How can i see imported particles circled on the micrographs?

I imported aligned images.
I imported particles successfully (associated with imported images).
how can I verify the particles are in the correct location visually?

when I curate micrographs and load particles it shows # of particles… but it doesnt circle them.

when I try to inspect particles and load micrographs and particles I get error: not all slots are connected: “missing_inputs” please connect all required inputs. … not connectedd: particles.pick_stats.

If you run an extract micrographs job you should be able to view them with inspect picks I think

but I agree it would be much better if it proceeded without the picking stats for cases like this


hey Oli, thanks.

unfortunately though can’t view after the extract. My pipeline was to import mics, CTF, import particles, extract, then to verify the extraction went as expected. However as far as I can tell there is no way to verify the particle locations that you’ve imported. Flying blind here!

what happens after extraction? if you put the micrographs and particles from the extract job into an inspect picks job (or a manual pick job), does it give the same error?


yes exactly that’s where I ran into the error. I guess it’s looking for those autopicker scores (power score etc) but obviously won’t find it.

Kindof in a dilemma because I’m importing particles from a star file but if I run a 2D it is clear that something is wrong. The star file has gone from cryosparc --> relion --> back to cryosparc (using a stripped down star file with just X/Y coordinates when re-importing).

However, learning in the other thread that particles aren’t recentered. So those X/Y coordinates could be substantially off.

Also tried reversing the X/Y swap that I had to do in csparc2star. Clearly something went wrong in this process. agh.

did you try viewing in manual picker as well as inspect picks? maybe manual picker doesn’t require the pick stats?

thanks, that was a good idea. it worked. Weird I didn’t think of that…

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