Retrieve soma information for skeletons (specified via CATMAID tags)

Source: R/catmaid_tags.R

soma fetches the XYZ location of the soma

somaindex fetches the raw index of the skeleton node associated with the soma (in range 1..N, number of vertices)

somaid fetches the identifier of the skeleton node associated with the soma

soma(x, ...)

# S3 method for neuronlist
soma(x, ...)

# S3 method for neuron
soma(x, ...)

somaindex(x, ...)

# S3 method for neuronlist
somaindex(x, ...)

# S3 method for neuron
somaindex(x, ...)

somaid(x, ...)

# S3 method for neuronlist
somaid(x, ...)

# S3 method for neuron
somaid(x, ...)

Arguments

x

a neuron or neuronlist object

...

additional arguments passed to methods, i.e. nlapply

Value

An Nx3 matrix (soma) or an integer vector (somaid, somaindex) with missing values filled with NA. Should a neuron have multiple soma tags then somaid and somaindex will return both (resulting in the *.neuronlist methods returning a list not a vector) but soma will select the first coordinates (with a warning) so that it always returns just one xyz location.

Details

CATMAID access required. Data collected and described in cited publication.

References

Ohyama T, Schneider-Mizell CM, Fetter RD, Aleman JV, Franconville R, Rivera-Alba M, Mensh BD, Branson KM, Simpson JH, Truman JW, et al. (2015) A multilevel multimodal circuit enhances action selection in Drosophila. Nature.

See also

nsoma