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Specifications for Hard Condensed Matter Specimens for Three-Dimensional High-Resolution Tomographies

  • P. Bleuet (a1), G. Audoit (a1), J.-P. Barnes (a1), J. Bertheau (a2), Y. Dabin (a3), H. Dansas (a1), J.-M. Fabbri (a1), B. Florin (a1), P. Gergaud (a1), A. Grenier (a1), G. Haberfehlner (a1), E. Lay (a4), J. Laurencin (a4), R. Serra (a1) and J. Villanova (a3)...


Tomography is a standard and invaluable technique that covers a large range of length scales. It gives access to the inner morphology of specimens and to the three-dimensional (3D) distribution of physical quantities such as elemental composition, crystalline phases, oxidation state, or strain. These data are necessary to determine the effective properties of investigated heterogeneous media. However, each tomographic technique relies on severe sampling conditions and physical principles that require the sample to be adequately shaped. For that purpose, a wide range of sample preparation techniques is used, including mechanical machining, polishing, sawing, ion milling, or chemical techniques. Here, we focus on the basics of tomography that justify such advanced sample preparation, before reviewing and illustrating the main techniques. Performances and limits are highlighted, and we identify the best preparation technique for a particular tomographic scale and application. The targeted tomography techniques include hard X-ray micro- and nanotomography, electron nanotomography, and atom probe tomography. The article mainly focuses on hard condensed matter, including porous materials, alloys, and microelectronics applications, but also includes, to a lesser extent, biological considerations.


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Andersson, B.V., Herland, A., Masich, S. & Inganäs, O. (2009). Imaging of the 3D nanostructure of a polymer solar cell by electron tomography. Nano Lett 9(2), 853855.
Attwood, D. (2006). Microscopy: Nanotomography comes of age. Nature 442(7103), 642643.
Banhart, J. (2008). Advanced Tomographic Methods in Materials Research and Engineering. Oxford, UK: Oxford University Press.
Baruchel, J., Buffiere, J.-Y., Cloetens, P., Di Michiel, M., Ferrie, E., Ludwig, W., Maire, E. & Salvo, L. (2006). Advances in synchrotron radiation microtomography. Scripta Mater 55(1), 4146.
Baumeister, W., Grimm, R. & Walz, J. (1999). Electron tomography of molecules and cells. Trends Cell Biol 9(2), 8185.
Biermans, E., Molina, L., Batenburg, K.J., Bals, S. & Van Tendeloo, G. (2010). Measuring porosity at the nanoscale by quantitative electron tomography. Nano Lett 10(12), 50145019.
Blavette, D., Bostel, A., Sarrau, J.M., Deconihout, B. & Menand, A. (1993). An atom probe for three-dimensional tomography. Nature 363(6428), 432435.
Bonse, U., Busch, F., Günnewig, O., Beckmann, F., Pahl, R., Delling, G.N., Hahn, M. & Graeff, W. (1994). 3D computed X-ray tomography of human cancellous bone at 8 micron spatial and 10−4 energy resolution. Bone Miner 25(1), 2538.
Brochin, C. (1999). Fixing device with freezing or heating tray. France: AMCC, International Patent WO 99/33607.
Cantoni, M., Knott, G. & Hébert, C. (2010). FIB-SEM nanotomography in materials and life science at EPFL. Microsc Microanaly 16(Suppl 2), 226227.
Charles-Harris, M., Del Valle, S., Hentges, E., Bleuet, P., Lacroix, D. & Planell, J.A. (2007). Mechanical and structural characterisation of completely degradable polylactic acid/calcium phosphate glass scaffolds. Biomaterials 28(30), 44294438.
Cherns, P., Lorut, F., Dupré, C., Tachi, K., Cooper, D., Chabli, A. & Ernst, T. (2010). Electron tomography of gate-all-around nanowire transistors. J Phys Conf Ser 209, 012046.
Courdurier, M., Noo, F., Defrise, M. & Kudo, H. (2008). Solving the interior problem of computed tomography using a priori knowledge. Inverse Probl 24, 065001.
Deconihout, B., Bostel, A., Menand, A., Sarrau, J.M., Bouet, M., Chambreland, S. & Blavette, D. (1993). On the development of a 3D tomographic atom-probe. Appl Surf Sci 67(1-4), 444450.
Dierolf, M., Menzel, A., Thibault, P., Schneider, P., Kewish, C.M., Wepf, R., Bunk, O. & Pfeiffer, F. (2010). Ptychographic X-ray computed tomography at the nanoscale. Nature 467(7314), 436439.
Drouin, D., Couture, A.R., Joly, D., Tastet, X., Aimez, V. & Gauvin, R. (2007). CASINO V2.42—A fast and easy-to-use modeling tool for scanning electron microscopy and microanalysis users. Scanning 29(3), 92101.
Fanelli, D. & Oktem, O. (2008). Electron tomography: A short overview with an emphasis on the absorption potential model for the forward problem Inverse Probl 24, 013001.
Flannery, B.P., Deckman, H.W., Roberge, W.G. & D'amico, K.L. (1987). Three-dimensional X-ray microtomography. Science 237(4821), 14391444.
Frank, J., Wagenknecht, T., McEwen, B.F., Marko, M., Hsieh, C.-E. & Mannella, C.A. (2002). Three-dimensional imaging of biological complexity. J Struct Biol 138(1-2), 8591.
Gault, B., Vurpillot, F., Vella, A., Gilbert, M., Menand, A., Blavette, D. & Deconihout, B. (2006). Design of a femtosecond laser assisted tomographic atom probe. Rev Sci Instrum 77(4), 043705043708.
Giannuzzi, L.A., Kempshall, B.W., Schwarz, S.M., Lomness, J.K., Prenitzer, B.I. & Stevie, F.A. (2005). FIB lift-out specimen preparation techniques. In Introduction to Focused Ion Beams, pp. 201228. New York: Springer.
Giannuzzi, L.A. & Stevie, F.A. (1999). A review of focused ion beam milling techniques for TEM specimen preparation. Micron 30(3), 197204.
Grenier, A., Lardé, R., Cadel, E., Le Breton, J.M., Juraszek, J., Vurpillot, F., Tiercelin, N., Pernod, P. & Teillet, J. (2007). Structural investigation of TbCo2/Fe magnetostrictive thin films by tomographic atom probe and Mössbauer spectrometry. J Mag Mag Mater 310(2, Pt 3), 22152216.
Grew, K.N., Chu, Y.S., Yi, J., Peracchio, A.A., Izzo, J.R., Hwu, Y., De Carlo, F. & Chiu, W.K.S. (2010). Nondestructive nanoscale 3D elemental mapping and analysis of a solid oxide fuel cell anode. J Electrochem Soc 157(6), B783B792.
Grodzins, L. (1983). Critical absorption tomography of small samples: Proposed applications of synchrotron radiation to computerized tomography II. Nucl Instrum Methods Phys Res 206(3), 547552.
Grünewald, K., Desai, P., Winkler, D.C., Heymann, J.B., Belnap, D.M., Baumeister, W. & Steven, A.C. (2003). Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302(5649), 13961398.
Guan, Y., Li, W., Gong, Y., Liu, G., Zhang, X., Chen, J., Gelb, J., Yun, W., Xiong, Y., Tian, Y. & Wang, H. (2011). Analysis of the three-dimensional microstructure of a solid-oxide fuel cell anode using nano X-ray tomography. J Power Sources 196(4), 19151919.
Haberfehlner, G., Bayle-Guillemaud, P., Audoit, G., Lafond, D., Morel, P.H., Jousseaume, V., Ernst, T. & Bleuet, P. (2012). Four-dimensional spectral low-loss EFTEM tomography of silicon nanowire-based capacitors. Appl Phys Lett 101, 063108.
Haberfehlner, G., Smith, M.J., Idrobo, J.C., Auvert, G., Sher, M-J., Winkler, M.T., Mazur, E., Gambacorti, N., Gradečak, S. & Bleuet, P. (forthcoming). Selenium segregation in femtosecond-laser hyperdoped silicon revealed by electron tomography. Microsc Microanal (accepted for publication).
Hahn, B. & Louis, A.K. (2012). Reconstruction in the three-dimensional parallel scanning geometry with application in synchrotron-based X-ray tomography. Inverse Probl 28(4), 045013.
Hawkes, P. (2006). The electron microscope as a structure projector. In Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell, 2nd ed., Frank, J. (Ed.). New York: Springer.
Izzo, J.R., Joshi, A.S., Grew, K.N., Chiu, W.K.S., Tkachuk, A., Wang, S.H. & Yun, W. (2008). Nondestructive reconstruction and analysis of SOFC anodes using X-ray computed tomography at sub-50 Å nm resolution. J Electrochem Soc 155(5), B504B508.
Kak, A.C. & Slaney, M. (2001). Principles of Computerized Tomographic Imaging. Philadelphia, PA: Society for Industrial and Applied Mathematics.
Kawase, N., Kato, M., Nishioka, H. & Jinnai, H. (2007). Transmission electron microtomography without the “missing wedge” for quantitative structural analysis. Ultramicroscopy 107(1), 815.
Ke, X., Bals, S., Cott, D., Hantschel, T., Bender, H. & Tendeloo, G.V. (2010). Three-dimensional analysis of carbon nanotube networks in interconnects by electron tomography without missing wedge artifacts. Microsc Microanal 16, 210217.
Kelly, T.F. & Miller, M.K. (2007). Atom probe tomography. Rev Sci Instrum 78(3), 031101/1–20.
Koster, A.J., Grimm, R., Typke, D., Hegerl, R., Stoschek, A., Walz, J. & Baumeister, W. (1997). Perspectives of molecular and cellular electron tomography. J Struct Biol 120(3), 276308.
Kwakman, L., Franz, G., Klumpp, A. & Ramm, P. (2011). Characterization and failure analysis of 3D integrated systems using a novel plasma-FIB system. In Frontiers of Characterization and Metrology for Nanoelectronics, Seiler, D.G., Diebold, A., McDonald, R., Herr, D., Thompson, G. & Chabli, A. (Eds.). Grenoble, France: American Institute of Physics.
Kyrieleis, A., Ibison, M., Titarenko, V. & Withers, P.J. (2009). Image stitching strategies for tomographic imaging of large objects at high resolution at synchrotron sources. Nucl Instrum Methods Phys Res A 607(3), 677684.
Langer, M. & Peyrin, F. (2010). A wavelet algorithm for zoom-in tomography. In Proceedings of the 2010 IEEE International Conference on Biomedical Imaging: From Nano to Macro, pp. 608611. Rotterdam.
Larson, D.J., Wissman, B.D., Martens, R.L., Villieux, R.J., Kelly, T.F., Gribb, T.T., Erskine, H.F. & Tabat, N. (2001). Advances in atom probe specimen fabrication from planar multilayer thin film structures. Microsc Microanal 7(1), 2431.
Laurencin, J., Quey, R., Delette, G., Suhonen, H., Cloetens, P. & Bleuet, P. (2012). Characterisation of solid oxide fuel cell Ni-8YSZ substrate by synchrotron X-ray nano-tomography: From 3D reconstruction to microstructure quantification. J Power Sources 198, 182189.
Lombardo, J.J., Ristau, R.A., Harris, W.M. & Chiu, W.K. (2012). Focused ion beam preparation of samples for X-ray nanotomography. J Synchrotron Radiat 19(5), 189196.
Martinez-Criado, G., Tucoulou, R., Cloetens, P., Bleuet, P., Bohic, S., Cauzid, J., Kieffer, I., Kosior, E., Laboure, S., Petitgirard, S., Rack, A., Sans, J.A., Segura-Ruiz, J., Suhonen, H., Susini, J. & Villanova, J. (2012). Status of the hard X-ray microprobe beamline ID22 of the European Synchrotron Radiation Facility. J Synchrotron Radiat 19(1), 1018.
McKenzie, Z.R., Marquis, E.Q. & Munroe, P.R. (2010). Focused ion beam sample preparation for atom probe tomography. In Microscopy: Science, Technology, Applications and Education, Díaz, A. M.-V. a. J. (Ed.), pp. 18001810.
Midgley, P.A. & Dunin-Borkowski, R.E. (2009). Electron tomography and holography in materials science. Nat Mater 8(4), 271280.
Midgley, P.A. & Weyland, M. (2003). 3D electron microscopy in the physical sciences: The development of Z-contrast and EFTEM tomography. Ultramicroscopy 96, 413431.
Miller, M.K. (2005). Sculpting needle-shaped atom probe specimens with a dual beam FIB. Microsc Microanal 11(Suppl 2), 808809CD.
Miller, M.K., Kelly, T.F., Rajan, K. & Ringer, S.P. (2012). The future of atom probe tomography. Mater Today 15(4), 158165.
Miller, M.K., Russell, K.F. & Thompson, G.B. (2005). Strategies for fabricating atom probe specimens with a dual beam FIB. Ultramicroscopy 102(4), 287298.
Möbus, G. & Inkson, B.J. (2007). Nanoscale tomography in materials science. Mater Today 10(12), 1825.
Natterer, F. & Wübbeling, F. (2001). Mathematical Methods in Image Reconstruction. Philadelphia, PA: Society for Industrial and Applied Mathematics.
Pacureanu, A., Langer, M., Boller, E., Tafforeau, P. & Peyrin, F. (2012). Nanoscale imaging of the bone cell network with synchrotron X-ray tomography: Optimization of acquisition setup. Med Phys 39(4), 22292238.
Peter, Z., Bleuet, P., Lafage-Proust, M.H. & Peyrin, F. (2006). Feasibility of three-dimensional imaging of the Lacuno-Canalicular network from synchrotron radiation micro-CT. In 17th International Bone Densitometry Workshop, Kyoto, Japan.
Petherbridge, J.R., Scott, T.B., Glascott, J., Younes, C., Allen, G.C. & Findlay, I. (2009). Characterisation of the surface over-layer of welded uranium by FIB, SIMS and Auger electron spectroscopy. J Alloys Comp 476(1-2), 543549.
Quey, R., Suhonen, H., Laurencin, J., Cloetens, P. & Bleuet, P. (2013). Direct comparison between X-ray nanotomography and scanning electron microscopy for the microstructure characterization of a solid oxide fuel cell anode. Mater Charact 78, 8795.
Randolph, S.J., Fowlkes, J.D. & Rack, P.D. (2006). Focused, nanoscale electron-beam-induced deposition and etching. Crit Rev Solid State Mater Sci 31(3), 5589.
Reimer, L. (1998). Scanning Electron Microscopy: Physics of Image Formation and Microanalysis. New York: Springer.
Sasov, A.Y. (1987). Microtomography. J Microsc 147(2), 179192.
Saxey, D.W., Cairney, J.M., McGrouther, D. & Ringer, S.P. (2006). Atom probe specimen fabrication methods using a dual FIB/SEM. In Vacuum Nanoelectronics Conference, 2006 and the 2006 50th International Field Emission Symposium., IVNC/IFES 2006. Technical Digest. 19th International, pp. 145146.
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-angstrom resolution. Nature 483(7390), 444447.
Shearing, P.R., Gelb, J. & Brandon, N.P. (2010). X-ray nano computerised tomography of SOFC electrodes using a focused ion beam sample-preparation technique. J European Ceram Soc 30(8), 18091814.
Shearing, P.R., Golbert, J., Chater, R.J. & Brandon, N.P. (2009). 3D reconstruction of SOFC anodes using a focused ion beam lift-out technique. Chem Eng Sci 64(17), 39283933.
Shepp, L.A. & Logan, B.F. (1974). The Fourier reconstruction of a head section. IEEE Trans Nucl Sci 21, 2143.
Shukla, N., Tripathi, S.K., Banerjee, A., Ramana, A.S.V., Rajput, N.S. & Kulkarni, V.N. (2009). Study of temperature rise during focused Ga ion beam irradiation using nanothermo-probe. Appl Surf Sci 256(2), 475479.
Sousa, A.A., Hohmann-Marriott, M.F., Zhang, G. & Leapman, R.D. (2009). Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: Implications for tomography of thick biological sections. Ultramicroscopy 109(3), 213221.
Spanne, P. & Rivers, M.L. (1987). Computerized microtomography using synchrotron radiation from the NSLS. Nucl Instrum Methods Phys Res B 24–25 (Pt 2), 10631067.
Stock, S.R. (2008). Recent advances in X-ray microtomography applied to materials. Int Mater Rev 53(3), 129181.
Thompson, G.B., Miller, M.K. & Fraser, H.L. (2004). Some aspects of atom probe specimen preparation and analysis of thin film materials. Ultramicroscopy 100(1-2), 2534.
Van Aert, S., Batenburg, K.J., Rossell, M.D., Erni, R. & Van Tendeloo, G. (2011). Three-dimensional atomic imaging of crystalline nanoparticles. Nature 470(7334), 374377.
Vila-Comamala, J., Diaz, A., Guizar-Sicairos, M., Mantion, A., Kewish, C.M., Menzel, A., Bunk, O. & David, C. (2011). Characterization of high-resolution diffractive X-ray optics by ptychographic coherent diffractive imaging. Opt Express 19(22), 2133321344.
Vila-Comamala, J., Pan, Y., Lombardo, J., M. Harris, W., Chiu, W.K., David, C. & Wang, Y. (2012). Zone-doubled Fresnel zone plates for high-resolution hard X-ray full-field transmission microscopy. J Synchrotron Radiat 19, 705709.
Wei, K., Lin, B. & Tai, J. (2011). Copper pillar bump technology progress overview. In 2011 12th International Conference on Electronic Packaging Technology and High Density Packaging (ICEPT-HDP), pp. 15.
Weyland, M. & Midgley, P.A. (2003). Extending energy-filtered transmission electron microscopy (EFTEM) into three dimensions using electron tomography. Microsc Microanal 9, 542555.
Wilson, J.R., Kobsiriphat, W., Mendoza, R., Chen, H.-Y., Hiller, J.M., Miller, D.J., Thornton, K., Voorhees, P.W., Adler, S.B. & Barnett, S.A. (2006). Three-dimensional reconstruction of a solid-oxide fuel-cell anode. Nat Mater 5(7), 541544.
Withers, P.J. (2007). X-ray nanotomography. Mater Today 10(12), 2634.
Xiao, X., De Carlo, F. & Stock, S. (2008). X-ray zoom-in tomography of calcified tissue. In Proc SPIE 7078, Developments in X-ray Tomography VI, 707810.
Yaguchi, T., Konno, M., Kamino, T. & Watanabe, M. (2008). Observation of three-dimensional elemental distributions of a Si device using a 360 degrees tilt FIB and the cold field-emission STEM system. Ultramicroscopy 108(12), 16031615.
Ziegler, J.F., Ziegler, M.D. & Biersack, J.P. (2010). SRIM—The stopping and range of ions in matter. Nucl Instrum Methods Phys Res B 268(11-12), 18181823.


Specifications for Hard Condensed Matter Specimens for Three-Dimensional High-Resolution Tomographies

  • P. Bleuet (a1), G. Audoit (a1), J.-P. Barnes (a1), J. Bertheau (a2), Y. Dabin (a3), H. Dansas (a1), J.-M. Fabbri (a1), B. Florin (a1), P. Gergaud (a1), A. Grenier (a1), G. Haberfehlner (a1), E. Lay (a4), J. Laurencin (a4), R. Serra (a1) and J. Villanova (a3)...


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