Return connector table for a given neuron

catmaid_get_connector_table(skids, direction = c("both", "incoming",
  "outgoing"), partner.skids = TRUE, get_partner_names = FALSE,
  get_partner_nodes = FALSE, pid = 1, conn = NULL, raw = FALSE,



Numeric skeleton ids


whether to find incoming or outgoing connections


Whether to include information about the skid of each partner neuron (NB there may be multiple partners per connector)

get_partner_names, get_partner_nodes

Whether to fetch the names and/or number of nodes for the partner neurons.


Project id (default 1)


A catmaid_connection objection returned by catmaid_login. If NULL (the default) a new connection object will be generated using the values of the catmaid.* package options as described in the help for catmaid_login.


Whether to return completely unprocessed data (when TRUE) or to convert the nodes and connectors lists into processed data.frames (when FALSE, the default)


Additional arguments passed to the catmaid_fetch function


As of CATMAID v2016.10.18 this returns a data.frame with columns

  • skid

  • connector_id

  • x

  • y

  • z

  • confidence

  • user_id

  • treenode_id (NB this is always the treenode id of the query skeleton whether or not incoming or outgoing connections are requested)

  • last_modified

  • partner_skid

Prior to this it returned a data.frame with columns

  • connector_id

  • partner_skid

  • x

  • y

  • z

  • s

  • confidence

  • tags

  • nodes_in_partner

  • username

  • treenode_id

  • last_modified

See also


if (FALSE) { # fetch connector table for neuron 10418394 ct=catmaid_get_connector_table(10418394) # compare number of incoming and outgoing synapses table(ct$direction) ## Look at synapse location in 3d # plot the neuron skeleton in grey for context library(nat) nopen3d() plot3d(read.neurons.catmaid(10418394), col='grey') # note use of nat::xyzmatrix to get xyz positions from the ct data.frame # colour synapses by direction points3d(xyzmatrix(ct), col=as.integer(ct$direction)) ## plot connected neurons in context of brain nopen3d() # fetch and plot brain model models=catmaid_fetch("1/stack/5/models") vs=matrix(as.numeric(models$cns$vertices), ncol=3, byrow = TRUE) points3d(vs, col='grey', size=1.5) # fetch and plot neurons plot3d(read.neurons.catmaid(10418394), col='black', lwd=3) points3d(xyzmatrix(ct), col=as.integer(ct$direction)) partner_neuron_ids=unique(na.omit(as.integer(ct$partner_skid))) partner_neurons=read.neurons.catmaid(partner_neuron_ids, .progress='text', OmitFailures = TRUE) plot3d(partner_neurons) }