If motion corrected micrographs are imported through a Live session, cryoSPARC makes copies in rather than symlinks as is done for movies. In retrospect I should have realized that would happen, since patch motion still runs and treats them as 1 frame movies.
Could this behavior perhaps be altered so that if the movies have 1 frame, patch motion is skipped and a symlink is made instead?
Hi @DanielAsarnow thanks for posting.
Right now this is not possible in a straightforward way because patch motion also does background subtraction, and so the output micrograph from patch motion is different than the input (even if it’s a 1 frame micrograph) and the downstream steps in Live require that the micrographs they read are already background subtracted on disk (meaning that we still need to make a copy of the input micrograph).
Oh, interesting. What background is subtracted? In my case any live micrograph imports would have been motion corrected by some other pipeline provided by the facility, they already have gain and defect correction.
The background that is subtracted is essentially the “ice gradient” - in patch motion (and rigid motion also) we estimate a background to flatten out the overall gradients of contrast across the micrograph. You can see these backgrounds as *_background.mrc in the job dir of patch motion jobs. The micrographs that are written out are gain, defect, hot pix corrected and background subtracted. The bg subtraction also helps a lot for visualization during particle picking - without it you can’t see particles in the darker/lighter (thicker/thinner) regions of the micrographs
I see, thanks for explaining! This subtraction is only done if Patch Motion is run, correct?
@DanielAsarnow sorry for the delay - correct the subtraction is only done if Patch Motion (or Rigid Motion) are run