Analysis of plant stem, roots and froots

Can we analyze the plant roots and stems and fruits?
Dr. Sreenivas Alluri

Yes, people have done this before and reported good results (you might be able to find some publications on this). If you have good scans then a lot of the same tools should work, like segmentation, vessel analysis, etc.

Can you provide any journal papers for reference.

With this google search I found some good hits: