Files in jefferis/nat
NeuroAnatomy Toolbox for Analysis of 3D Image Data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/alphashape3d.R R/amiralandmarks-io.R R/amiramesh-io.R R/cmtk-reformat.R R/cmtk.R R/cmtk_geometry.R R/cmtk_io.R R/cmtkreg.R R/coordinates.R R/dist3D_Segment_to_Segment.R R/dotprops.R R/geometry.R R/graph-nodes.R R/hxsurf.R R/im3d.R R/nat-data.R R/nat-package.R R/ndigest.R R/neuron-io-amira.R R/neuron-io-fiji.R R/neuron-io-neuroml.R R/neuron-io.R R/neuron-plot.R R/neuron.R R/neuronlist.R R/neuronlist_interactive_3d.R R/neuronlist_sets.R R/neuronlistfh.R R/ngraph.R R/nrrd-io.R R/pop3d.R R/potential_synapses.R R/reglist.R R/seglist.R R/summary.R R/utils.R R/vaa3draw-io.R R/vtk-io.R R/xform.R R/xformimage.R R/xformpoints.R R/zzz.R README.md
_pkgdown.yml
build-cmtk.sh
build_docs.r cran-comments.md
data/Cell07PNs.rda
data/MBL.surf.rda
data/kcs20.rda
docs/articles/Installation.html
docs/articles/NeuroGeometry.html
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-1-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-10-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-12-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-13-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-16-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-4-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-6-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-7-1.png
docs/articles/NeuroGeometry_files/figure-html/unnamed-chunk-9-1.png
docs/articles/fig/neuron-graph.svg
docs/articles/fig/neuronlist-01.png
docs/articles/fig/neuronlist-subsets-01.png
docs/articles/fig/neuronlist-subsets.pdf docs/articles/fig/neuronlist.pdf
docs/articles/index.html
docs/articles/neurons-as-graph.html
docs/articles/neurons-as-graph_files/figure-html/unnamed-chunk-11-1.png
docs/articles/neurons-as-graph_files/figure-html/unnamed-chunk-3-1.png
docs/articles/neurons-as-graph_files/figure-html/unnamed-chunk-4-1.png
docs/articles/neurons-as-graph_files/figure-html/unnamed-chunk-5-1.png
docs/articles/neurons-intro.html
docs/articles/neurons-intro_files/figure-html/plot3d-legend-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-11-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-13-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-14-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-25-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-26-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-27-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-28-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-29-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-30-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-32-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-33-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-34-1.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-34-2.png
docs/articles/neurons-intro_files/figure-html/unnamed-chunk-6-1.png
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Cell07PNs.html
docs/reference/MBL.surf.html
docs/reference/affmat2cmtkparams.html
docs/reference/all.equal.dotprops.html
docs/reference/all.equal.im3d.html
docs/reference/all.equal.neuron.html
docs/reference/amiramesh-io.html
docs/reference/amiratype.html
docs/reference/as.hxsurf.html
docs/reference/as.im3d.html
docs/reference/as.mesh3d.html
docs/reference/as.neuronlist.html
docs/reference/as.neuronlist.neuronlistfh.html
docs/reference/boundingbox.html
docs/reference/c.neuronlist.html
docs/reference/clampmax.html
docs/reference/cmtk.bindir.html
docs/reference/cmtk.call.html
docs/reference/cmtk.dof2mat.html
docs/reference/cmtk.extract_affine.html
docs/reference/cmtk.mat2dof.html
docs/reference/cmtk.reformatx.html
docs/reference/cmtk.statistics.html
docs/reference/cmtk.targetvolume.html
docs/reference/cmtk.version.html
docs/reference/cmtkparams2affmat.html
docs/reference/cmtkreg.html
docs/reference/cmtkreglist.html
docs/reference/coord2ind.html
docs/reference/dotprops-arithmetic.html
docs/reference/dotprops.html
docs/reference/fileformats.html
docs/reference/find.neuron.html
docs/reference/find.soma.html
docs/reference/flip.html
docs/reference/get-set-neuronlist-data.frame.html
docs/reference/graph.nodes.html
docs/reference/im3d-coords.html
docs/reference/im3d-io.html
docs/reference/im3d.html
docs/reference/image.im3d.html
docs/reference/imexpand.grid.html
docs/reference/imscalebar.html
docs/reference/imslice.html
docs/reference/ind2coord.html
docs/reference/index.html
docs/reference/intersect.html
docs/reference/intersect_plane-1.png
docs/reference/intersect_plane.html
docs/reference/is.amiramesh.html
docs/reference/is.fijitraces.html
docs/reference/is.im3d.html
docs/reference/is.neuroml.html
docs/reference/is.neuronlist.html
docs/reference/is.nrrd.html
docs/reference/is.swc.html
docs/reference/is.vaa3draw.html
docs/reference/kcs20.html
docs/reference/makeboundingbox.html
docs/reference/mask-1.png
docs/reference/mask-2.png
docs/reference/mask-3.png
docs/reference/mask-4.png
docs/reference/mask-6.png
docs/reference/mask.html
docs/reference/materials.html
docs/reference/mirror.html
docs/reference/nat-package.html
docs/reference/ndigest.html
docs/reference/neuron-1.png
docs/reference/neuron-10.png
docs/reference/neuron-12.png
docs/reference/neuron-2.png
docs/reference/neuron-3.png
docs/reference/neuron-4.png
docs/reference/neuron-5.png
docs/reference/neuron-6.png
docs/reference/neuron-7.png
docs/reference/neuron-8.png
docs/reference/neuron-arithmetic.html
docs/reference/neuron.html
docs/reference/neuronlist-arithmetic.html
docs/reference/neuronlist-dataframe-methods.html
docs/reference/neuronlist.html
docs/reference/neuronlistfh.html
docs/reference/ngraph-1.png
docs/reference/ngraph.html
docs/reference/nlapply.html
docs/reference/nlscan.html
docs/reference/nopen3d.html
docs/reference/normalise_swc.html
docs/reference/npop3d.html
docs/reference/nrrd.voxdims.html
docs/reference/nvertices.html
docs/reference/nview3d.html
docs/reference/origin.html
docs/reference/pan3d.html
docs/reference/plane_coefficients.html
docs/reference/plot.neuron-1.png
docs/reference/plot.neuron-10.png
docs/reference/plot.neuron-2.png
docs/reference/plot.neuron-3.png
docs/reference/plot.neuron-4.png
docs/reference/plot.neuron-5.png
docs/reference/plot.neuron-8.png
docs/reference/plot.neuron.html
docs/reference/plot.neuronlist-1.png
docs/reference/plot.neuronlist-2.png
docs/reference/plot.neuronlist-3.png
docs/reference/plot.neuronlist-4.png
docs/reference/plot.neuronlist-6.png
docs/reference/plot.neuronlist-8.png
docs/reference/plot.neuronlist.html
docs/reference/plot3d.boundingbox.html
docs/reference/plot3d.cmtkreg.html
docs/reference/plot3d.dotprops.html
docs/reference/plot3d.html
docs/reference/plot3d.hxsurf.html
docs/reference/plot3d.neuron.html
docs/reference/plot3d.neuronlist.html
docs/reference/pointsinside.html
docs/reference/potential_synapses.html
docs/reference/projection.html
docs/reference/prune.html
docs/reference/prune_strahler-1.png
docs/reference/prune_strahler-4.png
docs/reference/prune_strahler.html
docs/reference/prune_vertices-1.png
docs/reference/prune_vertices-3.png
docs/reference/prune_vertices.html
docs/reference/read.cmtk.html
docs/reference/read.cmtkreg.html
docs/reference/read.hxsurf.html
docs/reference/read.landmarks.html
docs/reference/read.morphml.html
docs/reference/read.neuron.fiji.html
docs/reference/read.neuron.html
docs/reference/read.neuron.neuroml.html
docs/reference/read.neuron.swc.html
docs/reference/read.neuronlistfh.html
docs/reference/read.neurons.html
docs/reference/read.nrrd.html
docs/reference/read.vaa3draw.html
docs/reference/reglist.html
docs/reference/remotesync.html
docs/reference/resample.html
docs/reference/rootpoints.html
docs/reference/scale.neuron.html
docs/reference/seglengths-1.png
docs/reference/seglengths-4.png
docs/reference/seglengths.html
docs/reference/seglist.html
docs/reference/seglist2swc.html
docs/reference/segmentgraph-1.png
docs/reference/segmentgraph-4.png
docs/reference/segmentgraph.html
docs/reference/setdiff.html
docs/reference/simplify_reglist.html
docs/reference/smooth_neuron-1.png
docs/reference/smooth_neuron-3.png
docs/reference/smooth_neuron.html
docs/reference/spine.html
docs/reference/strahler_order.html
docs/reference/sub-.neuronlistfh.html
docs/reference/sub2ind.html
docs/reference/subset.dotprops.html
docs/reference/subset.html
docs/reference/subset.hxsurf.html
docs/reference/subset.neuron-1.png
docs/reference/subset.neuron-5.png
docs/reference/subset.neuron.html
docs/reference/subset.neuronlist.html
docs/reference/summary.neuron.html
docs/reference/threshold.html
docs/reference/union.html
docs/reference/unmask.html
docs/reference/voxdims.html
docs/reference/write.amiramesh.html
docs/reference/write.cmtk.html
docs/reference/write.cmtkreg.html
docs/reference/write.hxsurf.html
docs/reference/write.neuron.html
docs/reference/write.neuronlistfh.html
docs/reference/write.neurons.html
docs/reference/write.nrrd.html
docs/reference/write.vtk.html
docs/reference/xform.html
docs/reference/xformimage.html
docs/reference/xformpoints.html
docs/reference/xyzmatrix.html
inst/CITATION
man/Cell07PNs.Rd man/MBL.surf.Rd man/affmat2cmtkparams.Rd man/all.equal.dotprops.Rd man/all.equal.im3d.Rd man/all.equal.neuron.Rd man/amiramesh-io.Rd man/amiratype.Rd man/as.hxsurf.Rd man/as.im3d.Rd man/as.mesh3d.Rd man/as.neuronlist.Rd man/as.neuronlist.neuronlistfh.Rd man/boundingbox.Rd man/c.neuronlist.Rd man/clampmax.Rd man/cmtk.bindir.Rd man/cmtk.call.Rd man/cmtk.dof2mat.Rd man/cmtk.extract_affine.Rd man/cmtk.mat2dof.Rd man/cmtk.reformatx.Rd man/cmtk.statistics.Rd man/cmtk.targetvolume.Rd man/cmtk.version.Rd man/cmtkparams2affmat.Rd man/cmtkreg.Rd man/cmtkreglist.Rd man/coord2ind.Rd man/dotprops-arithmetic.Rd man/dotprops.Rd man/fileformats.Rd man/find.neuron.Rd man/find.soma.Rd man/flip.Rd man/get-set-neuronlist-data.frame.Rd man/graph.nodes.Rd man/im3d-coords.Rd man/im3d-io.Rd man/im3d.Rd man/image.im3d.Rd man/imexpand.grid.Rd man/imscalebar.Rd man/imslice.Rd man/ind2coord.Rd man/intersect.Rd man/intersect_plane.Rd man/is.amiramesh.Rd man/is.fijitraces.Rd man/is.im3d.Rd man/is.neuroml.Rd man/is.neuronlist.Rd man/is.nrrd.Rd man/is.swc.Rd man/is.vaa3draw.Rd man/kcs20.Rd man/makeboundingbox.Rd man/mask.Rd man/materials.Rd man/mirror.Rd man/nat-package.Rd man/ndigest.Rd man/neuron-arithmetic.Rd man/neuron.Rd man/neuronlist-arithmetic.Rd man/neuronlist-dataframe-methods.Rd man/neuronlist.Rd man/neuronlistfh.Rd man/ngraph.Rd man/nlapply.Rd man/nlscan.Rd man/nopen3d.Rd man/normalise_swc.Rd man/npop3d.Rd man/nrrd.voxdims.Rd man/nvertices.Rd man/nview3d.Rd man/origin.Rd man/pan3d.Rd man/plane_coefficients.Rd man/plot.neuron.Rd man/plot.neuronlist.Rd man/plot3d.Rd man/plot3d.boundingbox.Rd man/plot3d.cmtkreg.Rd man/plot3d.dotprops.Rd man/plot3d.hxsurf.Rd man/plot3d.neuron.Rd man/plot3d.neuronlist.Rd man/pointsinside.Rd man/potential_synapses.Rd man/projection.Rd man/prune.Rd man/prune_strahler.Rd man/prune_vertices.Rd man/read.cmtk.Rd man/read.cmtkreg.Rd man/read.hxsurf.Rd man/read.landmarks.Rd man/read.morphml.Rd man/read.neuron.Rd man/read.neuron.fiji.Rd man/read.neuron.neuroml.Rd man/read.neuron.swc.Rd man/read.neuronlistfh.Rd man/read.neurons.Rd man/read.nrrd.Rd man/read.vaa3draw.Rd man/reglist.Rd man/remotesync.Rd man/resample.Rd man/rootpoints.Rd man/scale.neuron.Rd man/seglengths.Rd man/seglist.Rd man/seglist2swc.Rd man/segmentgraph.Rd man/setdiff.Rd man/simplify_reglist.Rd man/smooth_neuron.Rd man/spine.Rd man/strahler_order.Rd man/sub-.neuronlistfh.Rd man/sub2ind.Rd man/subset.Rd man/subset.dotprops.Rd man/subset.hxsurf.Rd man/subset.neuron.Rd man/subset.neuronlist.Rd man/summary.neuron.Rd man/threshold.Rd man/union.Rd man/unmask.Rd man/voxdims.Rd man/write.amiramesh.Rd man/write.cmtk.Rd man/write.cmtkreg.Rd man/write.hxsurf.Rd man/write.neuron.Rd man/write.neuronlistfh.Rd man/write.neurons.Rd man/write.nrrd.Rd man/write.vtk.Rd man/xform.Rd man/xformimage.Rd man/xformpoints.Rd man/xyzmatrix.Rd
nat.Rproj
revdep/.gitignore
revdep/check.R tests/test-all.R tests/testthat/test-.neuron-io-remote-nocran.R tests/testthat/test-.neuronlistfh-remote-nocran.R tests/testthat/test-amiramesh-io.R tests/testthat/test-cmtk-reformat.R tests/testthat/test-cmtk.R tests/testthat/test-cmtk_geometry.R tests/testthat/test-cmtk_io.R tests/testthat/test-cmtkreg.R tests/testthat/test-coordinates.R tests/testthat/test-dotprops.R tests/testthat/test-geometry.R tests/testthat/test-graph-nodes.R tests/testthat/test-hxsurf.R tests/testthat/test-im3d.R tests/testthat/test-landmarks-io.R tests/testthat/test-ndigest.R tests/testthat/test-neuroml-io.R tests/testthat/test-neuron-fiji-io.R tests/testthat/test-neuron-io.R tests/testthat/test-neuron.R tests/testthat/test-neuronlist.R tests/testthat/test-neuronlistfh.R tests/testthat/test-ngraph.R tests/testthat/test-nrrd-io.R tests/testthat/test-pop3d.R tests/testthat/test-potential_synapses.R tests/testthat/test-reglist.R tests/testthat/test-seglist.R tests/testthat/test-summary.R tests/testthat/test-xform.R tests/testthat/test-xformimage.R tests/testthat/test-xformpoints.R
tests/testthat/testdata/amira/AL-a_M.am
tests/testthat/testdata/amira/JFRC2_MB_CA_L.rds
tests/testthat/testdata/amira/JFRC2_neuropils_almblh_ascii.surf
tests/testthat/testdata/amira/LHMask.Labels.rle.am
tests/testthat/testdata/amira/LHMask.zip.am
tests/testthat/testdata/amira/VerySmallLabelField.am
tests/testthat/testdata/amira/VerySmallLabelField.nrrd
tests/testthat/testdata/amira/landmarks.am
tests/testthat/testdata/amira/malformed_labels.surf
tests/testthat/testdata/amira/tetrahedron-colbrace.surf
tests/testthat/testdata/amira/tetrahedron-colswap.surf
tests/testthat/testdata/amira/tetrahedron.surf
tests/testthat/testdata/amira/tetrahedron_badtrianglenum.surf
tests/testthat/testdata/amira/tetrahedron_nocol.surf
tests/testthat/testdata/amira/tetrahedron_notriangles.surf
tests/testthat/testdata/cmtk/.gitattributes
tests/testthat/testdata/cmtk/FCWB_JFRC2_01_warp_level-01.list/registration.gz
tests/testthat/testdata/cmtk/FCWB_JFRC2_01_warp_level-01.list/settings
tests/testthat/testdata/cmtk/FCWB_JFRC2_01_warp_level-01.list/statistics
tests/testthat/testdata/cmtk/FCWB_JFRC2_01_warp_level-01.list/studylist
tests/testthat/testdata/cmtk/FCWB_mirror_level-01.list/registration.gz
tests/testthat/testdata/cmtk/FCWB_mirror_level-01.list/settings
tests/testthat/testdata/cmtk/FCWB_mirror_level-01.list/statistics
tests/testthat/testdata/cmtk/FCWB_mirror_level-01.list/studylist
tests/testthat/testdata/cmtk/dofv1.1wshears.list/registration
tests/testthat/testdata/cmtk/dofv1.1wshears.list/studylist
tests/testthat/testdata/cmtk/dofv2.4wshears.list/registration
tests/testthat/testdata/cmtk/dofv2.4wshears.list/studylist
tests/testthat/testdata/dotprops/masse/SAKW13-1_dots4.rda
tests/testthat/testdata/dotprops/masse/SAKW13-1_dots4_properties.rda
tests/testthat/testdata/landmarks/JFRC2.points
tests/testthat/testdata/landmarks/JFRC2_single.points
tests/testthat/testdata/neuroml/level1/CablesIncluded.swc
tests/testthat/testdata/neuroml/level1/CablesIncluded.xml
tests/testthat/testdata/neuroml/level1/L23PyrFRB.morph.xml
tests/testthat/testdata/neuroml/level1/Simple.morph.swc
tests/testthat/testdata/neuroml/level1/Simple.morph.xml
tests/testthat/testdata/neuroml/level1/SimpleNeuroML.xml
tests/testthat/testdata/neuroml2/catsmall.nml
tests/testthat/testdata/neuron/EBT7R.CNG.swc
tests/testthat/testdata/neuron/EBT7R.am
tests/testthat/testdata/neuron/EBT7R_nans.am
tests/testthat/testdata/neuron/MultiplePathsJoinedToMainPath.traces
tests/testthat/testdata/neuron/Neurites.am
tests/testthat/testdata/neuron/NeuritesWithIsolatedPoints_veryshort.am
tests/testthat/testdata/neuron/SequentiallyBranchingTrace.traces
tests/testthat/testdata/neuron/SinglePath.traces
tests/testthat/testdata/neuron/XT6L2.CNG.swc
tests/testthat/testdata/neuron/fitted.traces
tests/testthat/testdata/neuron/testCell07PNs1_spine.rds
tests/testthat/testdata/neuron/testneuron_am3d.am
tests/testthat/testdata/neuron/testneuron_am3d.am.gz
tests/testthat/testdata/neuron/testneuron_am3d_ascii.am.gz
tests/testthat/testdata/neuron/testneuron_fclineset.am.gz
tests/testthat/testdata/neuron/testneuron_lineset.am
tests/testthat/testdata/neuron/unfitted.swc
tests/testthat/testdata/nrrd/FCWB_2um_mask.nrrd
tests/testthat/testdata/nrrd/FruMARCM-F000002_seg001_03-acrop.nrrd
tests/testthat/testdata/nrrd/JFRC2-444_mask.nrrd
tests/testthat/testdata/nrrd/LHMask.nhdr
tests/testthat/testdata/nrrd/LHMask.nrrd
tests/testthat/testdata/nrrd/LHMask_sum.nrrd
tests/testthat/testdata/nrrd/badenc.nhdr
tests/testthat/testdata/nrrd/badtype.nhdr
tests/testthat/testdata/nrrd/datafile_list.nhdr
tests/testthat/testdata/nrrd/datafile_listslab.nhdr
tests/testthat/testdata/nrrd/dataforstats.nrrd
tests/testthat/testdata/selfun_cell07.rds
tests/testthat/testdata/summary_cell07pns.rda
tests/testthat/testdata/v3draw/L1DS1_crop_straight_crop.v3draw
tests/testthat/testdata/v3draw/L1DS1_crop_straight_crop_ch1.nhdr
tests/testthat/testdata/v3draw/L1DS1_crop_straight_crop_ch1.v3draw
tests/testthat/testdata/v3draw/L1DS1_crop_straight_crop_slice.v3draw
travisbuildchildren.sh
vignettes/Installation.Rmd vignettes/NeuroGeometry.Rmd
vignettes/fig/neuron-graph.svg
vignettes/fig/neuronlist-01.png
vignettes/fig/neuronlist-subsets-01.png
vignettes/fig/neuronlist-subsets.pdf vignettes/fig/neuronlist.pdf vignettes/neurons-as-graph.Rmd vignettes/neurons-intro.Rmd
jefferis/nat documentation built on Oct. 25, 2018, 6:29 p.m.