Judging from the one image I’d say it should be possible. Still, I think it would come with some major effort since the only solutions I can think of to automate this problem are not simple and require some serious ‘love’ to be parametrized usefully.
DISCLAIMER: below this line I just spell out what comes to my mind. Giving the problem more thought might make me change all uttered opinions…
I would try to:
- Perform a foreground/background segmentation in one of 1000 known ways.
- Then use the fluorescent nuclei (or whatever it is) as seed points, constraining the space of all possible solutions only to those that have precisely as many segmented objects as one detects nuclei.
- Use one of many existing methods developed in the context of e.g. blood-vessel segmentation or connectomics. What comes to (my) mind are the methods by Björn Andres or Pascal Fua (et al., of course). These methods can in principle incorporate constraints that express that cells, when crossing, continue on straight.
Here one such paper: Türetken, E., Benmansour, F., Andres, B., Pfister, H., & Fua, P. (2013). Reconstructing Loopy Curvilinear Structures Using Integer Programming. Presented at the CVPR '13: Proceedings of the 2013 IEEE Conference on Computer Vision and Pattern Recognition, IEEE Computer Society.
If anybody reads this and thinks: good, this Florian guy must be quite old… I’d be happy to hear about more modern approaches for such problems… please post your ideas!