Hi All,
The dip is an artifact of the boundary where phases are randomization and where they are experimental. The same artifact is seen in Relion’s phase randomization for mask correction and extensive discussions about it can be seen in ccpem’s archive. It has been suggested that the ‘dip’ points be removed from the curve to make it look nicer, but I believe it is preferable to leave them in to show that correction has been done. If the corrected FSC is lower than the tight masked FSC then the correction is doing its job: it is showing that some of the correlation in the tight masked FSC is due to masking artifacts. The corrected FSC should always be used to interpret resolution.
I will leave it to @apunjani to comment on the details of the automasking approach that he implemented.
Best regards,
John