CryoSPARC Guide

Job: MotionCor2 (Wrapper) (BETA)

How to use the wrapper for MotionCor2 available in CryoSPARC.


An algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Please ensure you review the MotionCor2 License Terms below.


  • Raw movies (with microscope parameters & gain reference files imported earlier)

Common Parameters

  • Path to MotionCor2 executable: The absolute path to the MotionCor2 binary. Note: Run cryosparcm cli 'set_project_param_default(proect_uid, 'exec_param', path)' (where project_uid is your project number (e.g 'P12') and path is the absolute path to the MotionCor2 binary) to keep this parameter consistent across this project.


  • Global and local (patch-based) motion corrected dose weighted micrographs
  • Global and local (patch-based) motion corrected non-dose weighted micrographs (for CTF Estimation)
  • Global and local (patch-based) motion trajectories

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.

Common Next Steps

  • CTF Estimation (ensure non-dose weighted micrographs are used)