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Gain file is by default named CountRef…mrc (with a pixel size of 1)
Defect file is by default a text file
When importing the movies you should give a defect map file as well as the gain reference file.
Load IMOD
module load imod (on cbi-... servers) setimod (on xtallo machines)
You can make a defect map from the text file with 'clip defect' in IMOD 4.10.7 or higher:
clip defect -D defects...txt fileWithFrames defects...mrc
where the fileWithFrames is used only to set the size of the output and can be any file of the right X and Y size.
If the defect text file is not recognized by cryoSPARC, the Gain file has to be modified to put a value of 0 on defective pixels (because any pixels that have a value of 0 in the gain reference file are treated as defects).
In the Gain file, the defective pixels have a value of 1, so you need to subtract the defects…mrc file from the Gain…mrc file
subimage Gain...mrc defects...mrc Gain_subimage...mrc
The pixel size will messed-up and has to be fixed to get back to a value of 1
alterheader -fixpixel Gain_subimage...mrc
Now the Gain_substracted…mrc file has a zero value for defective pixels instead of 1).
Gain/defect files coming from Glacios must be flipped along Y axis when imported in cryoSPARC.