Topaz extract equivalent of separation radius?

[marinegor]

Hi everyone, I was using Topaz integration with CryoSPARC and just noticed that the particles after Topaz extract overlap a lot. Is there a way to control somehow? I was looking for something like "overlap radius" in CryoSPARC's "Template picker", but couldn't find any. Any suggestions?

[tbepler]

I think the "radius" parameter of "topaz extract" is what you're looking for.

[marinegor]

In my hands (=using CryoSPARC's 3.2 interface) it does not influence the number of extracted particles. Using following line:

Starting extraction by running command /opt/conda3/envs/topaz/bin/topaz extract --radius 7 --threshold -6 --up-scale 4 --assignment-radius -1 --min-radius 300 --max-radius 400 --step-radius 5 --num-workers 8 --device 2 --model /data/cryosparc_projects/P3/J619/models/model_epoch030.sav -o /data/cryosparc_projects/P3/J707/topaz_particles_prediction.txt

When I set --min-radius 5 --max-radius 100, I get the same number of particles as with (300, 400) pair, which probably shouldn't be the case🤔

[tbepler]

The min and max radius parameters don't do anything in the cryoSPARC command. They exist for cross validating the radius parameter. The parameter you want to adjust is just --radius.

[marinegor]

Ok, indeed. Thanks a lot!

[olibclarke]

This parameter controls the overlap. If you set radius to 5 (for example) when running topaz extract, then the extracted particles centers cannot be closer than 5 pixels.

Just to double check this - the radius, not 2x the radius, is the minimum distance between particle centers?

[tbepler]

That's correct.