Electron tomography

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

Electron tomography (ET) is a tomography technique for obtaining detailed 3D structures[1] of sub-cellular, macro-molecular, or materials specimens. 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[2] 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.[3][4] Recently, atomic resolution in 3D electron tomography reconstructions has been demonstrated.[5][6]

BF-TEM and ADF-STEM tomography[edit]

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.[7] 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,[8] 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 materials science.[9] 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.[10]

Atomic Electron Tomography (AET)[edit]

Schematic showing the concept of electron tomography.

Atomic level resolution in 3D electron tomography reconstructions has been demonstrated. Reconstructions of crystal defects such as stacking faults, grain boundaries, dislocations, and twinning in structures have been achieved.[11] This method is relevant to the physical sciences, where cryo-EM techniques cannot always be used to locate the coordinates of individual atoms in disordered materials. AET reconstructions are achieved using the combination of an ADF-STEM tomographic tilt series and iterative algorithms for reconstruction. Currently, algorithms such as the real-space algebraic reconstruction technique (ART) and the fast Fourier transform equal slope tomography (EST) are used to address issues such as image noise, sample drift, and limited data.[12] ADF-STEM tomography has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.[13][14][15][16] AET has also been used to find the 3D coordinates of 3,769 atoms in a tungsten needle with 19 pm precision[17] and 20,000 atoms in a multiply twinned palladium nanoparticle.[18] The combination of AET with electron energy loss spectroscopy (EELS) allows for investigation of electronic states in addition to 3D reconstruction.[19] Challenges to atomic level resolution from electron tomography include the need for better reconstruction algorithms and increased precision of tilt angle required to image defects in non-crystalline samples.

Different tilting methods[edit]

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.[20] Standard single-tilt sample holders have a limited rotation of ±80°, leading to a missing wedge in the reconstruction. A solution is to use needle shaped-samples to allow for full rotation. 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.[21]

See also[edit]

References[edit]

  1. ^ R. Hovden; D. A. Muller (2020). "Electron tomography for functional nanomaterials". MRS Bulletin. 45 (4): 298–304. arXiv:2006.01652. Bibcode:2020MRSBu..45..298H. doi:10.1557/mrs.2020.87. S2CID 216522865.
  2. ^ 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. S2CID 122980366.
  3. ^ Frank, Joachim (2006). Frank, Joachim (ed.). Electron Tomography. doi:10.1007/978-0-387-69008-7. ISBN 978-0-387-31234-7. S2CID 241282825.
  4. ^ 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.
  5. ^ 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. S2CID 4464276.
  6. ^ 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. S2CID 1600103.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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.
  11. ^ Miao, J.; Ercius, P.; Billinge, S. J. L. (23 September 2016). "Atomic electron tomography: 3D structures without crystals". Science. 353 (6306): aaf2157. doi:10.1126/science.aaf2157. PMID 27708010. S2CID 30174421.
  12. ^ Saghi, Zineb; Midgley, Paul A. (2012). "Electron Tomography in the (S)TEM: From Nanoscale Morphological Analysis to 3D Atomic Imaging". Annual Review of Materials Research. 42: 59–79. doi:10.1146/annurev-matsci-070511-155019. Retrieved 13 December 2022.
  13. ^ 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. S2CID 4410909.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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. S2CID 40526826.
  17. ^ Xu, Rui; Chen, Chien-Chun; Wu, Li; Scott, M. C.; Theis, W.; Ophus, Colin; Bartels, Matthias; Yang, Yongsoo; Ramezani-Dakhel, Hadi; Sawaya, Michael R.; Heinz, Hendrik; Marks, Laurence D.; Ercius, Peter; Miao, Jianwei (November 2015). "Three-dimensional coordinates of individual atoms in materials revealed by electron tomography". Nature Materials. 14 (11): 1099–1103. arXiv:1505.05938. doi:10.1038/nmat4426. PMID 26390325. S2CID 5455024.
  18. ^ Pelz, Philipp M.; Groschner, Catherine; Bruefach, Alexandra; Satariano, Adam; Ophus, Colin; Scott, Mary C. (25 January 2022). "Simultaneous Successive Twinning Captured by Atomic Electron Tomography". ACS Nano. 16 (1): 588–596. arXiv:2109.06954. doi:10.1021/acsnano.1c07772. PMID 34783237. S2CID 237513855.
  19. ^ Bals, Sara; Goris, Bart; De Backer, Annick; Van Aert, Sandra; Van Tendeloo, Gustaaf (1 July 2016). "Atomic resolution electron tomography". MRS Bulletin. 41 (7): 525–530. doi:10.1557/mrs.2016.138. hdl:10067/1356900151162165141. S2CID 139058353.
  20. ^ 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.
  21. ^ 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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