{
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  "Title": "NeuroAnatomy Toolbox for Analysis of 3D Image Data",
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  "Description": "NeuroAnatomy Toolbox (nat) enables analysis and\nvisualisation of 3D biological image data, especially traced\nneurons. Reads and writes 3D images in NRRD and 'Amira'\nAmiraMesh formats and reads surfaces in 'Amira' hxsurf format.\nTraced neurons can be imported from and written to SWC and\n'Amira' LineSet and SkeletonGraph formats. These data can then\nbe visualised in 3D via 'rgl', manipulated including applying\ncalculated registrations, e.g. using the 'CMTK' registration\nsuite, and analysed. There is also a simple representation for\nneurons that have been subjected to 3D skeletonisation but not\nformally traced; this allows morphological comparison between\nneurons including searches and clustering (via the 'nat.nblast'\nextension package).",
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  "Date/Publication": "2026-04-16 09:24:14 UTC",
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    {
      "page": "get-set-neuronlist-data.frame",
      "title": "Get or set the attached data.frame of a neuronlist",
      "topics": [
        "as.data.frame.neuronlist",
        "data.frame<-",
        "data.frame<-.neuronlist"
      ]
    },
    {
      "page": "as.hxsurf",
      "title": "Convert an object to a nat hxsurf object",
      "concept": [
        "hxsurf"
      ],
      "topics": [
        "as.hxsurf",
        "as.hxsurf.mesh3d"
      ]
    },
    {
      "page": "as.im3d",
      "title": "Convert a suitable object to an im3d object.",
      "concept": [
        "im3d"
      ],
      "topics": [
        "as.im3d",
        "as.im3d.im3d",
        "as.im3d.matrix"
      ]
    },
    {
      "page": "as.mesh3d",
      "title": "Convert an object to an rgl mesh3d",
      "concept": [
        "hxsurf"
      ],
      "topics": [
        "as.mesh3d",
        "as.mesh3d.ashape3d",
        "as.mesh3d.boundingbox",
        "as.mesh3d.hxsurf"
      ]
    },
    {
      "page": "as.neuronlist",
      "title": "Make a list of neurons that can be used for coordinate plotting/analysis",
      "topics": [
        "as.neuronlist",
        "as.neuronlist.default"
      ]
    },
    {
      "page": "as.neuronlist.neuronlistfh",
      "title": "convert neuronlistfh to a regular (in memory) neuronlist",
      "topics": [
        "as.neuronlist.neuronlistfh"
      ]
    },
    {
      "page": "boundingbox",
      "title": "Get the bounding box of an image volume or object containing 3D vertices",
      "concept": [
        "im3d"
      ],
      "topics": [
        "boundingbox",
        "boundingbox.character",
        "boundingbox.default",
        "boundingbox.im3d",
        "boundingbox<-"
      ]
    },
    {
      "page": "hxsurf-ops",
      "title": "Concatenate HyperSurface objects",
      "topics": [
        "c.hxsurf"
      ]
    },
    {
      "page": "c.neuronlist",
      "title": "Combine multiple neuronlists into a single list",
      "topics": [
        "c.neuronlist"
      ]
    },
    {
      "page": "Cell07PNs",
      "title": "Cell07PNs: 40 Sample Projection Neurons from Jefferis, Potter et al 2007",
      "concept": [
        "nat-data"
      ],
      "topics": [
        "Cell07PNs"
      ]
    },
    {
      "page": "clampmax",
      "title": "Return function that finds maximum of its inputs within a clamping range",
      "topics": [
        "clampmax"
      ]
    },
    {
      "page": "cmtk.bindir",
      "title": "Return path to directory containing CMTK binaries",
      "topics": [
        "cmtk",
        "cmtk.bindir"
      ]
    },
    {
      "page": "cmtk.call",
      "title": "Utility function to create and run calls to CMTK command line tools",
      "topics": [
        "cmtk.call",
        "cmtk.system2"
      ]
    },
    {
      "page": "cmtk.dof2mat",
      "title": "Convert CMTK registration to homogeneous affine matrix with dof2mat",
      "concept": [
        "cmtk-commandline",
        "cmtk-geometry"
      ],
      "topics": [
        "cmtk.dof2mat"
      ]
    },
    {
      "page": "cmtk.extract_affine",
      "title": "Extract affine registration from CMTK registration file or in-memory list",
      "concept": [
        "cmtk-io"
      ],
      "topics": [
        "cmtk.extract_affine"
      ]
    },
    {
      "page": "cmtk.mat2dof",
      "title": "Use CMTK mat2dof to convert homogeneous affine matrix into CMTK registration",
      "concept": [
        "cmtk-commandline",
        "cmtk-geometry"
      ],
      "topics": [
        "cmtk.mat2dof"
      ]
    },
    {
      "page": "cmtk.reformatx",
      "title": "Reformat an image with a CMTK registration using the reformatx tool",
      "topics": [
        "cmtk.reformatx"
      ]
    },
    {
      "page": "cmtk.statistics",
      "title": "Calculate image statistics for a nrrd or other CMTK compatible file",
      "topics": [
        "cmtk.statistics"
      ]
    },
    {
      "page": "cmtk.targetvolume",
      "title": "Defines a target volume for a CMTK reformatx operation",
      "topics": [
        "cmtk.targetvolume",
        "cmtk.targetvolume.character",
        "cmtk.targetvolume.default",
        "cmtk.targetvolume.im3d",
        "cmtk.targetvolume.list"
      ]
    },
    {
      "page": "cmtk.version",
      "title": "Return cmtk version or test for presence of at least a specific version",
      "topics": [
        "cmtk.version"
      ]
    },
    {
      "page": "cmtkparams2affmat",
      "title": "Compose homogeneous affine matrix from CMTK registration parameters",
      "concept": [
        "cmtk-geometry"
      ],
      "topics": [
        "cmtkparams2affmat"
      ]
    },
    {
      "page": "cmtkreg",
      "title": "Create and test cmtkreg objects that specify path to a CMTK registration",
      "topics": [
        "as.cmtkreg",
        "as.cmtkreg.default",
        "as.cmtkreg.matrix",
        "as.cmtkreg.reglist",
        "cmtkreg",
        "is.cmtkreg"
      ]
    },
    {
      "page": "cmtkreglist",
      "title": "Make in-memory CMTK registration list from affine matrix or CMTK parameters",
      "topics": [
        "cmtkreglist"
      ]
    },
    {
      "page": "coord2ind",
      "title": "Find 1D or 3D voxel indices into a 3D image given spatial coordinates",
      "topics": [
        "coord2ind",
        "coord2ind.default"
      ]
    },
    {
      "page": "correct_root",
      "title": "Interactively re-root neurons (usually to their soma)",
      "topics": [
        "correct_root"
      ]
    },
    {
      "page": "distal_to",
      "title": "Return indices of points in a neuron distal to a given node",
      "topics": [
        "distal_to"
      ]
    },
    {
      "page": "dl1neuron",
      "title": "Olfactory Projection Neuron reconstructed from EM data",
      "topics": [
        "dl1neuron"
      ]
    },
    {
      "page": "dotprops",
      "title": "dotprops: Neurons as point clouds with tangent vectors (but no connectivity)",
      "topics": [
        "as.dotprops",
        "dotprops",
        "dotprops.character",
        "dotprops.default",
        "dotprops.dotprops",
        "dotprops.im3d",
        "dotprops.neuron",
        "dotprops.neuronlist",
        "is.dotprops"
      ]
    },
    {
      "page": "fileformats",
      "title": "Set or return list of registered file formats that we can read",
      "topics": [
        "fileformats",
        "getformatreader",
        "getformatwriter",
        "registerformat"
      ]
    },
    {
      "page": "find.neuron",
      "title": "Find neurons within a 3D selection box (usually drawn in rgl window)",
      "topics": [
        "find.neuron"
      ]
    },
    {
      "page": "find.soma",
      "title": "Find neurons with soma inside 3D selection box (usually drawn in rgl window)",
      "topics": [
        "find.soma"
      ]
    },
    {
      "page": "flip",
      "title": "Flip an array, matrix or vector about an axis",
      "topics": [
        "flip",
        "flip.array"
      ]
    },
    {
      "page": "dotprops-topo",
      "title": "Get topological features per each node",
      "topics": [
        "get_distance_to_soma",
        "get_topo_features"
      ]
    },
    {
      "page": "graph.nodes",
      "title": "Return root, end, or branchpoints of an igraph object",
      "topics": [
        "graph.nodes"
      ]
    },
    {
      "page": "im3d",
      "title": "Construct an im3d object representing 3D image data, densities etc",
      "concept": [
        "im3d"
      ],
      "topics": [
        "im3d"
      ]
    },
    {
      "page": "im3d-coords",
      "title": "Interconvert pixel and physical coordinates",
      "concept": [
        "im3d"
      ],
      "topics": [
        "ijkpos",
        "im3d-coords",
        "xyzpos"
      ]
    },
    {
      "page": "im3d-io",
      "title": "Read/Write calibrated 3D blocks of image data",
      "concept": [
        "im3d"
      ],
      "topics": [
        "im3d-io",
        "read.im3d",
        "write.im3d"
      ]
    },
    {
      "page": "image.im3d",
      "title": "Method to plot spatially calibrated image arrays",
      "topics": [
        "image.im3d"
      ]
    },
    {
      "page": "imexpand.grid",
      "title": "Convert locations of im3d voxel grid into XYZ coordinates",
      "concept": [
        "im3d"
      ],
      "topics": [
        "imexpand.grid"
      ]
    },
    {
      "page": "imscalebar",
      "title": "Make a scalebar to accompany an image.im3d plot",
      "topics": [
        "imscalebar"
      ]
    },
    {
      "page": "imslice",
      "title": "Slice out a 3D subarray (or 2d matrix) from a 3D image array",
      "concept": [
        "im3d"
      ],
      "topics": [
        "imslice"
      ]
    },
    {
      "page": "ind2coord",
      "title": "Find XYZ coords corresponding to 1D indices into a 3D image",
      "topics": [
        "ind2coord",
        "ind2coord.array",
        "ind2coord.default",
        "ind2coord.im3d"
      ]
    },
    {
      "page": "intersect",
      "title": "Find the intersection of two collections of objects",
      "topics": [
        "intersect",
        "intersect.default",
        "intersect.neuronlist"
      ]
    },
    {
      "page": "intersect_plane",
      "title": "Find the points on a plane that are intersected by an object",
      "concept": [
        "geometry"
      ],
      "topics": [
        "intersect_plane",
        "intersect_plane.default",
        "intersect_plane.neuron"
      ]
    },
    {
      "page": "is.amiramesh",
      "title": "Check if file is AmiraMesh format",
      "concept": [
        "amira"
      ],
      "topics": [
        "is.amiramesh"
      ]
    },
    {
      "page": "is.fijitraces",
      "title": "Check whether a file is in Fiji's simple neurite tracer format",
      "topics": [
        "is.fijitraces"
      ]
    },
    {
      "page": "is.im3d",
      "title": "Test if an object is of class im3d",
      "concept": [
        "im3d"
      ],
      "topics": [
        "is.im3d"
      ]
    },
    {
      "page": "is.neuroml",
      "title": "Check whether a file is in NeuroML format",
      "topics": [
        "is.neuroml"
      ]
    },
    {
      "page": "is.neuronlist",
      "title": "Test objects of neuronlist class to store multiple neurons",
      "concept": [
        "neuronlist"
      ],
      "topics": [
        "is.neuronlist"
      ]
    },
    {
      "page": "is.nrrd",
      "title": "Check if a file is a NRRD file",
      "concept": [
        "nrrd"
      ],
      "topics": [
        "is.nrrd"
      ]
    },
    {
      "page": "is.swc",
      "title": "Test if a file is an SWC format neuron",
      "topics": [
        "is.swc"
      ]
    },
    {
      "page": "is.vaa3draw",
      "title": "Check if a file is in the raw image format used by Hanchuan Peng's Vaa3D",
      "topics": [
        "is.vaa3draw"
      ]
    },
    {
      "page": "kcs20",
      "title": "List of 20 Kenyon Cells from Chiang et al 2011 converted to dotprops objects",
      "concept": [
        "nat-data"
      ],
      "topics": [
        "kcs20"
      ]
    },
    {
      "page": "make_model",
      "title": "Generate a 3D model from connector and/or tree node data",
      "topics": [
        "make_model"
      ]
    },
    {
      "page": "makeboundingbox",
      "title": "Construct a 3D bounding box object",
      "topics": [
        "makeboundingbox"
      ]
    },
    {
      "page": "mask",
      "title": "Mask an object, typically to produce a copy with some values zeroed out",
      "concept": [
        "im3d"
      ],
      "topics": [
        "mask",
        "mask.im3d"
      ]
    },
    {
      "page": "materials",
      "title": "Extract or set the materials for an object",
      "concept": [
        "hxsurf"
      ],
      "topics": [
        "materials",
        "materials.character",
        "materials.default",
        "materials.hxsurf"
      ]
    },
    {
      "page": "MBL.surf",
      "title": "Surface object (hxsurf) for the left mushroom body in FCWB template space",
      "concept": [
        "nat-data"
      ],
      "topics": [
        "MBL.surf"
      ]
    },
    {
      "page": "mirror",
      "title": "Mirror 3D object about a given axis, optionally using a warping registration",
      "topics": [
        "mirror",
        "mirror.character",
        "mirror.default",
        "mirror.neuronlist"
      ]
    },
    {
      "page": "nclear3d",
      "title": "Clear the rgl or plotly 3D scene",
      "topics": [
        "nclear3d"
      ]
    },
    {
      "page": "ndigest",
      "title": "Calculated normalised digest value for an object",
      "topics": [
        "ndigest",
        "ndigest.dotprops",
        "ndigest.neuron",
        "ndigest.neuronlistfh"
      ]
    },
    {
      "page": "neuron",
      "title": "neuron: class to represent traced neurons",
      "concept": [
        "neuron"
      ],
      "topics": [
        "as.neuron",
        "as.neuron.data.frame",
        "as.neuron.default",
        "as.neuron.igraph",
        "as.neuron.ngraph",
        "is.neuron",
        "neuron"
      ]
    },
    {
      "page": "neuronlist",
      "title": "Create a neuronlist from zero or more neurons",
      "concept": [
        "neuronlist"
      ],
      "topics": [
        "neuronlist"
      ]
    },
    {
      "page": "neuronlist-dataframe-methods",
      "title": "Methods for working with the dataframe attached to a neuronlist",
      "concept": [
        "neuronlist"
      ],
      "topics": [
        "droplevels",
        "droplevels.neuronlist",
        "head",
        "head.neuronlist",
        "neuronlist-dataframe-methods",
        "tail",
        "tail.neuronlist",
        "with",
        "with.neuronlist",
        "[.neuronlist",
        "[<-.neuronlist"
      ]
    },
    {
      "page": "neuronlistfh",
      "title": "neuronlistfh - List of neurons loaded on demand from disk or remote website",
      "concept": [
        "neuronlist",
        "neuronlistfh"
      ],
      "topics": [
        "as.neuronlistfh",
        "as.neuronlistfh.neuronlist",
        "c.neuronlistfh",
        "is.neuronlistfh",
        "neuronlistfh"
      ]
    },
    {
      "page": "neuronlistz",
      "title": "A neuronlist object that will read neurons from a zip file on demand",
      "concept": [
        "neuronlist"
      ],
      "topics": [
        "as.neuronlist.neuronlistz",
        "neuronlistz"
      ]
    },
    {
      "page": "ngraph",
      "title": "ngraph: a graph to encode a neuron's connectivity",
      "concept": [
        "neuron"
      ],
      "topics": [
        "as.ngraph",
        "as.ngraph.data.frame",
        "as.ngraph.neuron",
        "ngraph"
      ]
    },
    {
      "page": "nlapply",
      "title": "lapply and mapply for neuronlists (with optional parallelisation)",
      "concept": [
        "neuronlist"
      ],
      "topics": [
        "nlapply",
        "nmapply",
        "progress_natprogress"
      ]
    },
    {
      "page": "nlscan",
      "title": "Scan through a set of neurons, individually plotting each one in 3D",
      "topics": [
        "nlscan"
      ]
    },
    {
      "page": "nopen3d",
      "title": "Open customised rgl window",
      "topics": [
        "nopen3d"
      ]
    },
    {
      "page": "normalise_swc",
      "title": "Normalise an SWC format block of neuron morphology data",
      "topics": [
        "normalise_swc"
      ]
    },
    {
      "page": "npop3d",
      "title": "Remove plotted neurons or other 3D objects",
      "topics": [
        "npop3d"
      ]
    },
    {
      "page": "nrrd.voxdims",
      "title": "Return voxel dimensions (by default absolute voxel dimensions)",
      "concept": [
        "nrrd"
      ],
      "topics": [
        "nrrd.voxdims"
      ]
    },
    {
      "page": "nvertices",
      "title": "Find the number of vertices in an object (or each element of a neuronlist)",
      "topics": [
        "nvertices",
        "nvertices.default",
        "nvertices.igraph",
        "nvertices.neuronlist",
        "nvertices.shapelist3d"
      ]
    },
    {
      "page": "nview3d",
      "title": "Set the 3D viewpoint of an RGL window using anatomical terms",
      "topics": [
        "nview3d"
      ]
    },
    {
      "page": "dotprops-arithmetic",
      "title": "Arithmetic for nat dotprops and surface objects",
      "topics": [
        "Ops.dotprops",
        "Ops.hxsurf",
        "Ops.mesh3d"
      ]
    },
    {
      "page": "neuron-arithmetic",
      "title": "Arithmetic for neuron coordinates",
      "topics": [
        "Ops.neuron"
      ]
    },
    {
      "page": "origin",
      "title": "Return the space origin of a 3D image object",
      "concept": [
        "im3d"
      ],
      "topics": [
        "origin"
      ]
    },
    {
      "page": "overlap_score",
      "title": "Generate a connectivity matrix based on euclidean distance between points",
      "topics": [
        "overlap_score"
      ]
    },
    {
      "page": "pan3d",
      "title": "Some useful extensions / changes to rgl defaults",
      "topics": [
        "pan3d"
      ]
    },
    {
      "page": "plane_coefficients",
      "title": "Find the coefficients of the plane equation",
      "concept": [
        "geometry"
      ],
      "topics": [
        "plane_coefficients"
      ]
    },
    {
      "page": "plot.neuron",
      "title": "Plot a 2D projection of a neuron",
      "concept": [
        "neuron"
      ],
      "topics": [
        "plot.dotprops",
        "plot.neuron"
      ]
    },
    {
      "page": "plot.neuronlist",
      "title": "2D plots of the elements in a neuronlist, optionally using a subset expression",
      "topics": [
        "plot.neuronlist"
      ]
    },
    {
      "page": "plot3d",
      "title": "plot3d methods for different nat objects",
      "topics": [
        "plot3d"
      ]
    },
    {
      "page": "plot3d.boundingbox",
      "title": "Plot a bounding box in 3D",
      "topics": [
        "plot3d.boundingbox"
      ]
    },
    {
      "page": "plot3d.cmtkreg",
      "title": "Plot the domain of a CMTK registration",
      "topics": [
        "plot3d.cmtkreg"
      ]
    },
    {
      "page": "plot3d.dotprops",
      "title": "3D plots of dotprops objects using rgl package",
      "topics": [
        "plot3d.dotprops"
      ]
    },
    {
      "page": "plot3d.hxsurf",
      "title": "Plot amira surface objects in 3D using rgl",
      "concept": [
        "hxsurf"
      ],
      "topics": [
        "plot3d.hxsurf"
      ]
    },
    {
      "page": "plot3d.neuron",
      "title": "Plot neurons in 3D using rgl library or plotly module",
      "topics": [
        "plot3d.neuron"
      ]
    },
    {
      "page": "plot3d.neuronlist",
      "title": "3D plots of the elements in a neuronlist, optionally using a subset expression",
      "topics": [
        "plot3d.character",
        "plot3d.neuronlist"
      ]
    },
    {
      "page": "plot3d.ngraph",
      "title": "Plot 3d representation of neuron (ngraph) with directed edges",
      "topics": [
        "plot3d.ngraph"
      ]
    },
    {
      "page": "pointsinside",
      "title": "Find which points of an object are inside a surface",
      "topics": [
        "pointsinside",
        "pointsinside.default"
      ]
    },
    {
      "page": "potential_synapses",
      "title": "Calculate number of potential synapses between two neurons",
      "concept": [
        "neuron"
      ],
      "topics": [
        "potential_synapses",
        "potential_synapses.dotprops",
        "potential_synapses.neuron",
        "potential_synapses.neuronlist"
      ]
    },
    {
      "page": "projection",
      "title": "Make 2D (orthogonal) projection of 3D image data",
      "concept": [
        "im3d"
      ],
      "topics": [
        "projection"
      ]
    },
    {
      "page": "prune",
      "title": "prune an object by removing points near (or far) from a target object",
      "concept": [
        "neuron"
      ],
      "topics": [
        "prune",
        "prune.default",
        "prune.dotprops",
        "prune.neuron",
        "prune.neuronlist"
      ]
    },
    {
      "page": "prune_in_volume",
      "title": "Prune neuron(s) within a volume defined by a 3D mesh",
      "topics": [
        "prune_in_volume",
        "prune_in_volume.neuron",
        "prune_in_volume.neuronlist"
      ]
    },
    {
      "page": "prune_online",
      "title": "Prune a neuron interactively in an rgl window",
      "topics": [
        "prune_online",
        "prune_online.neuron",
        "prune_online.neuronlist"
      ]
    },
    {
      "page": "prune_strahler",
      "title": "Prune a neuron by removing segments with a given Strahler order",
      "topics": [
        "prune_strahler"
      ]
    },
    {
      "page": "prune_twigs",
      "title": "Remove all twigs less than a certain path length from a neuron",
      "topics": [
        "prune_twigs",
        "prune_twigs.neuron",
        "prune_twigs.neuronlist"
      ]
    },
    {
      "page": "prune_vertices",
      "title": "Prune selected vertices or edges from a neuron",
      "topics": [
        "prune_edges",
        "prune_vertices"
      ]
    },
    {
      "page": "amiramesh-io",
      "title": "Read AmiraMesh data in binary or ascii format",
      "concept": [
        "amira"
      ],
      "topics": [
        "read.amiramesh",
        "read.amiramesh.header"
      ]
    },
    {
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