Error: Just part of image can be recognized during Inspect particle?


Have anyone experienced such an error that just part of image can be recognized when Inspecting particles after template-based autopicking in cryosparc v3.1.0?
These movies were recorded using K3 camera and motion-corrected by MotionCor2 and then CTF-calculated by Cttfind4, which both are integrated in the cryosparc interface. However, it seems OK if we initially processed the same movies using Patch-motion and Ctffind4.
I searched the discussion and found that similar errores happened in the previous version of cryosparc. Is still there some incompatible thing when using MotionCor2 in cryosparc v3.1.0. Is there any way to solve this error if using MotionCor2?
Thanks a lot!


I have not used cryosparc to pick K3 images, but this looks very much like what you get with gautomatch on rectangular micrographs. It only picks within a square area, leaving the edge out, which is probably what you are seeing. Either use a different picker, or split each image into two overlapping squares (in imod: clip resize -x 0,4092 -y 0,4092; clip resize -x 1668,5760 -y 0,4092) and then merge particle sets (after removing overlapping ones and adjusting X within the right square, of course). Some pain, but in this way you recover ~40% more data, so it is worth it, although you will not be able to do all that within cryosparc.

Hi @niu,

Thanks for reporting - this may be related to a bug we recently discovered in the MotionCor2 wrapper that sometimes changes the order of x,y axes of the micrographs after motion correction. We are hoping to fix this soon.

Is there a reason you’d like to use MotionCor2 instead of Patch-motion?

Thanks for your reply. I just want to adjust a small deformation by using the commond “-Mag n n n”. But I can not find any input for this commond in Patch-motion. So…

Thanks. It looks like just a bug in using MotionCor2 wrapper. If we firstly do it using MotionCor2 out of Cryosparc and then import the micrographs into Cryosparc, everything will go well next.

Thanks for confirming @niu, the fix will be in the next release.

Patch v3.2.0+210601 released yesterday resolves this issue: Patch 210601 is available for cryoSPARC v3.2.0