Hello
  I have been using the MOST tracing plugin to trace vascular networks in my datasets. I want to optimise the parameters for it in the same way as they did in the original paper, but to do that I think I need the output of the segmentation (the vessel scooping) before the skeletonisation (radius-adjustable sphere algorithm). Or I need to create a binary image based on a slice through the swc recorded nodes and radii. I was wondering if anyone knew how I could get the plugin to output a version of the images after the vessel scooping, or if anyone knew of code to do the swc to binary label (with radius info)?


Many Thanks
Claire

"if anyone knew of code to do the swc to binary label (with radius info)?"
---- you may use the Vaa3D plugin "swc_to_mask_img" which turns a swc file into a binary mask image.

Originally posted by Claire Walsh:

Many thanks, exactly what I need, do you know where the documentation is for this plugin as I am just trying to work out how it chooses the scaling i.e the voxl sizes on the mask image (I did a test run and the mask that the plugin provides has different image size to the original image used to make the skeletonisation.)

I don't think there is a 'documentation' for this function which is fairly straightforward. the information may be fetched from the source code itself quickly.


Originally posted by Claire Walsh: