segmentation of plant stems

[Aryeh Weiss]

I am working on analysis of images of soybean plants. A typical image and
the segmented plants can be found via this link:
https://drive.google.com/drive/folders/1Lxjx2JX5hDAf2J61pjaSuvoQ98qT94hz?usp=sharing

One of the things that I would like to do is extract the stems
(essentially, strip off the pods.. in isolated stems, that seems doable
(eg, using opening, or other operators that take advantage of the stems
being thinner than the pods).
However , the  stems may be close together (especially near the bottom of
the plant), and in those areas the image can be  quite messy. Yet, a human
observer can "interpolate"  past the messy areas and come up with a
reasonable estimate of the stem.
Even if that estimate is not exact , I would at least like to be able to
find the skeleton along the stem.

So, any ideas on how that might be done will be very welcome.

Thanks in advance
--aryeh

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