Extract particles from denoised micrographs

Application
1

Hi cryoSPARC Team and users,

I want to extract particles from the denoised micrographs, not the motion corrected. I am fully aware, that this must not be done for processing and 3D reconstruction.

But I would like to visually inspect my particles for illustrative purposes, rather than continue in processing.

Unfortunatelly, the Extract from Micrograph jobs does not allow me to select “From denoised” (most likely for the abovementioned risk of accidentially using them in refinement). So is there a way (right now), to extract from the denoised? Either via the GUI or the cryosparc-tools?

Thanks

Best
Christian

2

You can do this using the low level inputs (replacing the mic slot with the denoised one). Just remember that the denoised mics are F-cropped, so you will need to adjust box size accordingly

3

Thanks. I tried after a denoiser, but I missed the fact, that I can exchange the micrograph blob with the denoised blob.