Job: Extract from Micrographs


  • Extract picked particles from micrographs using a specified box size.


  • Aligned/motion-corrected micrographs
  • Particle locations

Common Parameters

  • Extraction box size: This controls the size of the extraction box, in pixels
  • You can set the Number of GPUs parameter to 0 to run the job exclusively on the CPU
  • Recenter using aligned shifts
    • Activated by default, this will cause the extracted picks to be re-centered if the 2D or 3D shifts are present from previous 2D classification or 3D reconstruction/refinement jobs
    • Re-centering will update both the location results (to store the new extraction centres) and alignments2D or alignments3D results (to store the residual <1 pixel shift after updating the locations)


  • Particles

Notes and Limitations

  • Do not extract particles from micrographs if you plan to run Local Motion Correction, as this latter job type will perform extraction.
  • Particles too close to the edges of a micrograph will not be included in the particles output from this job. See the job stream log for more information on how many particles were not included.