Man pages for alexanderbates/catnat
Analyse neuronal morphology and connectivity (extends catmaid and nat)
| arbour.clusters | Segregate neurite compartments from a neuron/neuronlist based... |
| ashape2mesh3d | Convert an alpha shape to a mesh3D object |
| as.mesh3d.kde | Convert a 3D Kernel Density Estimate (package ks) into rgl... |
| assign_cable.polarity | Assign axon/dendrite split to skeletons |
| assign.connector.info | Give connector data in a CATMAID neuron the same attributes... |
| assign_lh_neuron | Assign identity to lateral horn neurons |
| assignside | Assign cell body side based on neuron name |
| assign_strahler | Assign Strahler stream order to neurites |
| average.tracts | Average non-branching tracts |
| catmaid_annotate_partners | Annotate CATMAID partners |
| catmaid_connector_nodes | Get information on a CATMAID connector node |
| catmaid_controlled_upload | Interactively upload neuron(s) to CATMAID |
| catmaid_delete | Function used to delete single neurons from CATMAID based on... |
| catmaid_duplicated | Try to detect whether a neuron your are about to import into... |
| catmaid_find_likely_merge | Find the TODO tagged merge sites between a given neuron and... |
| catmaid_get_neuronid | Get the CATMAID neuron ID that corresponds to the skeleton ID |
| catmaid_get_server | Get CATMAID server |
| catmaid_get_tag | Find the location of specified tags for a CATMAID neuron |
| catmaid_interactive_join | Interactively choose to join neurons in CATMAID, visualising... |
| catmaid_interactive_name_transfer | Interactively transfer names and annotations between neurons... |
| catmaid_join_skeletons | Programmatically join CATMAID skeletons |
| catmaid_link_connectors | Add synaptic links between connectors and treenodes |
| catmaid_lock_neurons | Lock or unlock a CATMAID neuron reconstruction |
| catmaid_node_time | Get the UTC creation / edit time for a CATMAID node |
| catmaid_set_meta_annotations | Meta-annotate CATMAID annotations |
| catmaid_skeletons_in_bbx | Search for CATMAID skeletons within a volume |
| catmaid_update_radius | Update radius information for tree nodes in a CATMAID... |
| catmaid_upload_neurons | Upload neuron(s) to CATMAID |
| catnat-package | catnat: Analyse neuronal morphology and connectivity (extends... |
| clusterbysynapses | Cluster neurons by pre- and postsynapse positions |
| cluster_synapses_within_skeleton | Cluster synapses within a neuron's skeleton |
| combine.alphashape | Combine alphashapes generated by the alphashapes package |
| connectivity_matrix | Generate connectivity matrix |
| connectivity_similarity | Calculate a connectivity similarity score between two... |
| connector_URL | Generate URLs to CATMAID connector location |
| contribution.to.skeletons | Get data tracers' contributions to skeletons |
| correctsoma | Re-root neurons to their soma |
| create_skeleton_from_nrrd | Create a skeleton from a skeletonised neuron saved as a .Nrrd... |
| create_tracing_samplesheet | Create or update a googlesheet of randomised tracing targets... |
| distance.from.first.branchpoint | Calculate geodesic distance from nodes to a neuron's... |
| downstream.deletion.test | Find how many downstream partners tracers have connected up |
| extract_cable | Extract axonic/dendritic points/cable from a... |
| fafb_frags | Fetch the up or outgoing auto-traced FAFB fragments from a... |
| fafb_neuron_details | Find out what is already known about a neuron's connectivity... |
| fafb_seg | Use any CATMAID function in the v14-seg environment, without... |
| fafb_seg_conn | Log into the v14-seg CATMAID instance for FAFB v14 Adult... |
| fafbseg_join_connectors_in_ngl_volumes | Join free connectors in a CATMAID instance to skeletons if... |
| fafb_segs_stitch_volumes | Get neuron volumes and stitch them into a cohesive neuron, or... |
| fafbseg_transfer | Transfer information between v14 and v14-seg neurons |
| flow.centrality | Determine dendritic/axonal by calculating flow centrality |
| get_connected_skeletons | Retrieving CATMAID neuron skeletons connected to query... |
| get.hxsurf | Read Amira surface (aka HxSurface or HyperSurface) files into... |
| get.skeleton.from.flycircuit | Fetch FlyCircuit neuron skeletons from the Taiwan FlyCircuit... |
| get.synapses | Get 3D coordinates of synapse (not connector) positions |
| inside_neuropils | Calculate the cable length inside of different neuropils in a... |
| label_neuron.class | See neurons with chosen neuropils to determine their types |
| local_conn | Connect to a local CATMAID server |
| make.anatomical.model | Generate a neuroanatomical alpha shape from connector and/or... |
| make.mirror.transform | Get the transformation matrix from the Morpho::mirror... |
| manually_assign_axon_dendrite | Manually assign the dendrite and axon to a neuron |
| map_fafbsegs_to_neuron | Find out what is already known about a neuron's connectivity... |
| microtubules | Functions to assign and visualise microtubule rich and twig... |
| napplyTransform | Apply a transform to a neuron/neuronlist |
| nblast_bothways | NBLAST two different sets of neurons forwards and backwards |
| neurites | Segregate neurite compartments from a neuron/neuronlist |
| neurons.inside | Find neurites inside of an alphashape |
| open_l1 | Jump from R into the L1 larval EM data in CATMAID |
| overlap.connectivity.matrix | Generate a connectivity matrix based on euclidean distance... |
| pointsinsidemesh | Find neurites inside of an mesh3d object |
| primary.neurite | Returns the primary neurite of a neuron |
| prune_by_tag | Prune neuron by splitting it at CATMAID tags |
| prune.catmaidneuron | Prune nodes from a catmaid neuron, keeping the synapses |
| prune_distal | Prune nodes from a neuron, keeping the root node |
| prune_in_volume | Prune neuron within neuropil volume |
| prune_online | Prune a neuron interactively |
| prune_strahler.catmaidneuron | Prune a CATMAID neuron by removing segments with a given... |
| prune_vertices.catmaidneuron | Prune vertices from a CATMAID neuron, keeping the synapses |
| read.neurons.catmaid.meta | Read neurons from CATMAID with extra meta-data |
| read.neurons.fafbseg | Read neurons from the FAFB segmentation instance (temporary) |
| resample.catmaidneuron | Resample a CATMAID neuron |
| rescue.dps | Generate a dps object without dropping small neurons |
| scan4matching | Scan through suggested pairs of neurons |
| seebroken3d | Plot neurons split up by synapse clusters |
| seesplit3d | Plot neurons split up by flow centrality |
| segments_ranked | Ranked sampling |
| select_neurons | Select neurons in space |
| select_points | Select 3D points in space |
| set_segmentation_location | Calculate a connectivity similarity score between two... |
| shift.neurons | Shift neurons in space |
| sholl_data | Sholl analysis on neuron skeletons |
| soma | Functions for retrieving soma data |
| subtree | Get a subtree in a neuron object as a separate neuron object |
| synapsecolours.neuron | Plot a neuron with different coloured synapses depending on... |
| tracer.plot | Get data and plots describing tracer activity statistics |
| transform3dalphashape | Transform the 3D vertices of an alphashape |
| update.neuronlist | Update a local neuronlist with new CATMAID data |
| write.spin.swc | Write ordered swc |
| WriteVTKalphashape | Write alphashape as a .vtk file |
