Grid bar cleaning strategy

Dear colleagues,

Is there an effective strategy for cleaning the particles that were picked on the grid bar (in addition to inspecting/curation/2D classification/manual)?

image

Thank you.

Kind regards,
Dmitry

Hi Dmitry,

You should be able to remove most of these using the “Inspect Particle Picks” job. Setting a lower threshold for the power score removes picks with high pixel intensities, such as on the foil or on ice contamination. You can find more information on this tutorial page.

Cheers,
cbeck

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Dear @cbeck,

Many thanks for your answer.

I tried this option before, too, but it remains suboptimal in my case—changing the threshold or moving another toolbar removes quite a few potentially good particles.
Of course, this is all about balance and me being too demanding to result sometimes :slight_smile:

Kind regards,
Dmitry

I find this a pretty fair request. We’ve been shooting Lacey grids, and always getting a lot of particles on carbon. There are ways to remove them using curate exposures and inspect picks, but they are not 100% selective. Maybe Cryosparc could give the option to eliminate picks on darker background?

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An intensity (or maybe segment-anything? https://segment-anything.com) histogram based mask would be useful for picking, to avoid contaminants, carbon & gold. Also might be useful for helping patch based algorithms for motion correction & CTF estimation to avoid these regions, which can cause trouble.

EDIT: just for fun - segment anything does pretty well at masking contaminants!