Particle sets tool logic?


How does the particle sets tool decide which particles to take from which set (A or B), in the event that one set has a different box size or pixel size from the other?

E.g. let’s say I have two sets of particles, A and B. There is 80% overlap between the particles based on the UUID, but set B has been re-extracted with recentering at full scale after heterogeneous refinement, while set A is the originally extracted particles, binned 4x.

For the set corresponding to the intersection, will cryoSPARC take particles from set A, set B, or both, and what controls this choice? It does not say in the log file - maybe this would be worthwhile adding for clarity (or maybe add some way to quickly inspect the particles blob in the output to see the box size & pixel size)?

(I am assuming it will take the particle set with the larger box or the least Fourier cropping, but the exact rules would be good to know for more subtle cases - e.g. let’s say both sets have the same binning and box size but different recentering parameters…?)


Hi @olibclarke,

In intersect mode, Particle Sets Tool will take the all of the result groups (in common from set A and B) from set A in the intersect output. This includes the blob, ctf, alignments, etc. – and in particular particle sets tool won’t determine this logic from the box sizes or Fourier cropping of the inputs. Also note, sets A_minus_B and B_minus_A pull result groups from input sets A and B respectively. We’ll add a note in the event log to document this better.


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Thanks Michael, that is very clear and helpful! Might be worth copying that verbatim into the documentation for the Particle Sets job too! :slight_smile:

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