Input for Topaz


In Topaz train there is an tes/no option of “use denoised micrographs” which say: Use denoised micrographs in job if denoised beforehand.
So may question is do the input mic should be the denoised micrographs or the micrographs and CS will “know” to use the denoised?

Hi Elad,

This is a great question and I’m not sure what the answer is. I think @jyoo wrote this part of CryoSPARC and hopefully can answer.


Hi @Elad, yes cryoSPARC does know to use the denoised micrographs when the specified input group contains output from a denoise job (in the form of a micrograph_blob_denoised output - see screenshot below) and you have that switch enabled. Otherwise it defaults to the non-denoised micrographs.

Topaz Train job with micrograph_blob_denoised as input

Hope that helps!