I am trying to extract information on the orientation of vascular canals in the cortex of mouse bones from high-resolution CT data. I have used Skeletonize 3D followed by Analyze Skeleton 3D with the option for extra information on the vertex coordinates, branch lengths and Euclidean distance between them. The issue is that the difference between the Euclidean and branch lengths can be up to 50%, i.e., the branch representing the canal is significantly more tortuous than the vertices suggest. Is there a way that the branches from the skeletonization process can be further divided into shorter segments whose orientation could then be determined from their vertices (using a 3D specific plugin)? This would be especially relevant for canals that are circumferential, by their nature more curved than radial and longitudinal.
Here's a link to a recent article that discusses a method with an ImageJ plugin, but it relies on prior processing using the LineSet file format from Amira (using its AutoSkeleton feature). Ideally I'd like to automate this all in ImageJ/BoneJ.
Any thoughts or pointing to relevant plugins would be much appreciated!