One application is to be able to follow the deformation of a fiber during e.g. tensile tests in future research, to learn more about the behavior of the microstructure of the material. I honestly don't know much about the details.

Apparently, classic segmentation techniques have been tested before, but haven't worked well enough. My thesis project is basically about trying a machine learning approach, and seeing how well that can work.

Any ideas are appreciated. :)

If I understand you correctly, this would be a way to merge the results for smaller parts of an image? Unfortunately, I haven't really managed to achieve any good results on such smaller image parts either. For that reason I haven't tested the merging algorithm presented in the paper, so I don't know how well that one works.