Measuring branches

Henri

Hi Forum,

I'm trying to measure the branches of a neuron. Thanks to older threads in this forum I succeeded in using the branch end filter, thus classifying branch points, end points and the spine.
However, I would additionally like to measure the length of my branches. Is there a way to identify my 'spine'/ the longest continues line. Currently, it is not being picked up as a single long axon, but as multiple smaller segments, separated by my branch points. If there was an easier approach to select only the branches, please let me know.

Below are pictures of my skeletonised classification and the original image.
Thanks a lot,
Henri 

YuriG

Hi Henri,

Regarding measurement of the longest spine: you can apply Pruning filter (2D or 3D) with "Retain long branches" option, select the number of iterations (passes) to remove only short spines, and you will end up with only the long spine.

Note that you can measure length of the segments on the image using the "Vectorize" option (Measurements Options panel, Count Options group, Object drop down).

Yuri

Henri

Thanks Yuri!

This is what I was looking for. Could you briefly explain the effect of iterations? I couldn't see much of a difference. Presumably, more iterations means more branches removed?

Thanks again!

YuriG

Hi Henri,
The number of passes defines the length of the branches to cut. For example, set 50 if your branches are less than 50 pixels long.
Yuri