RELION

RELION is the open-source cryo-EM processing package from the MRC LMB, built on an empirical Bayesian approach to refinement and classification. It defined how the field processes data and, being fully open, it remains the reference against which other implementations are judged.

What it does

It covers the full single-particle workflow plus sub-tomogram averaging, with 3D classification, multi-body refinement for flexible assemblies, Bayesian polishing and CTF refinement. Because the statistical model is published and the code is open, choices in the pipeline can be inspected rather than trusted — which matters when a structure is contested.

Strengths

• Free and fully open source, with published methodology.
• The reference implementation for regularised likelihood refinement.
• Multi-body refinement for genuinely flexible complexes.
• Sub-tomogram averaging for cryo-electron tomography.
• Scriptable and cluster-friendly for large projects.

Limitations

The learning curve is steep and the interface is unapologetically utilitarian next to CryoSPARC’s. Processing is slow and compute-hungry, and getting good results depends on understanding what each parameter does. Most labs now run both — CryoSPARC for speed, RELION for refinement and for anything that must be independently defensible.