Alignment of cryo-EM movies of individual particles by optimization of image translations

TL;DR

This paper introduces a novel algorithm for aligning cryo-EM movies of individual particles by optimizing image translations, improving 3D map quality without relying on frame averaging or linear trajectory assumptions.

Contribution

The authors present a new method for aligning individual <1 MDa particle images in cryo-EM movies that avoids frame averaging and linear trajectory fitting, enhancing motion correction accuracy.

Findings

Improved alignment of cryo-EM particle images.

Enhanced quality of 3D reconstructions.

Effective correction of local beam-induced motion.

Abstract

Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the specimen, due both to instabilities in the microscope specimen stage and electron beam-induced movement. Unlike specimen stage drift, beam-induced movement is not always homogeneous within an image. Local correlation in the trajectories of nearby particles suggests that beam-induced motion is due to deformation of the ice layer. Algorithms have already been described that can correct movement for large regions of frames and for > 1 MDa protein particles. Another algorithm allows individual < 1 MDa protein particle trajectories to be estimated, but requires rolling averages to be calculated from frames and fits linear trajectories for particles. Here we describe an algorithm that allows for individual < 1 MDa particle images to be aligned without frame averaging or linear trajectories. The algorithm maximizes the overall correlation of the shifted frames with the sum of the shifted frames. The optimum in this single objective function is found efficiently by making use of analytically calculated derivatives of the function. To smooth estimates of particle trajectories, rapid changes in particle positions between frames are penalized in the objective function and weighted averaging of nearby trajectories ensures local correlation in trajectories. This individual particle motion correction, in combination with weighting of Fourier components to account for increasing radiation damage in later frames, can be used to improve 3-D maps from single particle cryo-EM.