If one provides pre-aligned sums to Live, e.g. aligned in appion, Live seems to still try to run Patch Motion on each exposure, taking a bit of time. It would be better I think in this case if Live recognized that the supplied mrc has a single frame and skipped directly to Patch CTF.
This is a good point - thanks for bringing it up. Currently, the motion correction job generates some metadata that the downstream jobs require, which is why it’s not possible to skip motion correction completely. We do plan to develop a workaround to calculate the required metadata without running through the entire motion correction algorithm, but I can’t at this time say exactly when that will be available.
May 4, 2022, 11:43am
Was there any update for this or it is not possible to use cryoSPARC Live without performing motion correction?
@olibclarke @hsnyder any cheat to import corrected aligned weighted sums?
Likewise it would be great to be able to use the Motioncor2 wrapper inside CS Live.
@DanielAsarnow Would you mind sharing with us the reason behind your preference for MotionCor2 in cryoSPARC Live?
Motioncor2 has several nice features:
Explicit motion model including sample doming
Can provide a tilt angle which is used by the motion model
Deconvolution of in-frame motion (using vectors interpolated from between-frame vectors)
Arbitrary Fourier cropping ratios (the whole movie has a very high spectral resolution, you can match pixel sizes between datasets using exact fractions)
.star file output for Relion particle polishing (suppose I could implement this in csparc2star.py)
Use the SerialEM defect file directly (believe this was requested elsewhere for Patch Motion)
Grouping of frames for movies with low doses or sparse particles (e.g. < 0.5 e-/Å^2)
Throw frames from beginning or end of movie
Anisotropic magnification correction at motion correction stage
Good outlier pixel rejection (I suppose Patch Motion does as well)
Output of dose subset micrographs (e.g. from 0.5 to 30 e-/Å^2, useful for making lower total dose reconstructions)
Output of even and odd sums for denoising
Output of aligned frames
And also certain people really want me to use it…but the first 4 points are the significant ones to me.
FWIW we simply want to run Live in a location where we don’t want to transfer frames.
Thank you for your work. This would save much time by not having to run motion correction with relion to polish cryosparc particles.
you can run Live on aligned mics - it just treats it as a one-frame movie and tries to run Patch Motion - it does still work though
Thanks. Do you use an empty gain reference image?
I think so? I can’t remember honestly, it’s been a while since I tried, I just remember that it worked