Hi,
AFAIK, RELION flips TIFF images along the slow axis (i.e. flip in y-axis). In contrast, cryoSPARC reads TIFF data in the order it’s written on disk (i.e. does not flip in y-axis). If your data (e.g. .tiff stacks, .mrc gain reference) required a flip in y transform in RELION, then this is not required in cryoSPARC due to the aforementioned difference.
Whenever in doubt, you can try it both ways and inspect the resulting thumbnail preview. It is often fairly obvious.
Cheers,
Yang
PS, If, however, you plan to use the MotionCor2 wrapper from within cryoSPARC, then a flip may again be required. MotionCor2 and RELION share the same TIFF reading convention.