Measuring length of curved lumen

Posted by clach on Jul 06, 2015; 6:18pm
URL: http://imagej.273.s1.nabble.com/Measuring-length-of-curved-lumen-tp5013440.html

Hi, I'm looking to measure the length of curved lumens in c. elegans.

I have a tiff stack of around 30 images, and while it is possible/easy to measure the length in 2 dimensions for one image in the stack, I want to be able to account for the length that the lumen curves in the Z dimension. I would also like this process to be relatively automatic so I can use it for all of my files.

I have been attempting to use binary/skeletonize/analyze skeleton, but it seems the lumen is too thick (?) resulting in skeletons that do not accurately represent the lumens (instead of giving one line for the lumen, it sometimes gives two for the perimeter or border of the lumen).  Additionally, I am not sure of the units in which "length" is given when I use analyze skeleton... and is that the entire length of the skeleton found in all images in the stack?

If skeletonize is not the best method, please let me know! Thanks for any and all help!