After a while processing data we have encountered that the pixel size was wrong, so in order to do it properly I just wanted to re-import the dataset with the correct pixel size, run again the pre-processing and use the latest particles from the wrong pixel size to extract them from the correct ones. Some colleagues have done it with previous versions of CS without any issue, but I encountered that the job runs, but no particles are found.
Previous times when having issues with the names of the files it would just give an error message, but here the job finishes without error messages.
If you started again from scratch, CryoSPARC may have added a different UID to each micrograph than the originally processed set. No particle positions match micrographs, thus, no extraction. First thing to check.
You might want to use the job “reassign particles to micrographs”.
It takes particles and a micrograph set as input, and uses the micrograph name (minus unique id) and the pixel size + particle coordinates to do the remapping.
After that re-extract, and you should be ok.
Thank you for the replies. Indeed it was the issue with the UID and the reassign job solved it. For some reason I assumed that since I was not importing it from relion or anything similar this issue would not arise, not sure why did not happen previously.