Obtain the centerlines from 3D binary mask

[qiang-zhang-neu]

Obtain the centerlines from 3D binary mask

[ungarj]

Hi @qiang-zhang-neu,

I'm not sure what you mean by "3D binary mask". I guess a 2D binary mask in this context is a raster dataset, so in order to use it with this tool you can try to vectorize the raster into a feature and then apply the centerlines algorithm. I don't think this would work for a 3D dataset though.

You use the skeleton as an alternative to the Voronoi approach here? We use the networkx package to build a temporary network graph and then calculate the longest path of all possible paths on that graph. (see https://github.com/ungarj/label_centerlines/blob/master/label_centerlines/_src.py#L66)

Then the tool smoothes the linestring by using NumPy and a Gaussian filter on the xy coordinates: https://github.com/ungarj/label_centerlines/blob/master/label_centerlines/_src.py#L146

I guess this approach will work with a skimage skeleton as well as long as you manage to convert the skeleton into a networkx graph.