CryoSPARC Guide
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Job: Restack Particles

Restack particles to manage your particle files and speed up caching
Input particles can be distributed across many .mrc files, and often only a subset of each file is being used for downstream operations. Restack will consolidate the particles from many files into a smaller number of files that don’t include unused particles, therefore taking up less disk space.


Re-write input particles to new consolidated output particle files. Restack Particles is useful for filtering unused particles from.mrc files, can speed up caching, and helps with data management. Restacking will not change results of downstream processing.
During particle data processing, particles are distributed across many particle .mrc files (typically one file per micrograph from extraction) and usually only a subset of all extracted particles will be used downstream. Restack Particles will read, consolidate and write out particle data into new files - allowing the original particle files, which also include unused particles, to be removed. This process also usually results in particles being aggregated into a smaller number of larger files, speeding up filesystem operations including caching performance.


  • Particles

Common parameters

  • Particle batch size: number of particles that will be written per output file
  • Save results in 16-bit floating point: Saves the output particles in float16 format (CryoSPARC v4.4+).


  • Restacked particles

Common Next Steps

  • Running 2D Classification, 3D Classification, 3D Variability Analysis or Heterogeneous Refinement on restacked particles
  • Clearing the particle extraction job(s) that produced the input particles to save storage space