[3dem] Autopicking

[Bullitt, Esther]

Hello,

I have a few questions about Autopicking in Relion.

I would like to have a more reasoned approach for choosing --min_avg_noise and --max_avg_noise.
is there a calculation somewhere of these values for either single or groups of micrographs?
more fundamentally, can I see a histogram of intensities of my images?
Any other details on find parameters for autopicking to pick filaments rather than background (which it is doing exclusively on my new dataset; see attached) would be appreciated -- and yes, the regions below the green circles are background; not a single filament segment picked.

In Relion 3.1.1, I could see the results of autopicking with the command (e.g.):

`which relion_manualpick` --i Select/job011/micrographs_split1.star --odir AutoPick/job002/ --pickname autpic --allow_save  --selection Select/job003/micrographs_selected.star --scale 0.2 --sigma_contrast 3 --black 0 --white 0 --lowpass 20 --ctf_scale 1 --particle_diameter 100

but I cannot find anything equivalent in Relion 4.0. Is it somewhere else?

thanks very much.

Sincerely,
Esther[X]

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