Picking particles within other particles


I have a list of particles i’ve imported from cryolo. Using a topaz trained model for a smaller particle I want to pick particles only within particles picked by cryolo. Having a hard time figuring out how to do this well in cryosparc, any help appreciated.


Could you import the particle stack as micrographs?

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Would be interested to see if this (@ccgauvin94 's idea) works well!

Pick with topaz, everything. Import the cryolo picks and reextract (so they get cryosparc UID). Remove duplicates with tiny distance with “remove duplicates completely” flag. This will generate an output of those which are in the same place from both particle sets?

This is the strategy i’m trying now, combining the extracted cryolo pick particles and my topaz picked particles and removing duplicates with a minimum distance so the “rejected” particles are those that were close between the two sets.

Problem is I also get all those topaz picked particles that happened to be close to each other, since cryosparc doesn’t know to remove duplicates only between 2 separate lists.

I think i’m just gonna have to use a python script of the two lists of coordinates with the cryolo picks as the reference coordinates.

run remove duplicates on topaz list alone before running again on mixed list.

If you have not already, you may want to check out cryosparc-tools, which facilitate “pythonic” interactions with CryoSPARC workflows.

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