Gain reference problem

Troubleshooting
1

Dear all,

I am importing dark subtracted .tif movies and want to do gain referencing while importing. I have my gain reference file converted with IMOD’s dm2mrc and then import to cryoSPARC. The importing fails with the following error:

Traceback (most recent call last):
File “cryosparc2_master/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/imports/run.py”, line 564, 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 (3838,3710) (3710,3838)

I know that my gainref file should be rotated 90 degrees and also flipped against x axis. However using rotate and flip options does not help. I am able to import the images without using gain reference.

Has anyone encountered similar problems?

Best wishes,
Valtteri

2

Hi @Valtteri_Jarvinen,

Do you get the same error message when you import with the rotate and flip settings set?
This should actually solve this problem (the shapes of the movies and the gain reference indicate that they are off by 90 degrees)

Ali