Initially I imported subtracted particles in relion to cspar, by directly importing from the star file. After some processing, now I want to import back to relion to undo the subtraction. However, when using the cs2star.py, including the --copy-micrograph-coordinates, the resulting star file does not contain the _rlnImageOriginalName. Is there a way to fix this issue?
cryosparc writes the information in two files; particles.cs & passthrough_particles.cs
Possibly the original micrograph name is written in the passthrough file (for my subtraction job that was the case). To combine the information of both files you have to include it in the csparc2star.py command. E.g.: csparc2star.py JX_particles.cs JX_passthrough_particles.cs JX_004_particles.star --swapxy.
Not sure, if you tried this, but for me this did the trick some time ago.