Files in alexanderbates/catnat
Analyse neuronal morphology and connectivity (extends catmaid and nat)
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/Amira.R
R/CTEDIT.R
R/FAFB.R
R/alphashape.R
R/auxillary.R
R/catmaid.R
R/catnat-package.R
R/clusterbysynapse.R
R/clustersynapses.R
R/connectivity.R
R/connectivitysimilarity.R
R/create_skeleton.R
R/dendritic.R
R/editcatmaid.R
R/fafbseg.R
R/flowcentrality.R
R/flycircuit.R
R/getsynapses.R
R/googlesheets.R
R/inside_neuropils.R
R/kde.R
R/microtubules.R
R/modelmaking.R
R/neurites.R
R/neuronlist.R
R/neuronvolume.R
R/open_l1.R
R/prune.R
R/rankedSampling.R
R/sampling.R
R/scanning.R
R/selections.R
R/shiftneurons.R
R/shollanalysis.R
R/somas.R
R/sorting.R
R/tracerstats.R
R/zzz.R
README.md
_pkgdown.yml
catnat.Rproj
doc/edit_catmaid.R
doc/edit_catmaid.Rmd
doc/edit_catmaid.html
docs/articles/edit_catmaid.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/WriteVTKalphashape.html
docs/reference/arbour.clusters.html
docs/reference/as.mesh3d.kde.html
docs/reference/ashape2mesh3d.html
docs/reference/assign.connector.info.html
docs/reference/assign_cable.polarity.html
docs/reference/assign_lh_neuron.html
docs/reference/assign_strahler.html
docs/reference/assignside.html
docs/reference/average.tracts.html
docs/reference/catmaid_annotate_partners.html
docs/reference/catmaid_connector_nodes.html
docs/reference/catmaid_controlled_upload.html
docs/reference/catmaid_delete.html
docs/reference/catmaid_duplicated.html
docs/reference/catmaid_find_likely_merge.html
docs/reference/catmaid_get_neuronid.html
docs/reference/catmaid_get_server.html
docs/reference/catmaid_get_tag.html
docs/reference/catmaid_interactive_join.html
docs/reference/catmaid_interactive_name_transfer.html
docs/reference/catmaid_join_skeletons.html
docs/reference/catmaid_link_connectors.html
docs/reference/catmaid_lock_neurons.html
docs/reference/catmaid_node_time.html
docs/reference/catmaid_set_meta_annotations.html
docs/reference/catmaid_skeletons_in_bbx.html
docs/reference/catmaid_update_radius.html
docs/reference/catmaid_upload_neurons.html
docs/reference/catnat-package.html
docs/reference/cluster_synapses_within_skeleton.html
docs/reference/clusterbysynapses.html
docs/reference/combine.alphashape.html
docs/reference/connectivity_matrix.html
docs/reference/connectivity_similarity.html
docs/reference/connector_URL.html
docs/reference/contribution.to.skeletons.html
docs/reference/correctsoma.html
docs/reference/create_skeleton_from_nrrd.html
docs/reference/create_tracing_samplesheet.html
docs/reference/distance.from.first.branchpoint.html
docs/reference/downstream.deletion.test.html
docs/reference/extract_cable.html
docs/reference/fafb_frags.html
docs/reference/fafb_neuron_details.html
docs/reference/fafb_seg.html
docs/reference/fafb_seg_conn.html
docs/reference/fafb_segs_stitch_volumes.html
docs/reference/fafbseg_join_connectors_in_ngl_volumes.html
docs/reference/fafbseg_transfer.html
docs/reference/flow.centrality.html
docs/reference/get.hxsurf.html
docs/reference/get.skeleton.from.flycircuit.html
docs/reference/get.synapses.html
docs/reference/get_connected_skeletons.html
docs/reference/index.html
docs/reference/inside_neuropils.html
docs/reference/label_neuron.class.html
docs/reference/local_conn.html
docs/reference/make.anatomical.model.html
docs/reference/make.mirror.transform.html
docs/reference/manually_assign_axon_dendrite.html
docs/reference/map_fafbsegs_to_neuron.html
docs/reference/microtubules.html
docs/reference/napplyTransform.html
docs/reference/nblast_bothways.html
docs/reference/neurites.html
docs/reference/neurons.inside.html
docs/reference/open_l1.html
docs/reference/overlap.connectivity.matrix.html
docs/reference/pointsinsidemesh.html
docs/reference/primary.neurite.html
docs/reference/prune.catmaidneuron.html
docs/reference/prune_by_tag.html
docs/reference/prune_distal.html
docs/reference/prune_in_volume.html
docs/reference/prune_online.html
docs/reference/prune_strahler.catmaidneuron.html
docs/reference/prune_vertices.catmaidneuron.html
docs/reference/read.neurons.fafbseg.html
docs/reference/resample.catmaidneuron.html
docs/reference/rescue.dps.html
docs/reference/scan4matching.html
docs/reference/seebroken3d.html
docs/reference/seesplit3d.html
docs/reference/select_neurons.html
docs/reference/select_points.html
docs/reference/set_segmentation_location.html
docs/reference/shift.neurons.html
docs/reference/sholl_analysis.html
docs/reference/soma.html
docs/reference/subtree.html
docs/reference/synapsecolours.neuron.html
docs/reference/tracer.plot.html
docs/reference/transform3dalphashape.html
docs/reference/update.neuronlist.html
docs/reference/write.spin.swc.html
inst/WORDLIST
inst/extdata/InitialAffine/finalaffine_ChiangFemaleTowardsFCWB.rds
inst/extdata/InitialAffine/finalaffine_ChiangMaleTowardsFCWB.rds
inst/extdata/InitialAffine/initialiseCMTKreg_ChiangFemaleTowardsFCWB.rds
inst/extdata/InitialAffine/initialiseCMTKreg_ChiangMaleTowardsFCWB.rds
inst/extdata/affine/FCWB_typicalbrainfemale_01_9dof.list/cmd.sh
inst/extdata/affine/FCWB_typicalbrainfemale_01_9dof.list/registration
inst/extdata/affine/FCWB_typicalbrainfemale_01_9dof.list/settings
inst/extdata/affine/FCWB_typicalbrainfemale_01_9dof.list/statistics
inst/extdata/affine/FCWB_typicalbrainfemale_01_9dof.list/studylist
inst/extdata/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list/cmd.sh
inst/extdata/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list/registration.gz
inst/extdata/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list/settings
inst/extdata/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list/statistics
inst/extdata/warp/FCWB_typicalbrainfemale_01_warp_m0g80c8e1e-1x26r4.list/studylist
inst/extdata/warp/FCWB_typicalbrainmale_01_warp_m0g80c8e1e-1x26r4.list/cmd.sh
inst/extdata/warp/FCWB_typicalbrainmale_01_warp_m0g80c8e1e-1x26r4.list/registration.gz
inst/extdata/warp/FCWB_typicalbrainmale_01_warp_m0g80c8e1e-1x26r4.list/settings
inst/extdata/warp/FCWB_typicalbrainmale_01_warp_m0g80c8e1e-1x26r4.list/statistics
inst/extdata/warp/FCWB_typicalbrainmale_01_warp_m0g80c8e1e-1x26r4.list/studylist
man/WriteVTKalphashape.Rd
man/arbour.clusters.Rd
man/as.mesh3d.kde.Rd
man/ashape2mesh3d.Rd
man/assign.connector.info.Rd
man/assign_cable.polarity.Rd
man/assign_lh_neuron.Rd
man/assign_strahler.Rd
man/assignside.Rd
man/average.tracts.Rd
man/catmaid_annotate_partners.Rd
man/catmaid_connector_nodes.Rd
man/catmaid_controlled_upload.Rd
man/catmaid_delete.Rd
man/catmaid_duplicated.Rd
man/catmaid_find_likely_merge.Rd
man/catmaid_get_neuronid.Rd
man/catmaid_get_server.Rd
man/catmaid_get_tag.Rd
man/catmaid_interactive_join.Rd
man/catmaid_interactive_name_transfer.Rd
man/catmaid_join_skeletons.Rd
man/catmaid_link_connectors.Rd
man/catmaid_lock_neurons.Rd
man/catmaid_node_time.Rd
man/catmaid_set_meta_annotations.Rd
man/catmaid_skeletons_in_bbx.Rd
man/catmaid_update_radius.Rd
man/catmaid_upload_neurons.Rd
man/catnat-package.Rd
man/cluster_synapses_within_skeleton.Rd
man/clusterbysynapses.Rd
man/combine.alphashape.Rd
man/connectivity_matrix.Rd
man/connectivity_similarity.Rd
man/connector_URL.Rd
man/contribution.to.skeletons.Rd
man/correctsoma.Rd
man/create_skeleton_from_nrrd.Rd
man/create_tracing_samplesheet.Rd
man/distance.from.first.branchpoint.Rd
man/downstream.deletion.test.Rd
man/extract_cable.Rd
man/fafb_frags.Rd
man/fafb_neuron_details.Rd
man/fafb_seg.Rd
man/fafb_seg_conn.Rd
man/fafb_segs_stitch_volumes.Rd
man/fafbseg_join_connectors_in_ngl_volumes.Rd
man/fafbseg_transfer.Rd
man/flow.centrality.Rd
man/get.hxsurf.Rd
man/get.skeleton.from.flycircuit.Rd
man/get.synapses.Rd
man/get_connected_skeletons.Rd
man/inside_neuropils.Rd
man/label_neuron.class.Rd
man/local_conn.Rd
man/make.anatomical.model.Rd
man/make.mirror.transform.Rd
man/manually_assign_axon_dendrite.Rd
man/map_fafbsegs_to_neuron.Rd
man/microtubules.Rd
man/napplyTransform.Rd
man/nblast_bothways.Rd
man/neurites.Rd
man/neurons.inside.Rd
man/open_l1.Rd
man/overlap.connectivity.matrix.Rd
man/pointsinsidemesh.Rd
man/primary.neurite.Rd
man/prune.catmaidneuron.Rd
man/prune_by_tag.Rd
man/prune_distal.Rd
man/prune_in_volume.Rd
man/prune_online.Rd
man/prune_strahler.catmaidneuron.Rd
man/prune_vertices.catmaidneuron.Rd
man/read.neurons.catmaid.meta.Rd
man/read.neurons.fafbseg.Rd
man/resample.catmaidneuron.Rd
man/rescue.dps.Rd
man/scan4matching.Rd
man/seebroken3d.Rd
man/seesplit3d.Rd
man/segments_ranked.Rd
man/select_neurons.Rd
man/select_points.Rd
man/set_segmentation_location.Rd
man/shift.neurons.Rd
man/sholl_data.Rd
man/soma.Rd
man/subtree.Rd
man/synapsecolours.neuron.Rd
man/tracer.plot.Rd
man/transform3dalphashape.Rd
man/update.neuronlist.Rd
man/write.spin.swc.Rd
tests/spelling.R
tests/testthat.R
tests/testthat/test-primary.neurite.R
tests/testthat/testdata/pnt1.rds
vignettes/.gitignore
vignettes/edit_catmaid.Rmd
