Job: Extract from Micrographs
Extract picked particles.

Description

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

Input

  • 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)

Output

  • 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.
Copy link
On this page
Description
Input
Common Parameters
Output
Notes and Limitations