Remove artefactual spikes in neuron tracing due to registration errors

unspike(x, threshold, ...)

# S3 method for neuron
unspike(x, threshold, ...)

# S3 method for neuronlist
unspike(x, threshold, ...)

Arguments

x	A neuron, or neuronlist
threshold	A numeric threshold for an XY distance that would be considered suspicious.
...	arguments passed to methods

Value

A neuron or neuronlist with artefactual spikes removed. Segments that cannot currently be fixed are left untouched with a warning issued.

Details

unspike currently uses a very simple algorithm to remove big jumps: it just looks for XY jumps bigger than a specified distance and removes the first associated node. It currently cannot deal with two slightly more difficult situations:

When there are two or more points that are far out of register.
When there a branch or end points that are out of register.

Handling consecutive points or end points should be a fairly straightforward addition. Branch points require a little more thought.

node ids and connectors

unspike has the side effect of losing the CATMAID node ids in the output neuron. connector/tag information is retained although the node ids are translated to the new numbering system.

Examples

# \donttest{
da1pns=read.neurons.catmaid("annotation:^glomerulus DA1$")
# set threshold to 5000 nm
da1pns.fix=unspike(da1pns, threshold=5000)
#> Warning: segment with one bad point
#> Warning: segment with one bad point
#> Warning: segment with one bad point
#> Warning: segment with one bad point
#> Warning: segment with one bad point
#> Warning: segment with one bad point
#> Warning: segment with one bad point
plot(da1pns, col='red', WithNodes=FALSE)
# overplot fixed neuron leaving red spikes visible
plot(da1pns.fix, col='black', WithNodes=FALSE, add=TRUE)
# }