I am trying to use BoneJ skeletonize function to skeletonize my tree like structure in 3D volume. Here is a small example example.tif (6.4 MB) .
I convert the image to binary, then use BoneJ>skeletonize. What I expected was getting the centerline of the entire tree like strcture connected as skeleton.
But I got this , which is not definitely centre line skeleton. I am not sure which mistake I did. I also tried fiji>plugin>skeleton>skeleton2D/3D. Gave me the same output. My actual data is bigger than the example, and when I run on the actual data, I also got the wired skeleton structure.
Can you please advise?