Read a neuron saved by Fiji's Simple Neurite Tracer Plugin
read.neuron.fiji( f, ..., simplify = TRUE, components = c("path", "fill"), Verbose = FALSE )
Path to a file
Additional arguments passed to
Whether to return a single neuron as a
rather than a
neuronlist of length 1.
Which components to read in (path or fill). Only paths are properly supported at present (see details).
Whether to print status messages during parsing.
simple neurite tracer .traces files are an XML based format so parsing it depends on installation of the suggested XML package.
They can contain both paths (skeleton lines) and fill information (saved as
XYZ coordinates of voxels inside the object). The latter cannot currently
be handled very well by
read.neuron. If you wish to access
them you will probably need to use the private
to do so (see examples).
Your best best if you want to produce a fully 3D object with "width"
information would be to generate a 3D mesh using Fiji's 3D viewer. You can
do this by selecting the object in the viewer and the choosing
... Export Surface ... Wavefront while the 3D viewer window is
active. The resultant obj file can then be read in by
read.neurons. You could use this mesh to find radius
information for a skeleton by shooting rays from skeleton to mesh to
estimate the radius.