CryoSPARC Guide
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CryoSPARC Tools

cryosparc-tools is an open-source Python library that enables powerful scripting access to CryoSPARC and is available for CryoSPARC v4.1+.
Use cases:
  • Programmatically read and write exposure, particle and volume data
  • Easily perform advanced operations on metadata (alignments, CTF, etc) and programmatically insert modified data back into CryoSPARC
  • Access project, workspace and job data
  • Build and run jobs to orchestrate custom cryo-EM workflows
  • Extend CryoSPARC functionality with third-party software packages
  • cryosparc-tools is on GitHub and available via pip and can be used outside of the CryoSPARC environment in your own programs and tools
The full documentation for cryosparc-tools is hosted at
cryosparc-tools source code is hosted on Github.
If you are using CryoSPARC v4.0 or older, please see: