dotprops: dotprops: Neurons as point clouds with tangent vectors (but...

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

dotprops: Neurons as point clouds with tangent vectors (but no connectivity)

Description

dotprops makes dotprops representation from raw 3D points (extracting vertices from S3 objects that have them)

dotprops.dotprops will default to the original vale of k and copy over all attributes that are not set by dotprops.default.

dotprops.neuronlist will run for every object in the neuronlist using nlapply. ... arguments will be passed to nlapply in addition to the named argument OmitFailures.

Usage

is.dotprops(x)

as.dotprops(x, ...)

dotprops(x, ...)

## S3 method for class 'character'
dotprops(x, ...)

## S3 method for class 'dotprops'
dotprops(x, k = attr(x, "k"), ...)

## S3 method for class 'im3d'
dotprops(x, ...)

## S3 method for class 'neuronlist'
dotprops(x, ..., OmitFailures = NA)

## S3 method for class 'neuron'
dotprops(x, Labels = NULL, resample = NA, ...)

## Default S3 method:
dotprops(x, k = NULL, Labels = NULL, na.rm = FALSE, ...)

Arguments

x	Object to be tested/converted
...	Additional arguments passed to methods
k	Number of nearest neighbours to use for tangent vector calculation (set to k=20 when passed NULL)
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an eror. For other values, see details.
Labels	Vector of labels for each point e.g. identifying axon vs dendrite. The default value NULL will produce class-specific default behaviour for different classes of input object, TRUE always uses labels when an incoming object has them and FALSE never uses labels.
resample	When finite, a new length to which all segmented edges will be resampled. See resample.neuron.
na.rm	Whether to remove NA points (default FALSE)

Details

k will default to 20 nearest neighbours when unset (i.e. when it has default value of NA) unless x is a dotprops object (when the original value of k is reused).

References

The dotprops format is essentially identical to that developed in:

Masse N.Y., Cachero S., Ostrovsky A., and Jefferis G.S.X.E. (2012). A mutual information approach to automate identification of neuronal clusters in Drosophila brain images. Frontiers in Neuroinformatics 6 (00021). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3389/fninf.2012.00021")}

See Also

nlapply

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