Measuring Skeleton length from seed point

Hi forum gurus.

I have a question for you. A user recently came to me with gorgeous 3D data of dendrites. We can segment the image very well and get a 3D skeleton using Skeletonize 3D.

Now, what we would need is: From a user-selected seed-point, output a new skeleton where the values represent the distance from the seed point along the skeleton.
The goal of the procedure is to keep the bits of the skeleton that are a certain distance away from the cell body.

I could do this by going through each part of the skeleton myself in 3D, adapting the discussion from

But if anyone has got something already in place, I’d be happy to hear from you :slight_smile:

Below is an example for just one part of the skeleton, done by hand. It’s sort of like a region growing from the seedpoint that computes the distance to that seedpoint along the skeleton.
The example is in 2D for now on a MIP of the dataset, but I would like to find a 3D solution. (We can ignore loops in the skeleton)

Hi Olivier

it sounds like a geodesic distance transform would help you. MorphoLibJ seems to have an interactive 3D Geodesic Transform : (Interactive Geodesic Reconstruction 3D, I haven’t tried it, though…



Could “Simple Neurite Tracer” do the measurement?


Hi and thanks for the reply! Absolutely! That’s the fantastic beast I was looking for! Thanks!