Pixel size change

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?

Hi @Ruben1,

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:

  1. find the job directory of your motion correction job
  2. inside the motion correction job you should find a passthrough_micrographs.cs file. Note the full path to this file.
  3. run:
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.

1 Like

Very nice, thank you!! I reprocessed the images from the beginning, which worked fine, but this is very helpful for the future.