unspike: Remove artefactual spikes in neuron tracing due to...

In natverse/elmr: Support for working with light and electron microscopy fly brain data

Remove artefactual spikes in neuron tracing due to registration errors

Description

Remove artefactual spikes in neuron tracing due to registration errors

Usage

unspike(x, threshold, ...)

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

## S3 method for class '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

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.

Value

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

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.

See Also

smooth_neuron

Examples

da1pns=read.neurons.catmaid("annotation:^glomerulus DA1$", conn=vfbcatmaid("fafb"))
# set threshold to 5000 nm
da1pns.fix=unspike(da1pns, threshold=5000)
plot(da1pns, col='red', WithNodes=FALSE)
# overplot fixed neuron leaving red spikes visible
plot(da1pns.fix, col='black', WithNodes=FALSE, add=TRUE)

natverse/elmr documentation built on Sept. 2, 2023, 9:30 a.m.