Noise models and cryo-EM drift correction with a direct-electron camera

Ultramicroscopy. 2013 Aug;131:61-9. doi: 10.1016/j.ultramic.2013.04.001. Epub 2013 Apr 18.


Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of "hot-pixel noise". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.

Keywords: CMOS; Complementary metal-oxide-semiconductor; Cross-correlation function; Cryo-EM; Electron cryomicroscopy; Transmission electron microscopy.

Publication types

  • Research Support, N.I.H., Extramural