potential_synapses: Calculate number of potential synapses between two neurons

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Calculate number of potential synapses between two neurons

Description

This implements the method of Stepanyants and Chklovskii

Usage

potential_synapses(a, b, s, ...)

## S3 method for class 'neuronlist'
potential_synapses(a, b, s, ...)

## S3 method for class 'neuron'
potential_synapses(
  a,
  b,
  s,
  sigma = s,
  bounds,
  method = c("direct", "approx"),
  ...
)

## S3 method for class 'dotprops'
potential_synapses(
  a,
  b,
  s,
  sigma = s,
  seglength = 1,
  bounds = NULL,
  method = c("direct", "approx"),
  ...
)

Arguments

a, b	neurons or neuronlists
s	the approach distance to consider a potential synapse
...	Additional arguments passed to methods (see details )
sigma	the smoothing parameter in the approximate method (see details)
bounds	Optional bounding box to restrict comparison
method	Whether to use the direct or approximate method (see details)
seglength	how long to consider each distance between points.

Details

Note that potential_synapses.neuronlist uses nlapply to process its first argument (a). This enables progress bars, robustness to errors and simple parallel execution. See the nlapply examples for further details of these arguments in action.

For this reason if you have two neuronlists of unequal sizes, it is recommended to put the larger one in argument a.

References

Neurogeometry and potential synaptic connectivity. Stepanyants A, Chklovskii DB. Trends Neurosci. 2005 Jul;28(7):387-94. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.tins.2005.05.006")}

See Also

Other neuron: neuron(), ngraph(), plot.neuron(), prune(), resample(), rootpoints(), spine(), subset.neuron()

Examples

potential_synapses(Cell07PNs[1], Cell07PNs[1:3], s=2)
## Not run: 
# if you have many neurons to calculate you should get a progress bar
potential_synapses(Cell07PNs[1:10], Cell07PNs[11:20], s=2)

# you can also use parallel execution, here over 7 cores
# doMC::registerDoMC(7)
potential_synapses(Cell07PNs[1:10], Cell07PNs[11:20], s=2, .parallel=TRUE)

## End(Not run)

nat documentation built on May 29, 2024, 10:36 a.m.