Dear @iarganda and Image J Community,
First off, thank you @iarganda for your work. I am a PhD student and this plugin is making my work possible. This particular project is for a poster in this years’ Society for Neuroscience conference.
I am using Analyze Skeleton to measure nerve terminals in a confocal image stack with fluorescence. I would like Analyze Skeleton to produce an image stack with numbers that identify the structure with the data.
This is my work-flow:
I measure the objects with Cell Object Counter 3D. This plug-in produces new image stacks that give a number for the structure identified so I can match the actual structure with the data. I am then taking one of these image stacks, skeletonizing it, and running it through Analyze Skeleton. Analyze Skeleton is recognizing the same 13 objects and measuring them. However, they are out of order when compared to Cell Object Counter 3D.
Is there any way to have Analyze Skeleton produce an image-set that shows the object ID number in the stack. I was hoping the “Skeleton-labeled-skeletons” image stack would have numbers that would identify the structures but I did not see it.
If we could get ID numbers within the image stack then we could organize the match the data from Analyze Skeleton with Cell Counter 3D. It would be great to match the data up so we can have volume, surface area, mgi and length!
Thank you for all of your hard work!