https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2021Himes_Simulation 2026-05-24T20:15:39Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2021Himes_Simulation&diff=4564&oldid=prev 2024-07-16T06:53:44Z

<p>Created page with &quot;== Citation == Himes, Benjamin / Grigorieff, Nikolaus. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. 2021. IUCrJ, Vol. 8, No. 6, p. 943-953 == Abstract == Image simulation plays a central role in the development and practice of highresolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in expe...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Himes, Benjamin / Grigorieff, Nikolaus. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. 2021. IUCrJ, Vol. 8, No. 6, p. 943-953<br /> <br /> == Abstract ==<br /> <br /> Image simulation plays a central role in the development and practice of highresolution<br /> electron microscopy, including transmission electron microscopy of<br /> frozen-hydrated specimens (cryo-EM). Simulating images with contrast that<br /> matches the contrast observed in experimental images remains challenging,<br /> especially for amorphous samples. Current state-of-the-art simulators apply post<br /> hoc scaling to approximate empirical solvent contrast, attenuated image<br /> intensity due to specimen thickness and amplitude contrast. This practice fails<br /> for images that require spatially variable scaling, e.g. simulations of a crowded or<br /> cellular environment. Modeling both the signal and the noise accurately is<br /> necessary to simulate images of biological specimens with contrast that is correct<br /> on an absolute scale. The ‘frozen plasmon’ method is introduced to explicitly<br /> model spatially variable inelastic scattering processes in cryo-EM specimens.<br /> This approach produces amplitude contrast that depends on the atomic<br /> composition of the specimen, reproduces the total inelastic mean free path as<br /> observed experimentally and allows for the incorporation of radiation damage<br /> in the simulation. These improvements are quantified using the matched filter<br /> concept to compare simulation and experiment. The frozen plasmon method, in<br /> combination with a new mathematical formulation for accurately sampling the<br /> tabulated atomic scattering potentials onto a Cartesian grid, is implemented in<br /> the open-source software package cisTEM.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://journals.iucr.org/m/issues/2021/06/00/rq5007/rq5007.pdf<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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