials.default | Extract or set the materials for an object |
| materials.hxsurf | Extract or set the materials for an object |
| MBL.surf | Surface object (hxsurf) for the left mushroom body in FCWB template space |
| mirror | Mirror 3D object about a given axis, optionally using a warping registration |
| mirror.character | Mirror 3D object about a given axis, optionally using a warping registration |
| mirror.default | Mirror 3D object about a given axis, optionally using a warping registration |
| mirror.neuronlist | Mirror 3D object about a given axis, optionally using a warping registration |
-- N --
| nat | Analyse 3D biological image data especially neurons |
| ndigest | Calculated normalised digest value for an object |
| ndigest.dotprops | Calculated normalised digest value for an object |
| ndigest.neuron | Calculated normalised digest value for an object |
| ndigest.neuronlistfh | Calculated normalised digest value for an object |
| neuron | neuron: class to represent traced neurons |
| neuronlist | Create a neuronlist from zero or more neurons |
| neuronlist-dataframe-methods | Methods for working with the dataframe attached to a neuronlist |
| neuronlistfh | neuronlistfh - List of neurons loaded on demand from disk or remote website |
| ngraph | ngraph: a graph to encode a neuron's connectivity |
| nlapply | lapply and mapply for neuronlists (with optional parallelisation) |
| nlscan | Scan through a set of neurons, individually plotting each one in 3D |
| nmapply | lapply and mapply for neuronlists (with optional parallelisation) |
| 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 dimensions) |
| nvertices | Find the number of vertices in an object (or each element of a neuronlist) |
| nvertices.default | Find the number of vertices in an object (or each element of a neuronlist) |
| nvertices.igraph | Find the number of vertices in an object (or each element of a neuronlist) |
| nvertices.neuronlist | Find the number of vertices in an object (or each element of a neuronlist) |
| nview3d | Set the 3D viewpoint of an RGL window using anatomical terms |
-- O --
| origin | Return the space origin of a 3D image object |
-- P --
| pan3d | Some useful extensions / changes to rgl defaults |
| plot.neuron | Plot a 2D projection of a neuron |
| plot.neuronlist | 2D plots of the elements in a neuronlist, optionally using a subset expression |
| plot3d | plot3d methods for different nat objects |
| plot3d.boundingbox | Plot a bounding box in 3D |
| plot3d.character | 3D plots of the elements in a neuronlist, optionally using a subset expression |
| 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 subset expression |
| pointsinside | Find which points of an object are inside a surface |
| pointsinside.default | Find which points of an object are inside a surface |
| potential_synapses | Calculate number of potential synapses between two neurons |
| potential_synapses.dotprops | Calculate number of potential synapses between two neurons |
| potential_synapses.neuron | Calculate number of potential synapses between two neurons |
| potential_synapses.neuronlist | 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 target object |
| prune.default | prune an object by removing points near (or far) from a target object |
| prune.dotprops | prune an object by removing points near (or far) from a target object |
| prune.neuron | prune an object by removing points near (or far) from a target object |
| prune.neuronlist | prune an object by removing points near (or far) from a target object |
| prune_edges | Prune selected vertices or edges from a neuron |
| prune_strahler | Prune a neuron by removing segments with a given Strahler order |
| prune_vertices | Prune selected vertices or edges from a neuron |
-- R --
| read.amiramesh | Read AmiraMesh data in binary or ascii format |
| read.amiramesh.header | Read AmiraMesh data in binary or ascii format |
| 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 hxsurf object |
| read.im3d | Read/Write calibrated 3D blocks of image data |
| read.landmarks | Generic functions to read/write landmarks in any supported format |
| 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.neuron.neuroml | Read one or more neurons from a NeuroML v1 file |
| read.neuron.swc | Read a neuron in swc file format |
| read.neuronlistfh | Read a local, or remote, neuronlistfh object saved to a file. |
| read.neurons | Read one or more neurons from file to a neuronlist in memory |
| read.ngraph.swc | Read a neuron in swc file format |
| read.nrrd | Read nrrd file into an array in memory |
| read.nrrd.header | Read nrrd file into an array in memory |
| read.vaa3draw | Read Vaa3d format image data |
| registerformat | Set or return list of registered file formats that we can read |
| reglist | A simple wrapper class for multiple transformations |
| remotesync | Synchronise a remote object |
| remotesync.neuronlistfh | Synchronise a remote object |
| resample | Resample an object with a new spacing |
| resample.neuron | Resample an object with a new spacing |
| rootpoints | Return the root or branch points of a neuron or graph |
| rootpoints.default | Return the root or branch points of a neuron or graph |
| rootpoints.igraph | Return the root or branch points of a neuron or graph |
| rootpoints.neuron | Return the root or branch points of a neuron or graph |
-- S --
| scale | Scale and centre neuron 3D coordinates |
| scale.dotprops | Scale and centre neuron 3D coordinates |
| 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 object |
| seglist2swc | Recalculate Neurons's SWCData using SegList and point information |
| segmentgraph | Return a simplified segment graph for a neuron |
| setdiff | Find the (asymmetric) difference between two collections of objects |
| setdiff.default | Find the (asymmetric) difference between two collections of objects |
| setdiff.neuronlist | Find the (asymmetric) difference between two collections of objects |
| simplify_reglist | Simplify a registration list |
| smooth_neuron | Smooth the 3D coordinates of a neuron skeleton |
| smooth_segment_gauss | 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 |
| 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 conditions |
| subset.neuronlist | Subset neuronlist returning either new neuronlist or names of chosen neurons |
| summary | Summary statistics for neurons (e.g. cable length, number of nodes) |
| summary.dotprops | Summary statistics for neurons (e.g. cable length, number of nodes) |
| summary.neuron | Summary statistics for neurons (e.g. cable length, number of nodes) |
| summary.neuronlist | Summary statistics for neurons (e.g. cable length, number of nodes) |
-- T --
| tail | Methods for working with the dataframe attached to a neuronlist |
| tail.neuronlist | Methods for working with the dataframe attached to a neuronlist |
| threshold | Threshold an object, typically to produce a mask |
| threshold.im3d | Threshold an object, typically to produce a mask |
-- U --
| union | Find the union of two collections of objects |
| union.default | Find the union of two collections of objects |
| union.neuronlist | Find the union of two collections of objects |
| unmask | Make im3d image array containing values at locations defined by a mask |
-- V --
| voxdims | Return voxel dimensions of an object |
| voxdims.character | Return voxel dimensions of an object |
| voxdims.default | Return voxel dimensions of an object |
| voxdims.im3d | Return voxel dimensions of an object |
-- W --
| with | Methods for working with the dataframe attached to a neuronlist |
| with.neuronlist | Methods for working with the dataframe attached to a neuronlist |
| 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 .surf file. |
| write.im3d | Read/Write calibrated 3D blocks of image data |
| write.landmarks | Generic functions to read/write landmarks in any supported format |
| 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, or a zip archive |
| write.nrrd | Write data and metadata to NRRD file or create a detached NRRD (nhdr) file. |
| write.nrrd.header | Write data and metadata to NRRD file or create a detached NRRD (nhdr) file. |
| write.nrrd.header.for.file | Write data and metadata to NRRD file or create a detached NRRD (nhdr) file. |
| write.vtk | Write object to VTK file |
| write.vtk.neuron | Write object to VTK file |
-- X --
| xform | Transform the 3D location of objects such as neurons |
| xform.character | Transform the 3D location of objects such as neurons |
| xform.data.frame | Transform the 3D location of objects such as neurons |
| xform.default | Transform the 3D location of objects such as neurons |
| xform.dotprops | Transform the 3D location of objects such as neurons |
| xform.list | Transform the 3D location of objects such as neurons |
| xform.neuron | Transform the 3D location of objects such as neurons |
| xform.neuronlist | Transform the 3D location of objects such as neurons |
| xform.shape3d | Transform the 3D location of objects such as neurons |
| xformimage | Transform image files using a registration or affine matrix |
| xformimage.character | Transform image files using a registration or affine matrix |
| xformimage.cmtkreg | Transform image files using a registration or affine matrix |
| xformimage.default | Transform image files using a registration or affine matrix |
| xformimage.reglist | Transform image files using a registration or affine matrix |
| xformpoints | Transform 3D points using a registration, affine matrix or function |
| xformpoints.character | Transform 3D points using a registration, affine matrix or function |
| xformpoints.cmtkreg | Transform 3D points using a registration, affine matrix or function |
| xformpoints.default | Transform 3D points using a registration, affine matrix or function |
| xformpoints.reglist | Transform 3D points using a registration, affine matrix or function |
| xyzmatrix | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.default | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.dotprops | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.hxsurf | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.igraph | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.mesh3d | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.neuron | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix.neuronlist | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<- | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.dotprops | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.hxsurf | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.igraph | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.neuron | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.neuronlist | Get and assign coordinates for classes containing 3D vertex data |
| xyzmatrix<-.shape3d | Get and assign coordinates for classes containing 3D vertex data |
| xyzpos | Interconvert pixel and physical coordinates |
-- misc --
| *.dotprops | Arithmetic for dotprops objects |
| *.neuron | Arithmetic for neuron coordinates |
| *.neuronlist | Arithmetic for neuron coordinates applied to neuronlists |
| +.dotprops | Arithmetic for dotprops objects |
| +.neuron | Arithmetic for neuron coordinates |
| +.neuronlist | Arithmetic for neuron coordinates applied to neuronlists |
| -.dotprops | Arithmetic for dotprops objects |
| -.neuron | Arithmetic for neuron coordinates |
| -.neuronlist | Arithmetic for neuron coordinates applied to neuronlists |
| /.dotprops | Arithmetic for dotprops objects |
| /.neuron | Arithmetic for neuron coordinates |
| /.neuronlist | Arithmetic for neuron coordinates applied to neuronlists |
| [.neuronlist | Methods for working with the dataframe attached to a neuronlist |
| [.neuronlistfh | Extract from neuronlistfh object or its attached data.frame |
| [<-.neuronlist | Methods for working with the dataframe attached to a neuronlist |