Job: MotionCor2 (Wrapper) (BETA)

How to use the wrapper for MotionCor2 available in CryoSPARC.

At a Glance

Perform motion correction using MotionCor2 as a wrapper within CryoSPARC.


MotionCor2 models the anisotropic motion of electron microscopy movies using a smooth deformation model. More details are available in Zheng, 2017.

Please ensure that you review the MotionCor2 License Terms before using it in your project.

MotionCor2 License Terms

CryoSPARC does not distribute MotionCor2 binaries. Please ensure you have your own copy of MotionCor2 installed under the terms of the MotionCor2 Non-Commercial Software License Agreement available at: For-profit users must contact David Agard for licensing information prior to download. Structura Biotechnology Inc. makes no warranty regarding MotionCor2.



MotionCor2 requires movies as an input, typically from an Import Movies job.

Commonly Adjusted Parameters

Patch Value

MotionCor2 requires users to input the number of patches in the X and Y axes. Note that this setting is distinct from Patch Motion Correction’s knots settings.



MotionCor2 outputs motion-corrected micrographs.

Common Next Steps

Micrographs typically require CTF estimation in Patch CTF Estimation for further downstream processing.


  1. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods 14, 331–332 (2017).

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