Electron tomography

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]

## Contents

* 1 BF-TEM and ADF-STEM tomography
* 1.1 Different tilting methods
* 2 See also
* 3 References

## 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.[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,Cite error: Closing `</ref>` missing for `<ref>` tag 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.[8] ADF-STEM tomography has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.Cite error: Closing `</ref>` missing for `<ref>` tag and 20,000 atoms in a multiply twinned palladium nanoparticle.[9] The combination of AET with electron energy loss spectroscopy (EELS) allows for investigation of electronic states in addition to 3D reconstruction.[10] 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

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.[11] 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 [math]\displaystyle{ \sqrt{2} }[/math] 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.[12]

## See also

* Tomography
* Tomographic reconstruction
* 3D reconstruction
* Cryo-electron tomography
* Positron emission tomography
* Crowther criterion
* X-ray computed tomography
* tomviz tomography software
* imod tomography software
* X-ray diffraction computed tomography

## References

1. ↑ R. Hovden; D. A. Muller (2020). "Electron tomography for functional nanomaterials". MRS Bulletin 45 (4): 298–304. doi:10.1557/mrs.2020.87. Bibcode: 2020MRSBu..45..298H.
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. doi:10.1098/rspa.1970.0119. Bibcode: 1970RSPSA.317..319C.
3. ↑ Frank, Joachim (2006). Electron Tomography. doi:10.1007/978-0-387-69008-7. ISBN 978-0-387-31234-7.
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 (2017). "Deciphering chemical order/disorder and material properties at the single-atom level". Nature 542 (7639): 75–79. doi:10.1038/nature21042. PMID 28150758. Bibcode: 2017Natur.542...75Y.
6. ↑ Scott, M. C.; Chen, C. C.; Mecklenburg, M.; Zhu, C.; Xu, R.; Ercius, P.; Dahmen, U.; Regan, B. C. et al. (2012). "Electron tomography at 2.4-ångström resolution". Nature 483 (7390): 444–7. doi:10.1038/nature10934. PMID 22437612. Bibcode: 2012Natur.483..444S. https://escholarship.org/content/qt4j80v2jt/qt4j80v2jt.pdf?t=oupzqq.
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. ↑ 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. https://www.annualreviews.org/doi/10.1146/annurev-matsci-070511-155019. Retrieved 13 December 2022.
9. ↑ 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" (in en). ACS Nano 16 (1): 588–596. doi:10.1021/acsnano.1c07772. PMID 34783237. https://pubs.acs.org/doi/10.1021/acsnano.1c07772.
10. ↑ Bals, Sara; Goris, Bart; De Backer, Annick; Van Aert, Sandra; Van Tendeloo, Gustaaf (1 July 2016). "Atomic resolution electron tomography" (in en). MRS Bulletin 41 (7): 525–530. doi:10.1557/mrs.2016.138. https://doi.org/10.1557/mrs.2016.138.
11. ↑ B.D.A. Levin (2016). "Nanomaterial datasets to advance tomography in scanning transmission electron microscopy". Scientific Data 3 (160041): 160041. doi:10.1038/sdata.2016.41. PMID 27272459. Bibcode: 2016NatSD...360041L.
12. ↑ 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. PMID 18417694.

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