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RNA Therapeutics Institute

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Biochemistry, Biophysics, and Structural Biology


Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The 'frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.


cryo-TEM, multislice wave propagation, cisTEM, frozen plasmon method

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Copyright © Himes and Grigorieff 2021. This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

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Himes B, Grigorieff N. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. IUCrJ. 2021 Sep 30;8(Pt 6):943-953. doi: 10.1107/S2052252521008538. PMID: 34804546; PMCID: PMC8562658. Link to article on publisher's site

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Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.