Job: Regroup 3D
Regroup 3D classes via spectral clustering
Description
Regroup 3D is new job in CryoSPARC v4.4+ that regroups particles from an upstream classification job into a smaller set of ‘superclasses’ using a light-weight 3D-voxel-based spectral clustering approach.
Input
Particles (
particles_all_classes
from 3D Classification or Heterogeneous Refinement)Volume series (from 3D Classification or Heterogeneous Refinement)
[Optional] Mask
Common Parameters
Class alignment3D prefix
By default, this parameter is set such that class assignments are expected to come from 3D classification. If using this job with an upstream heterogeneous refinement, this should be changed to the non-default value of
alignments_class_
.
Minimum class size (particles)
Only classes with this many particles will be regrouped. This parameter may be useful when there are (near-)empty classes with poorly resolved volumes.
Output
Regrouped particles
Note that all particle assignments are recomputed by maximizing over the class posteriors in the upstream dataset. Upstream posterior probabilities are ignored except as a proxy for class assignment. Regrouped particles are given ‘hard’ (one-hot) class posteriors based on the new set of superclasses.
Per-superclass particles
Superclass average volumes
These volumes are the real-space average of class volumes that belong to each superclass. To recover back-projected volumes from super-class particle assignments, use the Heterogeneous Reconstruction Only job with the
regrouped_particles
output group.
Superclass volume series
[If supplied] Mask
Remaining particles
Common Next Steps
Heterogeneous Reconstruction Only
Further 3D classification
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