Electron tomography

Electron tomography (ET) is a tomography technique for obtaining detailed 3D structures of sub-cellular macro-molecular objects. Electron tomography is an extension of traditional transmission electron microscopy and uses a transmission electron microscope to collect the data. In the process, a beam of electrons is passed through the sample at incremental degrees of rotation around the center of the target sample. This information is collected and used to assemble a three-dimensional image of the target. For biological applications, the typical resolution of ET systems[1] are in the 5–20 nm range, suitable for examining supra-molecular multi-protein structures, although not the secondary and tertiary structure of an individual protein or polypeptide.[2][3]

Basic principle of tomography: superposition free tomographic cross sections S1 and S2 compared with the projected image P

BF-TEM and ADF-STEM tomography

In the field of biology, bright-field transmission electron microscopy (BF-TEM) and high-resolution TEM (HRTEM) are the primary imaging methods for tomography tilt series acquisition. However, there are two issues associated with BF-TEM and HRTEM. First, acquiring an interpretable 3-D tomogram requires that the projected image intensities vary monotonically with material thickness. This condition is difficult to guarantee in BF/HRTEM, where image intensities are dominated by phase-contrast with the potential for multiple contrast reversals with thickness, making it difficult to distinguish voids from high-density inclusions.[4] Second, the contrast transfer function of BF-TEM is essentially a high-pass filter – information at low spatial frequencies is significantly suppressed – resulting in an exaggeration of sharp features. However, the technique of annular dark-field scanning transmission electron microscopy (ADF-STEM), which is typically used on material specimens,[5] more effectively suppresses phase and diffraction contrast, providing image intensities that vary with the projected mass-thickness of samples up to micrometres thick for materials with low atomic number. ADF-STEM also acts as a low-pass filter, eliminating the edge-enhancing artifacts common in BF/HRTEM. Thus, provided that the features can be resolved, ADF-STEM tomography can yield a reliable reconstruction of the underlying specimen which is extremely important for its application in material science.[6] For 3D imaging, the resolution is traditionally described by the Crowther criterion. In 2010, a 3D resolution of 0.5±0.1×0.5±0.1×0.7±0.2 nm was achieved with a single-axis ADF-STEM tomography.[7] Recently, atomic resolution in 3D electron tomography reconstructions has been demonstrated.[8][9] ADF-STEM tomography has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.[10][11][12][13]

Different tilting methods

The most popular tilting methods are the single-axis and the dual-axis tilting methods. The geometry of most specimen holders and electron microscopes normally precludes tilting the specimen through a full 180° range, which can lead to artifacts in the 3D reconstruction of the target.[14] By using dual-axis tilting, the reconstruction artifacts are reduced by a factor of compared to single-axis tilting. However, twice as many images need to be taken. Another method of obtaining a tilt-series is the so-called conical tomography method, in which the sample is tilted, and then rotated a complete turn.[15]

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gollark: > Why should states remain in the nation if they aren't having an equally powerful voice? For example, why should Iowa stick around if they're just subservient to California's whims?Don't different states have different amounts of electors?
gollark: The electoral college appears to do something you could approximately describe as that but which is weirdly skewed in some ways.
gollark: If you want representation to be based on rural-ness or not and not, well, actual vote count, it should be structured more sensibly.
gollark: He's on here, although might not read this channel much.

See also

References
  1. R. A. Crowther; D. J. DeRosier; A. Klug (1970). "The Reconstruction of a Three-Dimensional Structure from Projections and its Application to Electron Microscopy". Proc. R. Soc. Lond. A. 317 (1530): 319–340. Bibcode:1970RSPSA.317..319C. doi:10.1098/rspa.1970.0119.
  2. Frank, Joachim (2006). Electron Tomography. doi:10.1007/978-0-387-69008-7. ISBN 978-0-387-31234-7.
  3. Mastronarde, D. N. (1997). "Dual-Axis Tomography: An Approach with Alignment Methods That Preserve Resolution". Journal of Structural Biology. 120 (3): 343–352. doi:10.1006/jsbi.1997.3919. PMID 9441937.
  4. Bals, S.; Kisielowski, C. F.; Croitoru, M.; Tendeloo, G. V. (2005). "Annular Dark Field Tomography in TEM". Microscopy and Microanalysis. 11. doi:10.1017/S143192760550117X.
  5. B.D.A. Levin; et al. (2016). "Nanomaterial datasets to advance tomography in scanning transmission electron microscopy". Scientific Data. 3 (160041): 160041. arXiv:1606.02938. Bibcode:2016NatSD...360041L. doi:10.1038/sdata.2016.41. PMC 4896123. PMID 27272459.
  6. Midgley, P. A.; Weyland, M. (2003). "3D electron microscopy in the physical sciences: The development of Z-contrast and EFTEM tomography". Ultramicroscopy. 96 (3–4): 413–431. doi:10.1016/S0304-3991(03)00105-0. PMID 12871805.
  7. Xin, H. L.; Ercius, P.; Hughes, K. J.; Engstrom, J. R.; Muller, D. A. (2010). "Three-dimensional imaging of pore structures inside low-κ dielectrics". Applied Physics Letters. 96 (22): 223108. Bibcode:2010ApPhL..96v3108X. doi:10.1063/1.3442496.
  8. Y. Yang; et al. (2017). "Deciphering chemical order/disorder and material properties at the single-atom level". Nature. 542 (7639): 75–79. arXiv:1607.02051. Bibcode:2017Natur.542...75Y. doi:10.1038/nature21042. PMID 28150758.
  9. Scott, M. C.; Chen, C. C.; Mecklenburg, M.; Zhu, C.; Xu, R.; Ercius, P.; Dahmen, U.; Regan, B. C.; Miao, J. (2012). "Electron tomography at 2.4-ångström resolution" (PDF). Nature. 483 (7390): 444–7. Bibcode:2012Natur.483..444S. doi:10.1038/nature10934. PMID 22437612.
  10. Chen, C. C.; Zhu, C.; White, E. R.; Chiu, C. Y.; Scott, M. C.; Regan, B. C.; Marks, L. D.; Huang, Y.; Miao, J. (2013). "Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution". Nature. 496 (7443): 74–77. Bibcode:2013Natur.496...74C. doi:10.1038/nature12009. PMID 23535594.
  11. Midgley, P. A.; Dunin-Borkowski, R. E. (2009). "Electron tomography and holography in materials science". Nature Materials. 8 (4): 271–280. Bibcode:2009NatMa...8..271M. doi:10.1038/nmat2406. PMID 19308086.
  12. Ercius, P.; Weyland, M.; Muller, D. A.; Gignac, L. M. (2006). "Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography". Applied Physics Letters. 88 (24): 243116. Bibcode:2006ApPhL..88x3116E. doi:10.1063/1.2213185.
  13. Li, H.; Xin, H. L.; Muller, D. A.; Estroff, L. A. (2009). "Visualizing the 3D Internal Structure of Calcite Single Crystals Grown in Agarose Hydrogels". Science. 326 (5957): 1244–1247. Bibcode:2009Sci...326.1244L. doi:10.1126/science.1178583. PMID 19965470.
  14. B.D.A. Levin; et al. (2016). "Nanomaterial datasets to advance tomography in scanning transmission electron microscopy". Scientific Data. 3 (160041): 160041. arXiv:1606.02938. Bibcode:2016NatSD...360041L. doi:10.1038/sdata.2016.41. PMC 4896123. PMID 27272459.
  15. Zampighi, G. A.; Fain, N; Zampighi, L. M.; Cantele, F; Lanzavecchia, S; Wright, E. M. (2008). "Conical electron tomography of a chemical synapse: Polyhedral cages dock vesicles to the active zone". Journal of Neuroscience. 28 (16): 4151–60. doi:10.1523/JNEUROSCI.4639-07.2008. PMC 3844767. PMID 18417694.
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