Hi… I realize that I put the wrong pixelsize for a dataset when I imported it. Of course, I noticed this when the CTF determination went completely crazy. Since the step of unblurring took an inordinate amount of time, I would prefer just to be able to change it after this step. Is it possible to do that, or do I have to restart the whole process?
It is possible (though somewhat difficult) to change the pixel size, and also the pixel size is used to set/autotune parameters of the motion correction algorithms, so it may be worth re-processing anyway.
To change the pixel size:
- find the job directory of your motion correction job
- inside the motion correction job you should find a
passthrough_micrographs.csfile. Note the full path to this file.
cryosparcm icli # now in the cryosparc python shell from cryosparc2_compute import dataset d = dataset.from_file('<path to .cs file>') d.data['mscope_params/psize_A'] = <new pixel size> d.to_file('<path to .cs file>')
This will manually override the pixel size in the output of the motion correction job, and your subsequent CTF estimation job should work correctly.
Very nice, thank you!! I reprocessed the images from the beginning, which worked fine, but this is very helpful for the future.