Flipping and rotating gain reference

Dear cryoSparc team and users,
I have an unusual question. We know from our data collection, that the gain reference is flipped in X and rotated 180°. We gave these settings whenever we processed in Relion, as it was needed. Recently, someone told us that we should select these setting in cryosparc, because it does so automatically. Is it true? Does cryosparc handles .tiff and .mrc files differently during import? I don’t think there is any mention of this in the official guides.

Many thanks.


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.


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.

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Thank you, this was very helpful!