Hi @yanhezhao,
One option for you is to re-import the movies with the correct pixel size and re-run Patch Motion Correction, Patch CTF and particle re-extraction.
If you prefer to change the pixel size of Patch Motion Corrected micrographs and then only re-run Patch CTF and re-extraction of particles, then it is possible to perform pixel size adjustment on the motion corrected micrographs using cryosparc-tools, and we have provided an example script for this here. To run the script it would be something like:
python change_apix_micrographs.py P100,W1,J3 1.074 where the final number is the new pixel size that you are specifying.
The code allows you to adjust the pixel size of Patch Motion Corrected micrographs to whatever you like and will output the particles to the CryoSPARC GUI as an “external” job type with the title “micrographs_pix_updated”, and in the terminal will output a message to tell you what the external job number and updated pixel size is.
Using either of these strategies will mean that all downstream processing is at the correct pixel size and allow Reference-Based Motion Correction to run, if it is appropriate for the project.