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Transmission Electron Microscopy

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References

General Tomography References

  • Deans SR (2007) The Radon transform and some of its applications. Dover Publications, Mineola, New York (The most comprehensive and readable reference regarding the mathematics of the Radon transform. Best of all it contains an English translation of Radon’s original German paper. Unavailable for many years, this is a very welcome, and reasonably priced, reprint)

    Google Scholar 

  • Egerton RF, Li P, Malac M (2004) Radiation damage in the TEM and SEM. Micron 35(6):399–409 (Electron beam damage is a central concern in ET, as such comprehensive review of beam damage is invaluable)

    Article  Google Scholar 

  • Frank J (2006) Electron Tomography; Methods for Three-Dimensional Visualization of Structures in the Cell, 2nd edn. Springer, New York. (The standard ET ‘textbook’ for the biological sciences, in the absence of an equivalent for the materials sciences this is the best general reference)

    Google Scholar 

  • Midgley PA, Ward EPW, Hungría AB, Thomas JM (2007) Nanotomography in the chemical, biological and materials sciences. Chem Soc Rev 36:1477–1494 (A review of nanoscale electron tomography with comparisons with comparable X-ray experiments)

    Article  Google Scholar 

  • Saghi Z, Midgley PA (2012) Electron Tomography in the (S)TEM: From Nanoscale Morphological Analysis to 3D Atomic Imaging. Annual Rev Mater Res 42:59–79 (A review focusing primarily on STEM-based tomography. The volume also contains reviews on confocal STEM, cryo-tomography, X-ray tomography and atom probe tomography)

    Article  Google Scholar 

Specific References

  • Van Aert S, Batenburg KJ, Rossell MD, Erni R, Van Tendeloo G (2011) Three-dimensional atomic imaging of crystalline nanoparticles. Nature 470:374–377

    Article  Google Scholar 

  • Aoyama K, Takagi T, Hirase A, Miyazawa A (2008) STEM tomography for thick biological specimens. Ultramicroscopy 109:70–80

    Article  Google Scholar 

  • Bajaj C, Yu ZY, Auer M (2003) Volumetric feature extraction and visualization of tomographic molecular imaging. J Structural Biol 144(1–2):132–143

    Article  Google Scholar 

  • Barnard JS, Sharp J, Tong JR, Midgley PA (2006) High-Resolution Three-Dimensional Imaging of Dislocations. Science 313:319

    Article  Google Scholar 

  • Batenburg KJ, Bals S, Sijbers J, Kübel C, Midgley PA, Hernandez JC, Kaiser U, Encina ER, Coronado EA, Van Tendeloo G (2009) 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy 109:730–740

    Article  Google Scholar 

  • Baumeister W, Grimm R, Walz J (1999) Electron tomography of molecules and cells. Trends Cell Biol 9(2):81–85

    Article  Google Scholar 

  • van Benthem K, Lupini AR, Kim M, Baik HS, Doh S, Lee JH, Oxley MP, Findlay SD, Allen LJ, Luck JT, Pennycook SJ (2005) Three-dimensional imaging of individual hafnium atoms inside a semiconductor device. Appl Phys Lett 87:034104

    Article  Google Scholar 

  • Bracewell RN (1956) Strip Integration in Radio Astronomy. Aust J Phys 9:297–314

    Article  Google Scholar 

  • Candes EJ, Romberg J, Tao T (2006) Robust uncertainty principles: Exact signal reconstruction from highly incomplete frequency information. IEEE Trans Information Theory 52:489–509

    Article  Google Scholar 

  • Chen CC, Zhu C, White ER, Chiu CY, Scott MC, Regan BC, Marks LD, Huang Y, Miao J (2013) Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution. Nature 496:74–77

    Article  Google Scholar 

  • Crowther RA, de Rosier DJ, Klug A (1970) The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc Roy Soc Lond A 317:319–340

    Article  Google Scholar 

  • Dierksen K, Typke D, Hegerl R, Koster AJ, Baumeister W (1992) Towards Automatic Electron Tomography. Ultramicroscopy 40(1):71–87

    Article  Google Scholar 

  • Donoho DL (2006) Compressed Sensing. IEEE Trans Information Theory 52:1289–1306

    Article  Google Scholar 

  • Dwyer C, Weyland M, Chang LY, Muddle BC (2011) Combined electron beam imaging and ab initio modeling of T(1) precipitates in Al-Li-Cu alloys. Appl Phys Lett 98:201909

    Article  Google Scholar 

  • Van Dyck D, Chen FR (2012) ‘Big Bang’ tomography as a new route to atomic-resolution electron tomography. Nature 486:243–246

    Article  Google Scholar 

  • Egerton RF, Li P, Malac M (2004) Radiation damage in the TEM and SEM. Micron 35(6):399–409

    Article  Google Scholar 

  • Ercius P, Weyland M, Muller DA, Gignac LM (2006) Three -dimensional imaging of nanovoids in copper interconnects using incoherent bright field tomography. Appl Phys Lett 88(24):243116

    Article  Google Scholar 

  • Fernandez JJ, Li S, Crowther RA (2006) CTF determination and correction in electron cryotomography. Ultramicroscopy 106(7):587–596

    Article  Google Scholar 

  • Frangakis AS, Hegerl R (2002) Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis. J Structural Biol 138(1–2):105–113

    Article  Google Scholar 

  • Frigo SP, Levine ZH, Zaluzec NJ (2002) Submicron imaging of buried integrated circuit structures using scanning confocal electron microscopy. Appl Phys Lett 81:2112–2114

    Article  Google Scholar 

  • Gass MH, Koziol KK, Windle AH, Midgley PA (2006) 4-dimensional spectral-tomography of carbonaceous nano-composites. Nano Lett 6(3):376–379

    Article  Google Scholar 

  • Gilbert P (1972) Iterative Methods for the Three-dimensional Reconstruction of an Object from Projections. J Theoretical Biol 36:105–117

    Article  Google Scholar 

  • Gordon R, Bender R, Herman GT (1970) Algebraic Reconstruction Techniques (ART) for Three-dimensional Electron Microscopy and X-ray Photography. J Theor Biol 29:471–481

    Article  Google Scholar 

  • Goris B, Bals S, Van den Broek W, Carbó-Argibay E, Gómez-Graña S, Liz-Marzán LM, Van Tendeloo G (2012) Atomic-scale determination of surface facets in gold nanorods. Nature Mater 11:930–935

    Article  Google Scholar 

  • Haberfehlner G, Orthacker A, Albu M, Li J, Kothleitner G (2014) Nanoscale voxel spectroscopy by simultaneous EELS and EDS tomography. Nanoscale 6:14563–14569

    Article  Google Scholar 

  • Hawkes PW (1992) The Electron Microscope as a Structure Projector. In: Frank J (ed) Electron tomography: three-dimensional imaging with the transmission electron microscope. Plenum Press, London, pp 17–39

    Chapter  Google Scholar 

  • Hegerl R, Hoppe W (1976) Influence Of Electron Noise On 3-Dimensional Image-Reconstruction. Z Naturforschung Section A 31(12):1717–1721

    Google Scholar 

  • Houben L, Bar SM (2011) Refinement procedure for the image alignment in high-resolution electron tomography. Ultramicroscopy 111:1512–1520

    Article  Google Scholar 

  • Hyun JK, Ercius P, Muller DA (2008) Beam spreading and spatial resolution in thick organic specimens. Ultramicroscopy 109:1–7

    Article  Google Scholar 

  • Ikeda Y, Katoh A, Shimanuki J, Kohjiya S (2004) Nano-structural observation of in situ silica in natural rubber matrix by three dimensional transmission electron microscopy. Macromolecular Rapid Commun 25(12):1186–1190

    Article  Google Scholar 

  • Isabell TC, Fischione PE, O’Keefe C, Guruz MU, Dravid VP (1999) Plasma cleaning and its applications for electron microscopy. Microsc Microanal 5(2):126–135

    Article  Google Scholar 

  • Jarausch K, Thomas P, Leonard DN, Twesten R, Booth CR (2009) Four-dimensional STEM-EELS: Enabling nano-scale chemical tomography. Ultramicroscopy 109:326–337

    Article  Google Scholar 

  • Jinnai H, Nishikawa Y, Spontak RJ, Smith SD, Agard DA, Hashimoto T (2000) Direct measurement of interfacial curvature distributions in a bicontinuous block copolymer morphology. Phys Rev Lett 84(3):518–521

    Article  Google Scholar 

  • Kaiser U, Biskupek J, Meyer JC, Leschner J, Lechner L, Rose H, Stoger-Pollach M, Khlobystov AN, Hartel P, Muller H, Haider M, Eyhusen S, Benner G (2011) Transmission electron microscopy at 20 kV for imaging and spectroscopy. Ultramicroscopy 111:1239–1246

    Article  Google Scholar 

  • Kimura K, Hata S, Matsumura S, Horiuchi T (2005) Dark-field transmission electron microscopy for a tilt series of ordering alloys: toward electron tomography. J Electron Microsc 54(4):373–377

    Article  Google Scholar 

  • Koster AJ, Van Den BA, Van Der MKD (1987) An autofocus method for a TEM. Ultramicroscopy 21:209–222

    Article  Google Scholar 

  • Lade SJ, Paganin D, Morgan MJ (2005) Electron tomography of electromagnetic fields, potentials and sources. Optics Commun 253:392–400

    Article  Google Scholar 

  • Lawrence MC (1992) Least-Squares Method of Alignment Using Markers. In: Frank J (ed) Electron tomography: three-dimensional imaging with the transmission electron microscope. Plenum Press, London., pp 197–204

    Chapter  Google Scholar 

  • LeBeau JM, Findlay SD, Allen LJ, Stemmer S (2008) Quantitative atomic resolution scanning transmission electron microscopy. Phys Rev Lett 100:206101

    Article  Google Scholar 

  • Lepinay K, Lorut F, Pantel R, Epicier T (2013) Chemical 3D tomography of 28 nm high K metal gate transistor: STEM XEDS experimental method and results. Micron 47:43–49

    Article  Google Scholar 

  • Liu Y, Penczek PA, McEwen BF, Frank J (1995) A Marker- Free Alignment Method For Electron Tomography. Ultramicroscopy 58(3–4):393–402

    Article  Google Scholar 

  • Mastronarde DN (1997) Dual-axis tomography: An approach with alignment methods that preserve resolution. J Structural Biol 120(3):343–352

    Article  Google Scholar 

  • Mastronarde DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Structural Biol 152(1):36–51

    Article  Google Scholar 

  • Miao JW, Forster F, Levi O (2005) Equally sloped tomography with oversampling reconstruction. Phys Rev B 72:052103

    Article  Google Scholar 

  • Midgley PA, Weyland M (2003) 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 96(3–4):413–431

    Article  Google Scholar 

  • Midgley PA, Weyland M, Thomas JM, Johnson BFG (2001) Z-Contrast tomography: a technique in three-dimensional nanostructural analysis based on Rutherford scattering. Chem Commun 2001:907–908

    Article  Google Scholar 

  • Mobus G, Doole RC, Inkson BJ (2003) Spectroscopic electron tomography. Ultramicroscopy 96:433–451

    Article  Google Scholar 

  • Nicoletti O, de la Pena F, Leary RK, Holland DJ, Ducati C, Midgley PA (2013) Three-dimensional imaging of localized surface plasmon resonances of metal nanoparticles. Nature 502:80–84

    Article  Google Scholar 

  • Phatak C, Beleggia M, De Graef M (2008) Vector field electron tomography of magnetic materials: Theoretical development. Ultramicroscopy 108:503–513

    Article  Google Scholar 

  • Phatak C, Petford-Long AK, De Graef M (2010) Three-Dimensional Study of the Vector Potential of Magnetic Structures. Phys Rev Lett 104:253901

    Article  Google Scholar 

  • Qin W, Fraundorf P (2003) Lattice parameters from direct-space images at two tilts. Ultramicroscopy 94:245–262

    Article  Google Scholar 

  • Radermacher M (1988) 3-Dimensional Reconstruction of Single Particles From Random and Nonrandom Tilt Series. J Electron Microsc Techniq 9(4):359–394

    Article  Google Scholar 

  • Radon J (1917) Uber die Bestimmung von Funktionen durch ihre Intergralwerte langs gewisser Mannigfaltigkeiten. Ber Verh K Sachs Ges Wiss Leipzig, Math-Phys Kl 69:262–277

    Google Scholar 

  • De Rosier DJ, Klug A (1968) Reconstruction of Three Dimensional Structures from Electron Micrographs. Nature 217:130–134

    Article  Google Scholar 

  • Russ JC (2002) The Image Processing Handbook. CRC Press, London

    Google Scholar 

  • Saghi Z, Holland DJ, Leary R, Falqui A, Bertoni G, Sederman AJ, Gladden LF, Midgley PA (2011) Three-Dimensional Morphology of Iron Oxide Nanoparticles with Reactive Concave Surfaces. A Compressed Sensing-Electron Tomography (CS-ET) Approach. Nano Lett 11:4666–4673

    Article  Google Scholar 

  • Sawada H, Sasaki T, Hosokawa F, Yuasa S, Terao M, Kawazoe M, Nakamichi T, Kaneyama T, Kondo Y, Kimoto K, Suenaga K (2010) Higher-order aberration corrector for an image-forming system in a transmission electron microscope. Ultramicroscopy 110:958–961

    Article  Google Scholar 

  • Saxton WO, Baumeister W, Hahn M (1984) 3-Dimensional Reconstruction of Imperfect Two-Dimensional Crystals. Ultramicroscopy 13(1–2):57–70

    Article  Google Scholar 

  • Scott MC, Chen CC, Mecklenburg M, Zhu C, Xu R, Ercius P, Dahmen U, Regan BC, Miao J (2012) Electron tomography at 2.4-angstrom resolution. Nature 483:444–491

    Article  Google Scholar 

  • Spontak RJ, Williams MC, Agard DA (1988) 3- Dimensional Study Of Cylindrical Morphology In A Styrene Butadiene Styrene Block Copolymer. Polymer 29(3):387–395

    Article  Google Scholar 

  • Stolojan V, Dunin-Borkowski RE, Weyland M, Midgley PA (2001) Three-dimensional magnetic fields of nanoscale elements determined by electron-holographic tomography. Electron Microsc Anal 2001:243–246

    Google Scholar 

  • Tanaka M, Higashida K, Kaneko K, Hata S, Mitsuhara M (2008) Crack tip dislocations revealed by electron tomography in silicon single crystal. Scripta Mater 59:901–902

    Article  Google Scholar 

  • Twitchett-Harrison AC, Yates TJV, Dunin-Borkowski RE, Midgley PA (2008) Quantitative electron holographic tomography for the 3D characterization of semiconductor device structures. Ultramicroscopy 108:1401–1407

    Article  Google Scholar 

  • Volkmann N (2002) A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J Structural Biol 138(1–2):123–129

    Article  Google Scholar 

  • Voortman LM, Stallinga S, Schoenmakers RHM, van Vliet LJ, Rieger B (2011) A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM. Ultramicroscopy 111:1029–1036

    Article  Google Scholar 

  • Ward EPW, Yates TJV, Fernandez JJ, Vaughan DEW, Midgley PA (2007) Three-dimensional nanoparticle distribution and local curvature of heterogeneous catalysts revealed by electron tomography. J Phys Chem C 111:11501–11505

    Article  Google Scholar 

  • Weyland M, Midgley PA, Thomas JM (2001) Electron tomography of nanoparticle catalysts on porous supports: A new technique based on Rutherford scattering. J Phys Chem B 105(33):7882–7886

    Article  Google Scholar 

  • Weyland M, Yates TJV, Dunin-Borkowski RE, Laffont L, Midgley PA (2006) Nanoscale analysis of three-dimensional structures by electron tomography. Scripta Mater 55:29–33

    Article  Google Scholar 

  • Winkler H, Taylor KA (2006) Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106(3):240–254

    Article  Google Scholar 

  • Wolf D, Lubk A, Roeder F, Lichte H (2013) Electron holographic tomography. Current Opinion Solid State Mater Sci 17:126–134

    Article  Google Scholar 

  • Xin HL, Muller DA (2010) Three-Dimensional Imaging in Aberration-Corrected Electron Microscopes. Microsc Microanal 16:445–455

    Article  Google Scholar 

  • Zeise U, Janssen R, Geerts W, van der Krift T, van Balen A, de Ruijter H, de Jong K, Verkleij A, Koster B (2001) A novel method of data collection for automated electron tomography based upon pre-calibration of image shifts and defocus changes. Microsc Microanal. Springer, Long Beach, CA

    Google Scholar 

  • Zhang X, Jin L, Fang Q, Hui WH, Zhou ZH (2010) 3.3 angstrom Cryo-EM Structure of a Nonenveloped Virus Reveals a Priming Mechanism for Cell Entry. Cell 141:472–482

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Materials Science and Engineering, Monash University, Melbourne, Australia

    Matthew Weyland

  2. Department of Materials Science and Metallurgy, University of Cambridge, Cambridge, UK

    Paul Midgley

Authors
  1. Matthew Weyland
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  2. Paul Midgley
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Corresponding author

Correspondence to Paul Midgley .

Editor information

Editors and Affiliations

  1. University of Connecticut, Storrs, Connecticut, USA

    C. Barry Carter

  2. Ohio State University, Columbus, Ohio, USA

    David B. Williams

Appendix

Appendix

12.1.1 People

As microscopists, we may think of tomography as being a natural progression from stereo pairs, in which case you might be interested to read about Sir Charles Wheatstone (born February 6, 1802, died October 19, 1875) and Sir David Brewster (born December 11, 1781, died February 10, 1868); you’ve heard of each before in very different contexts! Explore the meaning of the word planography. Then look at the invention of Godfrey Newbold Hounsfield (born August 28, 1991, died August 12, 2004), who used computers and X-rays and shared a Nobel Prize in 1979.

12.1.2 Self-Assessment Questions

Q9.1:

Describe the importance of the Radon transform to (electron) tomography.

Q9.2:

Draw a diagram to illustrate what is meant by the projection slice theorem . Explain its implications for tomographic reconstruction.

Q9.3:

Describe one experimental situation/specimen (physical or biological) where electron tomography WOULD be of value.

Q9.4:

Suggest one experimental situation/specimen (physical or biological) where electron tomography WOULD NOT be of value.

Q9.5:

Explain some of the limitations that might be imposed by the electron microscope and specimen holder on the acquisition of tilt series. Suggest some means for overcoming these limitations.

Q9.6:

Describe some of the limitations that might be imposed by the specimen on the acquisition of tilt series. Suggest some means for overcoming these limitations.

Q9.7:

Before tomographic reconstruction can occur the tilt series needs to be aligned with respect to a common tilt axis. Describe the TWO parts of this alignment.

Q9.8:

Why is there more than one valid tomographic alignment for each tilt series?

Q9.9:

List the advantages and limitations of alignment by tracking of fiducial markers.

Q9.10:

List the advantages and limitations of alignment by cross-correlation.

Q9.11:

Derive the equation to generate an r-weighting filter for tomographic reconstruction.

Q9.12:

Under what circumstances would r-weighting reconstruction generate a ‘perfect’ reconstruction?

Q9.13:

Describe two different constraints that can be applied in tomographic reconstruction. Include a justification for their use.

Q9.14:

Compare and contrast slicing and surface rendering as means of visualizing tomographic reconstructions.

Q9.15:

What is the ‘projection requirement’ and why is it so important when carrying out electron tomography on engineering materials?

Q9.16:

Why is HAADF STEM an ideal imaging mechanism for ET?

Q9.17:

List the challenges in carrying out electron tomography using secondary X-ray signals. Suggest means to overcome these challenges.

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Weyland, M., Midgley, P. (2016). Electron Tomography. In: Carter, C., Williams, D. (eds) Transmission Electron Microscopy. Springer, Cham. https://doi.org/10.1007/978-3-319-26651-0_12

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