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

arbour.clustersSegregate neurite compartments from a neuron/neuronlist based...
ashape2mesh3dConvert an alpha shape to a mesh3D object
as.mesh3d.kdeConvert a 3D Kernel Density Estimate (package ks) into rgl...
assign_cable.polarityAssign axon/dendrite split to skeletons
assign.connector.infoGive connector data in a CATMAID neuron the same attributes...
assign_lh_neuronAssign identitiy to lateral horn neurons
assignsideAssign cell body side based on neuron name
assign_strahlerAssign Strahler stream order to neurites
average.tractsAverage non-branching tracts
catmaid_annotate_partnersAnnotate CATMAID partners
catmaid_set_meta_annotationsMeta-annotate CATMAID annotations
catnat-packageAlex Bates' functions for use with nat and rcatmaid
clusterbysynapsesCluster neurons by pre- and postsynapse positons
cluster_synapses_within_skeletonCluster synapses within a neuron's skeleton
combine.alphashapeCombine alphashapes generated by the alphashapes package
connectivity_matrixGenerate connectivity matrix
connectivity_similarityCalculate a connectivity similarity score between two... data tracers' contributions to skeletons
correctsomaRe-root neurons to their soma
create_skeleton_from_nrrdCreate a skeleton from a skeletonised neuron saved as a .Nrrd...
create_tracing_samplesheetCreate or update a googlesheet of randomised tracing targets...
distance.from.first.branchpointCalculate geodesic distance from nodes to a neuron's...
downstream.deletion.testFind how many downstream partners tracers have connected up
extract_cableExtract axonic/dendritic points from a neuron/neuronlist
flow.centralityDetermine dendritic/axonal by calculating flow centrality
get_connected_skeletonsRetrieving CATMAID neuron skeletons connected to query...
get.hxsurfRead Amira surface (aka HxSurface or HyperSurface) files into...
get.skeleton.from.flycircuitFetch Flycircuit neuron skeletons from the Tawian Flycircuit...
get.synapsesGet 3D coordinates of synapse (not connector) positions
inside_neuropilsCalculate the cable length inside of different neuropils in a...
label_neuron.classSee neurons with chosen neuropils to determine their types
make.anatomical.modelGenerate a neuroanatomicla alpha shape from connector and/or...
make.mirror.transformGet the transformation matrix from the Morpho::mirror...
manually_assign_axon_dendriteManually assign the dendrite and axon to a neuron
microtubulesFunctions to assign and visualise microtubule rich and twig...
napplyTransformApply a transform to a neruon/neuronlist
nblast_bothwaysNBlast two different sets of neurons forwards and backwards
neuritesSegregate neurite compartments from a neuron/neuronlist
neurons.insideFind neurites inside of an alphashape
open_l1Jump from R into the L1 larval EM data in CATMAID
overlap.connectivity.matrixGenerate a connectivity matrix based on euclidean distance...
pointsinsidemeshFind neurites inside of an mesh3d object
primary.neuriteReturns the primary neurite of a neuron
prune_by_tagPrune neuron by splitting it at CATMAID tags
prune.catmaidneuronPrune nodes from a catmaid neuron, keeping the synapses
prune_distalPrune nodes from a neuron, keeping the root node
prune_in_volumePrune neuron within neuropil volume
prune_onlinePrune a neuron interactively
prune_strahler.catmaidneuronPrune a CATMAID neuron by removing segments with a given...
prune_vertices.catmaidneuronPrune vertices from a CATMAID neuron, keeping the synapses
resample.catmaidneuronResample a CATMAID neuron
rescue.dpsGenerate a dps object without dropping small neurons
scan4matchingScan through suggested pairs of neurons
seebroken3dPlot neurons split up by synapse clusters
seesplit3dPlot neurons split up by flow centrality
select_neuronsSelect neurons in space
select_pointsSelect 3D points in space
shift.neuronsShift neurons in space
sholl_analysisSholl analysis on neuron skeletons
somaFunctions for retrieving soma data
subtreeGet a subtree in a neuron object as a separate neuron object
synapsecolours.neuronPlot a neuron with different coloured synapses depending on...
tracer.plotGet data and plots describing tracer activity statistics
transform3dalphashapeTransform the 3D vertices of an alphashape
update.neuronlistUpdate a local neuronlist with new CATMAID data
write.spin.swcWrite ordered swc
WriteVTKalphashapeWrite alphashape as a .vtk file
alexanderbates/catnat documentation built on Dec. 4, 2018, 6:57 a.m.