Using Kimimaro for vessel skeletonization

[RosieFerr]

Dear Seung Lab,

I was wondering if i could use kimimaro to skeletonize a treelike vascular structure.
I read that kimimaro was specifically was developed for skeletonizing neurons, however I know that TEASAR was developed to skeletonize all kinds of structures and it is advised in some papers to skeletonize teelike vascular structures with TEASAR. I was wondering if kimimaro would be suitable to use for vascular structures instead of neurons, what do you advise?
If the answer is yes, do you have any additional advice regarding the kimimaro parameters when used for vasculature?

[william-silversmith]

Hi Rosaria!

Thanks for checking out Kimimaro. Kimimaro was designed to work with dense neurons yes, but it can be applied to many different structures including vasculature.

It's a little tricky to give advice on parameters without knowing anything about the data or its resolution. However, I did write a guide that can help you figure it out:

https://github.com/seung-lab/kimimaro/wiki/Intuition-for-Setting-Parameters-const-and-scale

Of course, you can just run it and see what pops out with the defaults too.

Will