Job: MotionCor2 (Wrapper)


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)