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In the field of biology, bright-field [[transmission electron microscopy]] (BF-TEM) and high-resolution TEM ([[High-resolution transmission electron microscopy|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.<ref>{{Cite journal | doi = 10.1017/S143192760550117X| title = Annular Dark Field Tomography in TEM| journal = Microscopy and Microanalysis| volume = 11| year = 2005| last1 = Bals | first1 = S. | last2 = Kisielowski | first2 = C. F. | last3 = Croitoru | first3 = M. | last4 = Tendeloo | first4 = G. V. }}</ref> 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]]
In the field of biology, bright-field [[transmission electron microscopy]] (BF-TEM) and high-resolution TEM ([[High-resolution transmission electron microscopy|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.<ref>{{Cite journal | doi = 10.1017/S143192760550117X| title = Annular Dark Field Tomography in TEM| journal = Microscopy and Microanalysis| volume = 11| year = 2005| last1 = Bals | first1 = S. | last2 = Kisielowski | first2 = C. F. | last3 = Croitoru | first3 = M. | last4 = Tendeloo | first4 = G. V. }}</ref> 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,<ref>{{cite journal|author=B.D.A. Levin, et al.|title=Nanomaterial datasets to advance tomography in scanning transmission electron microscopy|journal=Scientific Data |year=2016|volume=3|page=160041
(ADF-STEM) 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.<ref>{{Cite journal | doi = 10.1016/S0304-3991(03)00105-0| title = 3D electron microscopy in the physical sciences: The development of Z-contrast and EFTEM tomography| journal = Ultramicroscopy| volume = 96| issue = 3–4| pages = 413–431| year = 2003| last1 = Midgley | first1 = P. A. | authorlink = Paul Midgley| last2 = Weyland | first2 = M. | pmid=12871805}}</ref> 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&nbsp;nm was achieved with a single-axis ADF-STEM tomography.<ref name="Xin2010">{{Cite journal | doi = 10.1063/1.3442496| title = Three-dimensional imaging of pore structures inside low-κ dielectrics| journal = Applied Physics Letters| volume = 96| issue = 22| pages = 223108| year = 2010| last1 = Xin | first1 = H. L. | last2 = Ercius | first2 = P. | last3 = Hughes | first3 = K. J. | last4 = Engstrom | first4 = J. R. | last5 = Muller | first5 = D. A. |bibcode = 2010ApPhL..96v3108X }}</ref> Presently, the highest electron tomography resolution is around 2.4 angstrom as demonstrated by UCLA Miao group using a gold nanoparticle.<ref name="Scott2012">{{Cite journal | doi = 10.1038/nature10934| title = Electron tomography at 2.4-ångström resolution| journal = Nature| volume = 483| issue = 7390| pages = 444–7| year = 2012| last1 = Scott | first1 = M. C.| last2 = Chen | first2 = C. C. | last3 = Mecklenburg | first3 = M. | last4 = Zhu | first4 = C. | last5 = Xu | first5 = R. | last6 = Ercius | first6 = P. | last7 = Dahmen | first7 = U. | last8 = Regan | first8 = B. C.| last9 = Miao | first9 = J. | pmid=22437612
|doi=10.1038/sdata.2016.41|url=http://www.nature.com/articles/sdata201641}}</ref> 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.<ref>{{Cite journal | doi = 10.1016/S0304-3991(03)00105-0| title = 3D electron microscopy in the physical sciences: The development of Z-contrast and EFTEM tomography| journal = Ultramicroscopy| volume = 96| issue = 3–4| pages = 413–431| year = 2003| last1 = Midgley | first1 = P. A. | authorlink = Paul Midgley| last2 = Weyland | first2 = M. | pmid=12871805}}</ref> 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&nbsp;nm was achieved with a single-axis ADF-STEM tomography.<ref name="Xin2010">{{Cite journal | doi = 10.1063/1.3442496| title = Three-dimensional imaging of pore structures inside low-κ dielectrics| journal = Applied Physics Letters| volume = 96| issue = 22| pages = 223108| year = 2010| last1 = Xin | first1 = H. L. | last2 = Ercius | first2 = P. | last3 = Hughes | first3 = K. J. | last4 = Engstrom | first4 = J. R. | last5 = Muller | first5 = D. A. |bibcode = 2010ApPhL..96v3108X }}</ref> Recently, atomic resolution in 3D electron tomography reconstructions has been demonstrated.<ref>{{cite journal|author=Y. Yang, et al.|title=Deciphering chemical order/disorder and material properties at the single-atom level|journal=SNature |year=2017|volume=542|page=75-79
⚫
|bibcode = 2012Natur.483..444S }}</ref> This technique has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.<ref name="cc2013">{{Cite journal | doi = 10.1038/nature12009| title = Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution| journal = Nature| volume = 496| issue = 7443| pages = 74–77| year = 2013| last1 = Chen | first1 = C. C. | last2 = Zhu | first2 = C. | last3 = White | first3 = E. R. | last4 = Chiu | first4 = C. Y. | last5 = Scott | first5 = M. C.| last6 = Regan | first6 = B. C.| last7 = Marks | first7 = L. D. | last8 = Huang | first8 = Y. | last9 = Miao | first9 = J.
|doi=10.1038/nature21042|url=http://www.nature.com/nature/journal/v542/n7639/full/nature21042.html}}</ref><ref name="Scott2012">{{Cite journal | doi = 10.1038/nature10934| title = Electron tomography at 2.4-ångström resolution| journal = Nature| volume = 483| issue = 7390| pages = 444–7| year = 2012| last1 = Scott | first1 = M. C.| last2 = Chen | first2 = C. C. | last3 = Mecklenburg | first3 = M. | last4 = Zhu | first4 = C. | last5 = Xu | first5 = R. | last6 = Ercius | first6 = P. | last7 = Dahmen | first7 = U. | last8 = Regan | first8 = B. C.| last9 = Miao | first9 = J. | pmid=22437612
⚫
|bibcode = 2012Natur.483..444S }}</ref> ADF-STEM tomography has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.<ref name="cc2013">{{Cite journal | doi = 10.1038/nature12009| title = Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution| journal = Nature| volume = 496| issue = 7443| pages = 74–77| year = 2013| last1 = Chen | first1 = C. C. | last2 = Zhu | first2 = C. | last3 = White | first3 = E. R. | last4 = Chiu | first4 = C. Y. | last5 = Scott | first5 = M. C.| last6 = Regan | first6 = B. C.| last7 = Marks | first7 = L. D. | last8 = Huang | first8 = Y. | last9 = Miao | first9 = J.
|bibcode = 2013Natur.496...74C }}</ref><ref>{{Cite journal | doi = 10.1038/nmat2406| title = Electron tomography and holography in materials science| journal = Nature Materials| volume = 8| issue = 4| pages = 271–280| year = 2009| last1 = Midgley | first1 = P. A. | authorlink1 = Paul Midgley| last2 = Dunin-Borkowski | first2 = R. E. | authorlink2 = Rafal E. Dunin-Borkowski | pmid=19308086|bibcode = 2009NatMa...8..271M }}</ref><ref>{{Cite journal | doi = 10.1063/1.2213185| title = Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography| journal = Applied Physics Letters| volume = 88| issue = 24| pages = 243116| year = 2006| last1 = Ercius | first1 = P. | last2 = Weyland | first2 = M. | last3 = Muller | first3 = D. A. | last4 = Gignac | first4 = L. M. |bibcode = 2006ApPhL..88x3116E }}</ref><ref>{{Cite journal | doi = 10.1126/science.1178583| title = Visualizing the 3D Internal Structure of Calcite Single Crystals Grown in Agarose Hydrogels| journal = Science| volume = 326| issue = 5957| pages = 1244–1247| year = 2009| last1 = Li | first1 = H.| last2 = Xin | first2 = H. L.| last3 = Muller | first3 = D. A.| last4 = Estroff | first4 = L. A. | pmid=19965470|bibcode = 2009Sci...326.1244L }}</ref>
|bibcode = 2013Natur.496...74C }}</ref><ref>{{Cite journal | doi = 10.1038/nmat2406| title = Electron tomography and holography in materials science| journal = Nature Materials| volume = 8| issue = 4| pages = 271–280| year = 2009| last1 = Midgley | first1 = P. A. | authorlink1 = Paul Midgley| last2 = Dunin-Borkowski | first2 = R. E. | authorlink2 = Rafal E. Dunin-Borkowski | pmid=19308086|bibcode = 2009NatMa...8..271M }}</ref><ref>{{Cite journal | doi = 10.1063/1.2213185| title = Three-dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography| journal = Applied Physics Letters| volume = 88| issue = 24| pages = 243116| year = 2006| last1 = Ercius | first1 = P. | last2 = Weyland | first2 = M. | last3 = Muller | first3 = D. A. | last4 = Gignac | first4 = L. M. |bibcode = 2006ApPhL..88x3116E }}</ref><ref>{{Cite journal | doi = 10.1126/science.1178583| title = Visualizing the 3D Internal Structure of Calcite Single Crystals Grown in Agarose Hydrogels| journal = Science| volume = 326| issue = 5957| pages = 1244–1247| year = 2009| last1 = Li | first1 = H.| last2 = Xin | first2 = H. L.| last3 = Muller | first3 = D. A.| last4 = Estroff | first4 = L. A. | pmid=19965470|bibcode = 2009Sci...326.1244L }}</ref>


===Different tilting methods===
===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.<ref>{{cite journal|author=B.D.A. Levin, et al.|title=Nanomaterial datasets to advance tomography in scanning transmission electron microscopy|journal=Scientific Data |year=2016|volume=3|page=160041

The most popular tilting methods are the single-axis and the dual-axis tilting methods. By using dual-axis tilting, the elongation effect is reduced by a factor of <math>\scriptstyle \sqrt{2}</math> however, twice as many images need to be taken. Another solution to obtain tilt-series is offered by the so-called conical tomography, during which the sample is tilted, and then rotated a complete turn.<ref>{{Cite journal
|doi=10.1038/sdata.2016.41|url=http://www.nature.com/articles/sdata201641}}</ref> By using dual-axis tilting, the reconstruction artifacts are reduced by a factor of <math>\scriptstyle \sqrt{2}</math> compared to single-axis tilting. However, twice as many images need to be taken. Another solution to obtain tilt-series is offered by the so-called conical tomography, during which the sample is tilted, and then rotated a complete turn.<ref>{{Cite journal
| pmid = 18417694
| pmid = 18417694
| pmc = 3844767
| pmc = 3844767

Revision as of 03:47, 1 March 2017

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 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]

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 solution to obtain tilt-series is offered by the so-called conical tomography, during which the sample is tilted, and then rotated a complete turn.[15]

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. London A. 317.
  2. ^ "Electron Tomography". 2006. doi:10.1007/978-0-387-69008-7. ISBN 978-0-387-31234-7. {{cite journal}}: Cite journal requires |journal= (help)
  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.
  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. doi:10.1038/sdata.2016.41. {{cite journal}}: Explicit use of et al. in: |author= (help)
  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". SNature. 542: 75-79. doi:10.1038/nature21042. {{cite journal}}: Explicit use of et al. in: |author= (help)
  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". 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.
  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. doi:10.1038/sdata.2016.41. {{cite journal}}: Explicit use of et al. in: |author= (help)
  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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