Hi @adesfosses,
Thanks for bearing with me. One other thing is coming to mind that may explain the increased amplitude at high resolution. In motion correction, dose weighting is done to upweight earlier frames at high resolution, and to downweight later frames at high resolution. However, at low resolution, frames get a closer to uniform weight. This is described a bit more on our guide pages.
This means that at high resolution compared to low resolution, there will be a larger variance in the noise in the images. This may be the underlying reason why there is a larger amplitude variation at high resolution (the power spectrum you’ve shown growing “whiter” near the periphery of the box)
I was thinking something worth trying could be to average together particle images that have been extracted without dose-weights applied. If you completed motion correction in CryoSPARC, there should be an output result of motion correction called micrograph_blob_non_dw. It might be worth trying to re-extract particles with this result overridden using the low-level results interface (described by Rich here), and then re-run 2D Class and Average Power Spectra.
I’m not entirely sure this would solve the increased amplitude at high resolution issue, but perhaps it is worth trying. If it doesn’t resolve it, my apologies I couldn’t be of more help
Best,
Michael