If I understand correctly, the electron beam causes ice-doming which can cause beam-induced particle motion in the x, y, and z axes.
Does cryoSPARC’s CTF estimation or per-particle CTF refinement correct for defocus changes across frames in a movie due to changes in particle position along the z-axis (z-height)?
I believe Gctf has implemented some sort of CTF correction across movie frames to correct for particle motion along the z-axis, but I am not sure if cryoSPARC’s version of CTF estimation or CTF refinement does as well.
Welcome to the forum @hickschadw! 
CryoSPARC’s motion correction algorithms currently only estimate and correct for motion in the xy plane of the particles; z motion is not estimated or corrected for. Thus, CTF estimation currently does not correct for defocus changes induced by motion along the z-axis of particles. In fact, CTF estimation only operates on micrographs and doesn’t currently use information from the raw movies.
We aren’t too familiar with the workings of GCTF, but this type of approach sounds interesting — let us know if you have a reference for this behaviour, as we would be curious to learn how it works.
Best,
Michael
Hi Michael,
Thanks for the response! I think that correcting particle motion along the z-axis would only matter at very high resolutions, but cryo-EM techniques seem to be getting better and better, so it might be useful to have this kind of correction.
Section 2.7 of (Zhang (2016) Gctf…) describes correcting for CTF across movie frames: “First, global CTF parameters are determined for the averaged micrograph of motion-corrected movies. Then based on the global values, parameters for each frame are refined using an equally weighted average of adjacent frames (suggested 5–10) to reduce the noise.”
Zhang, Kai. “Gctf: Real-time CTF determination and correction.” Journal of structural biology 193.1 (2016): 1-12.
Thanks!
-Chad