How to use the Frangi Filter in Fiji


#1

Could someone help with how to use the frangi filter to segment the venous structure? I do not quite understand the min and max values for the threshold.


#2

Hi @wei_liu,

Welcome to the forum!

Those parameters are not thresholds, they are scales. You should give large values of those parameters if you expect the “tubes” in your image are big/wide, and small values if you expect them to be small/thin. Details here.

Hope that helps,
John


#3

Hi John (@bogovicj),

Thanks for your reply. I do not get the desired results regardless which number I tried. Could it be due to the fact the images I used are SWI images with the venous structure showing in dark instead of bright?

Thanks,

Wei


#4

Hi Wei @wei_liu,

Yes, this could be the issue - have you tried inverting your images ( Edit > Invert ) before applying the Frangi filter?

If you are still getting unexpected results, perhaps consider posting your original and post-processed images to this forum post - that could be helpful for others to give you ideas.

Good luck,
John


#5

This does the trick. Thank you!