Job: Local Motion Correction

Local motion correction.

Due to beam-induced motion (see Patch Motion Correction), it can sometimes be beneficial to perform motion correction on each particle individually. However, it is only possible to do so once particle pick locations are available. The local motion correction job performs this per particle motion correction, taking full-frame-motion corrected movies and particle pick locations as inputs. A typical workflow would be to first use patch motion correction on the raw movies, perform picking, and then re-perform motion correction with full-frame and local motion correction.


Estimate and correct for anisotropic local beam-induced motion (per-particle) from movie data and a pre-estimated full-frame motion trajectory. Two versions are available - Local Motion Correction runs on a single GPU, while Local Motion Correction (Multi-GPU) uses multiple available GPUs to parallelize processing.

As of CryoSPARC v4.0, Local motion correction supports downsampling particles (via Fourier cropping) on the fly while performing motion correction. To use this, set the Fourier crop to box size (pix) parameter.


  • Raw movies

  • Rigid motion trajectory estimates

  • Particle locations

Common Parameters

  • Only process this many movies: Selects the first n movies to process, instead of processing the entire set. Helpful when working with a set of movies for the first time, to better understand the data quality.

  • Low-memory mode: When working with very large movies on GPUs with low memory (less than, say, 16 GB), it is possible to run out of GPU memory. If this happens, turning on low-memory mode will usually allow the processing to proceed. This option makes processing slightly slower, so it is turned off by default.

  • Extraction box size: This box size should be at least twice the particle width

  • Fourier crop to box size (pix): When set, the job will downsample the output particles to this box size, using Fourier cropping.

  • Override e/A^2/frame: Optional: When Apply exposure weighting is enabled, this parameter can be used to override the exposure level of the movie data, in case the level was not correctly set at import time. In contrast to the Import Movies job's Total exposure dose (e/A^2) parameter, Local Motion Correction's parameter must be specified per-frame. Local Motion Correction's exposure weighting method is based on the reference rotaviral protein 6 (Grant & Grigorieff, 2015).

  • Save results in 16-bit floating point: Saves the output micrographs in float16 format (CryoSPARC v4.4+).


  • Local motion-corrected particles

  • Local motion trajectories

Common Next Steps

  • 2D Classification

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