title: Robust image alignment for cryogenic transmission electron microscopy.
abstract: Cryo-electron microscopy recently experienced great improvements in structure resolution due to direct electron detectors with improved contrast and fast read-out leading to single electron counting. High frames rates enabled dose fractionation, where a long exposure is broken into a movie, permitting specimen drift to be registered and corrected. The typical approach for image registration, with high shot noise and low contrast, is multi-reference (MR) cross-correlation. Here we present the software package Zorro, which provides robust drift correction for dose fractionation by use of an intensity-normalized cross-correlation and logistic noise model to weight each cross-correlation in the MR model and filter each cross-correlation optimally. Frames are reliably registered by Zorro with low dose and defocus. Methods to evaluate performance are presented, by use of independently-evaluated even- and odd-frame stacks by trajectory comparison and Fourier ring correlation. Alignment of tiled sub-frames is also introduced, and demonstrated on an example dataset. Zorro source code is available at github.com/CINA/zorro.
authors.affiliation: Center for Cellular Imaging and NanoAnalytics, Biozentrum, Universität Basel, Basel, Switzerland. Electronic address: robbmcleod@gmail.com.
authors.forename: Robert A
authors.initials: RA
authors.lastname: McLeod
authors.affiliation: Center for Cellular Imaging and NanoAnalytics, Biozentrum, Universität Basel, Basel, Switzerland.
authors.forename: Julia
authors.initials: J
authors.lastname: Kowal
authors.affiliation: Center for Cellular Imaging and NanoAnalytics, Biozentrum, Universität Basel, Basel, Switzerland.
authors.forename: Philippe
authors.initials: P
authors.lastname: Ringler
authors.affiliation: Center for Cellular Imaging and NanoAnalytics, Biozentrum, Universität Basel, Basel, Switzerland.
authors.forename: Henning
authors.initials: H
authors.lastname: Stahlberg
mesh_terms: D020285:Cryoelectron Microscopy / Q000379:methods*; D046529:Microscopy, Electron, Transmission / Q000379:methods*; D008962:Models, Theoretical; D012984:Software
keywords: Cross correlation; Cryogenic transmission electron microscopy; Direct detection device; Dose fractionation; Image alignment; Image registration