Hello ImageJ/Fiji community,
I am looking for a solution to generate 3D skeleton from filtered images of blood vessel.
I attached a 2D max projection image for example, if neccessary I can also try to attach the original 3D stack:
To get this I started with a fairly noisy image and performed a multi-scale tubeness filtering, to enhance the vasculature structures. The filtered image stack can either be 8-bit or 32-bit gray image, but doesn’t matter too much. We would like to generate skeleton of the blood vessels from such image stack. The skeleton doesn’t need to be super precise but should decent enough to represent both thick vessel and thin vessel.
Currently I couldn’t find a good threshold value to satisfy both large and small vessel structures, to generate a binary mask. Alternatively I am thinking to just use the gray value image to generate the skeleton. However I couldn’t seem to find a plugin that doing this.
I found this:
But all links are broken now.
I don’t think I’m the first one that need a 3D skeletonize on gray value image, but couldn’t find a readily solution after half day of googling. I haven’t done research in method/algorithm yet, and that’s my next step if no available solution found. I wouldn’t mind to code a plugin or implement a nice algorithm from sketch to do that, but certainly don’t want to reinvent the wheels.
Any help or suggestions will be appreciated. Thanks.