Related Experiment Video
Updated: May 15, 2026

Workflow Using a Cryogenic Coincident Fluorescence, Electron, and Ion Beam Microscope for Targeted Milling of Cells
Published on: October 17, 2025
Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images
Fatemeh Karimi Nejadasl1, Manikandan Karuppasamy, Emily R Newman
1Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300RC Leiden, The Netherlands.
Abstract:
The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.
