skeletonise_error

[pr4deepr]

Hi Robert
I am having trouble with the skeletonise plugin in CLIJx.

I tried the Skeletonise2D/3D plugin (left column) and CLIJx skeletonise (right column). Last image is the maximum projection of each.

Sample image is here.

Cheers
Pradeep

[haesleinhuepf]

Hey @pr4deepr ,

thanks for reporting! We discussed that earlier on the forum:
https://forum.image.sc/t/clijx-skeletonize-wrong-skeleton/39362/5

Thanks for creating an issue here!

Afaik, there is no easy fix. That's why skeletonize is part of CLIJx ;-)

Do you by chance know good/fast lternatives except the one from Fiji?

Cheers,
Robert

[pr4deepr]

Aaah, I forgot to search the forum. I was looking at the issues here.
In terms of a fast alternative, I have not really tried any other alternatives, apart from what I have seen in skimage, but have you seen this CUDA implementation of skeletonise?
https://github.com/sahandKashani/skeletonization
Can this be adapted?

[pr4deepr]

As you have been looking at ITK filters, can these work? You may have come across this..
Fast Marching Minimal Path Extraction in ITK
ITK Thickness 3D