[Feature request] 3D Classification quick action: Build Local Refinement (Each Class)

Local Refinement
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I’ve found recently that I often want to do Local Refinements of all (or nearly all) classes after 3D classification (e.g. due to symmetry expansion).

So I’d like to request adding a quick action for Local Refinement, similar to the current quick actions for homogeneous and non-uniform refinement to quickly create all of the Local Refinement jobs. I imagine others would also find this useful.

3 Likes
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Hey @rbs_sci,

We are curious as to the use case for such a workflow, as the implementation of such a feature could be difficult to meet a broad set of user needs/intentions. I have a couple questions for you.

  1. How many classes are in the 3D classification jobs that you would be using this feature for?
  2. Are you working on a dataset where the classes all exhibit a lot of similarity? Does the use of latent mixing coefficients in classification help to reduce down to a few classes with the heterogeneity you are looking for?
  3. What masks would you want used here? The solvent of focus mask from 3D classification? An outside mask?
  4. Would a job with the volume and particles connected be sufficient and you supply the mask?
  5. Would a workflow solve this issue?

Best,
Kye

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To answer point by point…

  1. Varies, but often 24-36.
  2. Varies again; have two cases currently running, one shows a significant amount of heterogeneity which isn’t well classified by heterogeneous refinement but works well with repeated rounds of 3D classification → Local Refinement → Recombination as relevant → 3D classification → Local Refinement, another where at higher resolutions we’ve resolved some unexpected structural heterogeneity after symmetry expansion, 3D classification and Local refinement
  3. So far have used an extremely loose mask and focused masks (on sites of interest)
  4. Yes. Ideally, I want the Local refinement jobs populated with class volume and particles, I’ll attach whatever mask is desired myself.
  5. A very tight/short one might? I’ll do some playing around on this point when I have time, I guess.
1 Like
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Thanks for the suggestion @rbs_sci ! We’ve made a note to add this quick action

As an alternative way of quickly creating jobs with pre-connected inputs, you can use the outputs view on the cards/tree, select relevant groups and use the cart to build downstream jobs. This would work well in the case where you’re selecting different masks.

Regards,
Suhail