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)?


Thank you.

Kind regards,

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.


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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,

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? 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!