I’ve been messing around on Fiji/ImageJ with Image registration, but I was curious if this “GraspJ” superresolution solution might be helpful at all? A fair bit of this goes over my head, but it seems as if it potentially could be used to get best possible results from SR since it offers a lot of parameters you can change and even “shot detection” to some degree.
https://code.google.com/p/graspj/downloads/detail?name=user manual v3.pdf