Gain reference - Rotation Problem


I imported TIF movies and a MRC gain reference, setup (1) “Flip gain ref in X” & (2) “Rotate gain ref” by 90 degree (The same settings I used in MotionCor2), but got the following errors. I changed “Rotate gain ref” to 0, but still got the same errors. I am running cryosparc 2.11 on P100 GPUs.

Traceback (most recent call last):
  File "cryosparc2_master/cryosparc2_compute/", line 78, in
  File "cryosparc2_compute/jobs/imports/", line 616, in run_import_movies_or_micrographs
    imgdata = tiff.read_tiff(abs_path).sum(axis=0) * gainref
ValueError: operands could not be broadcast together with shapes (7676,7420) (7420,7676) 

Any suggestion would be greatly appreciated. Thanks a lot.


Hi Xing, Should you happen to want to rotate the gain reference counterclockwise 90 degrees (i.e., -RotGain 3 in MotionCor2) and then flip left-to-right (i.e., -FlipGain 2 in MotionCor2), Rotate gain ref = 1 in cryoSPARC should work, imho.


Hi, John,

Looks problem solved by flipping the gain reference top-to-down followed by rotating 270 degree using proc2d. Thanks a lot.