TOPAZ FoM equivalent in Cryosparc?

Particle Picking
1

Hi All,

Is there an equivalent of Relion’s FOM (Figure of Merit) when doing particle extraction with TOPAZ ? I found that “NCC score and Power score” are not easy do understand and not very useful for filtering good from bad particles…

With many thanks,

Gianluca

2

Hi @giax,

RELIONs FoM score is based on the difference image between each particle and its aligned template. Since Topaz doesnt use any templates for particle picking, the RELION FoM value for particles picked with Topaz should just be the particle probability value determined by Topaz.

In CS, there are currently two ways to interact with that value. The first being Topaz Extract has a parameter called “Particle Threshold” (default 0) and this can be used (similarly to Figure 4 of their paper) to threshold the particles at time of picking. During particle picking in CS, the predicted probability scores are normalized, scaled, and placed in the NCC and Power score slots.

Best,
Kye

3

Hi

and thank you.

this is the point. I find that in Relion, by playing with the FOM during extraction after topaz picking, is more easy to separate good particles from bad ones. In cryosparc is more complicated becaue you have 2 indicators (NCC and Power), not saying that is bad, but it’s less straightforward of just having one. I will try what you suggest, the Particle Threshold.

Thanks!

GIA

4

Hi @giax,

The particle probability score that we normalize, scale, and place into the power and NCC score slot is the same value for both score slots; this results in the diagonal line in inspect particle picks. These values are essentially the same as the normalization and scaling does not change ranking of the particles among their cohort.

Best,

Kye

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