Workflows and processing

A workflow is a versioned declaration of steps, parameters, inputs, decision points, and outputs. A run captures the exact workflow revision and values used for that session or analysis workspace.

Typical stages

1. Frame preparation and motion assessment
2. Micrograph and CTF quality assessment
3. Ice and contamination evaluation
4. Particle or feature detection
5. Extraction and classification
6. Refinement, reconstruction, validation, and reporting as configured

Not every deployment enables every stage. Availability depends on licensed integrations, approved extensions, compute resources, and the validation scope of the facility.

Running a workflow

• Select the session or analysis workspace and verify the intended inputs.
• Load an approved workflow revision or a saved project preset.
• Review parameters, resource estimates, external dependencies, and stop conditions.
• Start a bounded run, inspect early outputs, and expand only when results are plausible.
• Preserve failed and excluded items long enough to diagnose selection bias and operational problems.

Automated scores are evidence for review, not a substitute for scientific judgment.