API for alexanderbates/catnat
Analyse neuronal morphology and connectivity (extends catmaid and nat)

Global functions
Chiang2FCWB Man page Source code
WriteVTKalphashape Man page Source code
applyTransform.neuron Source code
applyTransform.neuronlist Source code
arbour.clusters Man page Source code
arbour.clusters.neuron Man page Source code
arbour.clusters.neuronlist Man page Source code
arbour_cable Man page Man page Source code Source code
arbour_cable.neuron Man page Man page Source code Source code
arbour_cable.neuronlist Man page Man page Source code Source code
arbours Man page Source code
arbours.neuron Man page Source code
arbours.neuronlist Man page Source code
as.mesh3d.kde Man page Source code
ashape2mesh3d Man page Source code
assign.connector.info Man page Source code
assign.connector.info.neuron Man page Source code
assign.connector.info.neuronlist Man page Source code
assign_cable.polarity Man page Source code
assign_lh_neuron Man page Source code
assign_strahler Man page Source code
assign_strahler.neuron Man page Source code
assign_strahler.neuronlist Man page Source code
assignside Man page Source code
assignside.names Source code
assignsides.l1 Source code
assignsynapses Source code
average.tracts Man page Source code
axonal_endings Man page Source code
axonic_cable Man page Source code
axonic_cable.neuron Man page Source code
axonic_cable.neuronlist Man page Source code
axonic_points Man page Source code
axonic_points.neuron Man page Source code
axonic_points.neuronlist Man page Source code
catmaid_annotate_partners Man page Source code
catmaid_get_annotated_partner Man page Source code
catmaid_set_meta_annotations Man page Source code
catmaid_urls Source code
catnat Man page
catnat-package Man page
cluster_synapses_within_skeleton Man page Source code
cluster_synapses_within_skeleton.neuron Man page Source code
cluster_synapses_within_skeleton.neuronlist Man page Source code
clusterbysynapses Man page Source code
combine.alphashape Man page Source code
connectivity_matrix Man page Source code
connectivity_similarity Man page Source code
connectivity_similarity.matrix Man page Source code
connectivity_similarity.numeric Man page Source code
connectivity_similarity_distance Man page Source code
connector_URL Source code
connectors.inside Source code
correctsoma Man page Source code
create_skeleton_from_nrrd Man page Source code
create_tracing_googlesheet Man page Source code
dendritic.morphogenisis Source code
dendritic.morphogenisis.neuronlist Source code
dendritic_cable Man page Source code
dendritic_cable.neuron Man page Source code
dendritic_cable.neuronlist Man page Source code
dendritic_endings Man page Source code
dendritic_points Man page Source code
dendritic_points.neuron Man page Source code
dendritic_points.neuronlist Man page Source code
deselect_neurons Man page Source code
distance.from.first.branchpoint Man page Source code
distance.from.first.branchpoint.neuron Man page Source code
distance.from.first.branchpoint.neuronlist Man page Source code
downstream.deletion.test Man page Source code
find.neuropil.points Source code
find.symmetric Source code
flow.centrality Man page Source code
flow.centrality.neuron Man page Source code
flow.centrality.neuronlist Man page Source code
get.connectors Source code
get.hxsurf Man page Source code
get.skeleton.from.flycircuit Man page Source code
get.synapses Man page Source code
get.synapses.neuron Man page Source code
get.synapses.neuronlist Man page Source code
get_connected_skeletons Man page Source code
in_neuropil Source code
in_neuropil.neuron Source code
in_neuropil.neuronlist Source code
inside_neuropils Man page Source code
inside_neuropils.neuron Man page Source code
inside_neuropils.neuronlist Source code
label_neuron.class Man page Source code
longestpathfromsoma Source code
make.3d.tract Source code
make.anatomical.model Man page Source code
make.mirror.transform Man page Source code
manually_assign_axon_dendrite Man page Source code
manually_assign_axon_dendrite.neuron Man page Source code
manually_assign_axon_dendrite.neuronlist Man page Source code
mark.microtubules Man page Source code
mark.microtubules.neuron Man page Source code
mark.microtubules.neuronlist Man page Source code
microtubules.errors Man page Source code
mixed_points Man page Source code
mixed_points.neuron Man page Source code
mixed_points.neuronlist Man page Source code
napplyTransform Man page Source code
napplyTransform.neuron Man page Source code
napplyTransform.neuronlist Man page Source code
nblast_bothways Man page Source code
neurites Man page Source code
neurites.neuron Man page Source code
neurites.neuronlist Man page Source code
neuron.heatmap Man page Source code
neurons.inside Man page Source code
neurons.inside.alphashape Source code
node.contribution.to.skeletons Man page Source code
onLoad Source code
open_l1 Man page Source code
overlap.connectivity.matrix Man page Source code
overlap.connectivity.matrix.catmaid Man page Source code
plot3d.split Man page Source code
points_in_neuropil Source code
pointsinsidemesh Man page Source code
polaritycluster Source code
primary.neurite Man page Source code
primary.neurite.neuron Man page Source code
primary.neurite.neuronlist Man page Source code
prune Man page
prune.catmaidneuron Man page Source code
prune_by_tag Man page Source code
prune_by_tag.catmaidneuron Man page Source code
prune_by_tag.neuron Man page Source code
prune_by_tag.neuronlist Man page Source code
prune_distal Man page Source code
prune_in_volume Man page Source code
prune_in_volume.neuron Man page Source code
prune_in_volume.neuronlist Man page Source code
prune_microtubules Man page Source code
prune_microtubules.neuron Man page Source code
prune_microtubules.neuronlist Man page Source code
prune_online Man page Source code
prune_online.neuron Man page Source code
prune_online.neuronlist Man page Source code
prune_strahler Man page
prune_strahler.catmaidneuron Man page Source code
prune_vertices Man page
prune_vertices.catmaidneuron Man page Source code
reroot.flycircuit.neuron Man page Source code
resample Man page
resample.catmaidneuron Man page Source code
resample.catmaidneuronlist Source code
resample.neuronlist Source code
rescue.dps Man page Source code
reverse.name.side Man page Source code
scan4matching Man page Source code
scan_lh_matches Man page Source code
seebroken3d Man page Source code
seesplit3d Man page Source code
select_neurons Man page Source code
select_points Man page Source code
shift.neurons Man page Source code
sholl_data Man page Source code
skeleton_connectivity_matrix Man page Source code
soma Man page Source code
soma.neuron Man page Source code
soma.neuronlist Man page Source code
somaid Man page Source code
somaid.neuron Man page Source code
somaid.neuronlist Man page Source code
somapos Man page Source code
somapos.neuron Man page Source code
somapos.neuronlist Man page Source code
spinny Source code
splitscan Man page Source code
starting.neurite Man page Source code
starting.neurite.neuron Man page Source code
starting.neurite.neuronlist Man page Source code
subtree Man page Source code
synapse.contribution.to.skeletons Man page Source code
synapsecolours.neuron Man page Source code
tracer.neuron.stats Man page Source code
tracer.plot Man page Source code
tracer.treenodes.plot Man page Source code
transform3dalphashape Man page Source code
unique.neurons.trace Source code
unsure_cable Man page Source code
unsure_cable.neuron Man page Source code
unsure_cable.neuronlist Man page Source code
update_names Man page Source code
update_neurons Man page Source code
update_tracing_googlesheet Man page Source code
update_tracing_sheet Source code
update_tracing_worksheet Man page Source code
visualise.microtubules Man page Source code
wind Source code
write.spin.split.swc Man page Source code
write.spin.swc Man page Source code
alexanderbates/catnat documentation built on April 8, 2018, 5:24 a.m.