Advice for Classification

Tips
1

Hi,

I would like to know a couple of things about classification in cryosparc:

  1. Since 2D classification is not available, how do you clean your datasets for contaminations? Do you plan to implement 2D classification in cryosparc?

  2. After refinement in cryosparc, if I select the particles from the refinement output, will the alignment parameters be used to perform a follow-up classification?

Thank you very much,
Clara

2

Hi Clara,

There are plans to include 2D classification in the next version of cryoSPARC. In the meantime our group tends to do 2D classification in Relion prior to importing particles to cryoSPARC. However, sometimes 2D classification isn’t necessary and we can go straight to 3D classification.

@apunjani is there a convenient way to do classification following refinement but disallow orientation searching during classification (keep orientations from the refinement)?

Best wishes,
John

3

Thanks John. Indeed we are currently working on 2D classification in cryoSPARC.

Currently there is not a way to classify only (and not re-align particles). When you select particles from a refinement output, only the identity of those particles is used, not their alignments, in further experiments. This is something we are building as we move to support local/masked refinement.

Ali

4

Thanks a lot for your answers!

I am glad to know that both will be available in the future.

Best
Clara

5