Importing particle picks from cryosparc to Relion


I picked particles using cryolo, imported the picks and the motion corrected micrographs to cryosparc. After 2D classification, I would like to import them back to Relion 3 but having new issues I have not seen before. I have previously imported the picks with the remove UID option and would run this command to generate the star files and the remainder of my pipeline went smoothly: particles_selected Jxx_passthrough_particles_selected.cs --micrograph-path MotionCorr/jobxxx/Frames --swapxy

This would strip the UID from micrographs because of the selected “remove UID option” while importing the picks. In the past, I have not had to pass the --strip-uid flag. With the new changes, I included --strip-uid flag as I noticed micrograph filename containing having UID without this flag and removed the --swapxy flag based on recent responses by developers here. I ran this command and performed a test classification after extraction in Relion: particles_selected Jxx_passthrough_particles_selected.cs --micrograph-path MotionCorr/jobxxx/Frames --strip-uid

Neverthless, the picks in Relion are in the wrong regions of the micrograph. Let me know if you have thoughts on how to fix this.


Contemporary versions of pyem initiate an inverty operation in the background. At a guess, this probably has to be undone in your case, i.e. by specifying an explicit --inverty flag, in order to maintain the same output coordinates.