Inaccurate gain correction


We recently upgraded the camera on our Krios to Direct Electron Apollo, and it appears that cryoSPARC (v 4.4) has some difficulty with gain correction in the process of motion correction. The attached image contains the gain (estimated from the data to eliminate the possibility of the camera software introducing unwanted rotations/flips), output of motion correction in relion and output of motion correction in cryoSPARC for the same movie. Because the movies are in tiff format, the gain was “flipped in Y” when importing the movies into cryoSPARC. This approach worked well for our old Gatan K2, but for the Apollo gain correction in cryoSPARC produces artifacts. Just in case, I experimented with various combinations of rotations and flips, but the results were clearly worse. What could be the reason fro this?

Thank you.