Job: Remove Duplicate Particles


Remove duplicate particle picks in a given input set of particles. This enables picks from various different pickers (e.g. template picker and blob picker) to be combined safely, by passing them through this job. It also can incorporate the alignment shifts, which makes it useful for removing duplicates after 2D classification, and before launching into ab-initio reconstruction or refinement. If pick stats are connected, duplicate particles with lower NCC score will be rejected in favour of higher NCC score particles.


  • Particles
    • location required
    • blob, pick_stats, alignments2D, alignments3D are optional
  • Micrographs (optional)
    • micrograph_blob (optional)


  • Minimum separation distance (A)
    • The desired minimum distance between particle centers (default 20 Å)
  • Micrograph pixel size (A)
    • If micrographs are not input to the job, then the micrograph pixel size in Angstroms must be set here
  • Shift key
    • This is used only if alignments2D or alignments3D are connected, in which case, the particle center coordinates will be determined by applying the additional shift offset (either from alignments2D, or alignments3D according to the shift key)


  • particles_kept: Particles kept after duplicates are removed
  • particles_rejected: Particles identified as duplicates

Example Plots

If micrographs are connected, the job will plot out an example micrograph with the kept and rejected coordinates. Shown below are example plots of duplicate removal on a template-picked dataset, with a high minimum separation distance of 100 Å.
On the left are kept particles; on the right are removed particles (too close to other particles).

Common Next Steps

  • Job: 2D Classification
  • Job: Ab-Initio Reconstruction
  • Job: Homogeneous Refinement (NEW)