Outlier pixel removal during gain correction?


We have been finding that on one of our scopes with K3 detector, gain references generated by leginon leave white spots after gain correction, when gain correction is carried out in cryosparc (but not in relion). These white spots affect motion correction, and lead to “ringing” in 2D classes.

Suspecting that maybe relion was performing some sort of normalization or outlier removal prior to gain correction, I manually removed outliers from the gain using the ‘remove_outlier_pixels’ utility of cistem. This fixes the issue during patch motion (see below for comparison).

Would it be possible to incorporate an outlier removal step during gain correction, to fix this kind of issue automatically?