Interactive Job: Manual Picker

Manual picking.

The information in this section applies to CryoSPARC ≤v3.3. For CryoSPARC v4.0+, please see:Interactive Jobs


  • Manually pick particles interactively from micrographs.


  • Aligned/motion-corrected micrographs

Common Parameters

  • Once the job is running, you can input and adjust the Box size in the job inspector/stream log. We recommend a box size that is at least double the diameter of the particle.

  • You can also adjust the Contrast Intensity Override slider to manually select the contrast bounds when viewing a micrograph.


  • Particles

Notes and Limitations

When manually picking particles with the goal of creating a template for auto-picking, we recommend picking particles from multiple micrographs with a range of defocus and CTF fit values to ensure a comprehensive template.

Manual picking is the most time consuming picking method. As such, this job is recommended for picking a small subset of micrographs for the purposes of providing initial picks to template picking and/or deep picking instead of picking entire datasets.

Common Next Steps

  • 2D Classification and Select 2D to generate templates for Template picking

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