How do I join edges from the results of AnalyzeSkeleton plugin?




I’m a bit stuck on working with the result of AnalyzeSkeleton. After I used the method on the plugin web page to prune very short end points, I re-analyzed the skeleton and this is the result (an example of many of the same problem):
how to join branch

As you can see, there is a junction despite not having a bifurcation. My question is: how would I go about combining the two edges?

Here’s what I have so far:
detect by gathering vertices that only connects 2 branches (no bifurcation therefore edges should be connected)
first idea: make a new graph with all existing edges and vertices except for the offending vertex and its 2 edges, make a new edge with the appropriate V1 and V2, and all the slab pixels from e1 and e2, then adds it to the new graph -> runs out of memory therefore inconclusive.
second idea: get p1 and p2 from the vertex, draw a line (3D) between the two points on the image stack then re-analyze. -> no change

The skeleton is fully connected in the imagestack, but AnalyzeSkeleton acts as they’re spereated and renders them accordingly on the 3D Viewer.


Ok I’m stupid, setting the analysis setting to detect and break cycles via “AnalyzeSkeleton_.SHORTEST_BRANCH” solved it. Maybe the skeleton isn’t as clean as I thought it was.