electron 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.{{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. | author1-link = Sara Bals | last2 = Kisielowski | first2 = C. F. | last3 = Croitoru | first3 = M. | last4 = Tendeloo | first4 = G. V. | doi-access = free }}{{cite journal |last1=Van Aarle |first1=W. |last2=Palenstijn |first2=WJ. |last3=De Beenhouwer|first3=J|last4=Alantzis|first4=T|last5=Bals|first5=S|last6=Batenburg|first6=J|last7=Sijbers|first7=J|title=The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography |journal=Ultramicroscopy |date=2015 |volume=157 |pages=35–47 |doi=10.1016/j.ultramic.2015.05.002|pmid=26057688 |hdl=10067/1278340151162165141|url=https://ir.cwi.nl/pub/23858 |hdl-access=free}} 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 journal|author=B.D.A. Levin|display-authors=etal|title=Nanomaterial datasets to advance tomography in scanning transmission electron microscopy|journal=Scientific Data |year=2016|volume=3|issue=160041|page=160041

|doi=10.1038/sdata.2016.41|pmid=27272459|pmc=4896123|arxiv=1606.02938|bibcode=2016NatSD...360041L}} 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.{{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}} 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.{{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 }}

File:Electron Tomography.tif

Atomic level resolution in 3D electron tomography reconstructions has been demonstrated. With the aid of computational ptychography, identification and precise 3D coordinates of every single atom[https://www.nature.com/articles/s41586-024-08278-z] in tiny objects have been imaged, clearly depicting molecular structures at large and small scales. Reconstructions of crystal defects such as stacking faults, grain boundaries, dislocations, and twinning in structures have been achieved.{{cite journal |last1=Miao |first1=J. |last2=Ercius |first2=P. |last3=Billinge |first3=S. J. L. |title=Atomic electron tomography: 3D structures without crystals |journal=Science |pages=aaf2157 |language=en |doi=10.1126/science.aaf2157 |date=23 September 2016|volume=353 |issue=6306 |pmid=27708010 |s2cid=30174421 |doi-access=free }} 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.{{cite journal |last1=Saghi |first1=Zineb |last2=Midgley |first2=Paul A. |title=Electron Tomography in the (S)TEM: From Nanoscale Morphological Analysis to 3D Atomic Imaging |url=https://www.annualreviews.org/doi/10.1146/annurev-matsci-070511-155019 |journal=Annual Review of Materials Research |year=2012 |volume=42 |pages=59–79 |doi=10.1146/annurev-matsci-070511-155019 |bibcode=2012AnRMS..42...59S |access-date=13 December 2022}} ADF-STEM tomography has recently been used to directly visualize the atomic structure of screw dislocations in nanoparticles.{{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 | pmid=23535594| s2cid = 4410909}}{{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 }}{{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 | doi-access = free }}{{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 | s2cid = 40526826}}

AET has also been used to find the 3D coordinates of 3,769 atoms in a tungsten needle with 19 pm precision{{cite journal |last1=Xu |first1=Rui |last2=Chen |first2=Chien-Chun |last3=Wu |first3=Li |last4=Scott |first4=M. C. |last5=Theis |first5=W. |last6=Ophus |first6=Colin |last7=Bartels |first7=Matthias |last8=Yang |first8=Yongsoo |last9=Ramezani-Dakhel |first9=Hadi |last10=Sawaya |first10=Michael R. |last11=Heinz |first11=Hendrik |last12=Marks |first12=Laurence D. |last13=Ercius |first13=Peter |last14=Miao |first14=Jianwei |title=Three-dimensional coordinates of individual atoms in materials revealed by electron tomography |url=https://www.nature.com/articles/nmat4426 |journal=Nature Materials |pages=1099–1103 |language=en |doi=10.1038/nmat4426 |date=November 2015|volume=14 |issue=11 |pmid=26390325 |s2cid=5455024 |arxiv=1505.05938 |bibcode=2015NatMa..14.1099X }} and 20,000 atoms in a multiply twinned palladium nanoparticle.{{cite journal |last1=Pelz |first1=Philipp M. |last2=Groschner |first2=Catherine |last3=Bruefach |first3=Alexandra |last4=Satariano |first4=Adam |last5=Ophus |first5=Colin |last6=Scott |first6=Mary C. |title=Simultaneous Successive Twinning Captured by Atomic Electron Tomography |url=https://pubs.acs.org/doi/10.1021/acsnano.1c07772 |journal=ACS Nano |pages=588–596 |language=en |doi=10.1021/acsnano.1c07772 |date=25 January 2022|volume=16 |issue=1 |pmid=34783237 |s2cid=237513855 |arxiv=2109.06954 }} The combination of AET with electron energy loss spectroscopy (EELS) allows for investigation of electronic states in addition to 3D reconstruction.{{cite journal |last1=Bals |first1=Sara |last2=Goris |first2=Bart |last3=De Backer |first3=Annick |last4=Van Aert |first4=Sandra |last5=Van Tendeloo |first5=Gustaaf |title=Atomic resolution electron tomography |url=https://doi.org/10.1557/mrs.2016.138 |journal=MRS Bulletin |pages=525–530 |language=en |doi=10.1557/mrs.2016.138 |date=1 July 2016|volume=41 |issue=7 |bibcode=2016MRSBu..41..525B |hdl=10067/1356900151162165141 |s2cid=139058353 |hdl-access=free }}{{cite journal |last1=Van Aarle |first1=W. |last2=Palenstijn |first2=WJ. |last3=De Beenhouwer|first3=J|last4=Alantzis|first4=T|last5=Bals|first5=S|last6=Batenburg|first6=J|last7=Sijbers|first7=J|title=The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography |journal=Ultramicroscopy |date=2015 |volume=157 |pages=35–47 |doi=10.1016/j.ultramic.2015.05.002|pmid=26057688 |hdl=10067/1278340151162165141|url=https://ir.cwi.nl/pub/23858 |hdl-access=free}} 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.

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.{{cite journal|author=B.D.A. Levin|display-authors=etal|title=Nanomaterial datasets to advance tomography in scanning transmission electron microscopy|journal=Scientific Data |year=2016|volume=3|issue=160041|page=160041

|doi=10.1038/sdata.2016.41|pmid=27272459|pmc=4896123|arxiv=1606.02938|bibcode=2016NatSD...360041L}}{{cite journal |last1=Van Aarle |first1=W. |last2=Palenstijn |first2=WJ. |last3=De Beenhouwer|first3=J|last4=Alantzis|first4=T|last5=Bals|first5=S|last6=Batenburg|first6=J|last7=Sijbers|first7=J|title=The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography |journal=Ultramicroscopy |date=2015 |volume=157 |pages=35–47 |doi=10.1016/j.ultramic.2015.05.002|pmid=26057688 |hdl=10067/1278340151162165141|url=https://ir.cwi.nl/pub/23858 |hdl-access=free}} 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 $\backslash sqrt\{2\}$ 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.{{Cite journal | pmid = 18417694| pmc = 3844767| year = 2008| last1 = Zampighi| first1 = G. A.| title = Conical electron tomography of a chemical synapse: Polyhedral cages dock vesicles to the active zone| journal = Journal of Neuroscience| volume = 28| issue = 16| pages = 4151–60| last2 = Fain| first2 = N| last3 = Zampighi| first3 = L. M.| last4 = Cantele| first4 = F| last5 = Lanzavecchia| first5 = S| last6 = Wright| first6 = E. M.| doi = 10.1523/JNEUROSCI.4639-07.2008}}

• 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

{{reflist}}

Category:Electron microscopy

Category:Multidimensional signal processing

Category:Condensed matter physics