Job: Full-Frame Motion Correction

At a Glance

Perform rigid motion correction of movies.

Description

Full-frame motion correction models and corrects movement of each full frame of the movie. It therefore cannot correct anisotropic movement, such as movement due to ice doming during movie collection. Full-frame motion correction also applies Dose Weighting.

See Motion Correction for more details about the different types of motion correction available in CryoSPARC.

Inputs

Movies

Full-Frame Motion Correction requires raw movies in .mrc , .tif , .eer, or .mrc.bz2 format, typically from an Import Movies job.

Commonly Adjusted Parameters

Only process this many movies

This parameter selects the first n movies to process, rather than the entire input stack. It is most useful when working with a subset of movies to assess data quality before committing to a full processing pipeline.

If collection parameters changed during the collection, it may be better to use an Exposure Sets Tool job to select a random subset instead.

Low GPU memory

Reading movie files from disk is slow. To speed up processing, motion correction jobs process one movie and load the next simultaneously. However, this can lead to GPUs with low memory (i.e., < 16 GB VRAM) to run out of memory. Turning this option on causes the job to wait to load the next movie until it has finished processing the current movie. This slows down the job, but can prevent out-of-memory errors.

Save results in 16-bit floating point

Saves the output micrographs in 16-bit floating point. We recommend that this option is turned on to save space at minimal loss of accuracy. See the 16-bit floating point article for more information.

Start frame and End frame

These parameters allow discarding frames from the start and end of the input movies, before motion correction is applied. This can be helpful in case there are artefacts or issues with early or late frames. For example, some cameras can have issues where they output one or more blank frames at the end of a movie, and these can disturb motion estimation.

Outputs

Micrographs

Aligned micrographs for further downstream preprocessing. These micrographs also have rigid motion estimates, which are required for jobs like Reference-Based Motion Correction and Local Motion Correction.

Micrographs incomplete

If alignment of any micrographs failed, the failed micrographs are collected in this output. If the micrographs failed because the GPU ran out of memory during processing, re-processing these movies after freeing some GPU memory may successfully resolve the issue. Otherwise, these movies may be corrupted.

Common Next Steps

Typically, micrographs have their CTF estimated by Patch CTF Estimation before any further processing occurs.

Recommended Alternatives

In almost all cases, Patch Motion Correction will outperform Full-Frame Motion Correction. Patch Motion Correction accounts for both rigid motion (as with Full-Frame) and the local, anisotropic motion which occurs in all cryoEM movies. We recommend that users prefer Patch Motion Correction unless they have very low SNR movies or very sparse particle distribution.