overlap.connectivity.matrix | R Documentation |
Generates an 'overlap matrix' of overlap scores between neurons in the 'neurons' and 'targets' pools. For every point in a given neuron in 'neurons', a distance score is calculated to every point in a neuron in 'targets'. The sum of this score is added to the final output matrix. The score is calculated as e(-d^2/2δ^2), where d is the euclidean distance between the two points, and δ is the expected distance in um that is considered 'close'.
overlap.connectivity.matrix(neurons, targets, neuropil = NULL, delta = 1)
overlap.connectivity.matrix.catmaid(
neurons,
targets,
neuropil = NULL,
delta = 1,
split = FALSE,
rval = c("score.matrix", "neuronlist")
)
neurons |
first set of neurons |
targets |
second set of neurons |
neuropil |
an as3d object of the neuropil in which to consider connectivity. Defaults to whole brain. |
delta |
the distance (in um) at which a synapse might occur |
split |
with a CATMAID neuron, whether or not to split the neuron using flow centrality |
rval |
whether to return an overlap score matrix or a neuronlist in which every point is given an overlap score against each of the target neurons |
... |
additional arguments passed to methods |
a matrix of 3D points
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