Crowther, RA, DeRosier, DJ, Klug, A: The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc. R. Soc. A. 317(1530), 319–340 (1970). doi:10.1098/rspa.1970.0119
Gilbert, P: Iterative methods for the three-dimensional reconstruction of an object from projections. J. Theor. Biol. 36(1), 105–117 (1972). doi:10.1016/0022-5193(72)90180-4
Midgley, PA, Ward, EPW, Hungria, AB, Thomas, JM: Nanotomography in the chemical, biological and materials sciences. Chem. Soc. Rev. 36, 1477–1494 (2007). doi:10.1039/B701569K
Banhart, J, (Ed): Advanced Tomographic Methods in Materials Research and Engineering. Oxford University Press, Oxford, UK (2008). ISBN: 9780199213245.
Midgley, PA, Weyland, M: 3D electron microscopy in the physical sciences: the development of z-contrast and EFTEM tomography. Ultramicroscopy. 96(3–4), 413–431 (2003). doi:10.1016/S0304-3991(03)00105-0
Ikeda, Y, Katoh, A, Shimanuki, J, Kohjiya, S: Nano-structural observation of in situ silica in natural rubber matrix by three dimensional transmission electron microscopy. Macromol. Rapid Commun. 25(12), 1186–1190 (2004). doi:10.1002/marc.200400053
Staniewicz, L, Vaudey, T, Degrandcourt, C, Couty, M, Gaboriaud, F, Midgley, P: Electron tomography provides a direct link between the payne effect and the inter-particle spacing of rubber composites. Sci. Rep. 4 (2014). doi:10.1038/srep07389
Zečević, J, van der Eerden, AMJ, Friedrich, H, de Jongh, PE, de Jong, KP: Heterogeneities of the nanostructure of platinum/zeolite Y catalysts revealed by electron tomography. ACS Nano. 7(4), 3698–3705 (2013). doi:10.1021/nn400707p
Yates, TJV, Thomas, JM, Fernandez, J-J, Terasaki, O, Ryoo, R, Midgley, PA: Three-dimensional real-space crystallography of mcm-48 mesoporous silica revealed by scanning transmission electron tomography. Chem. Phys. Lett. 418(4–6), 540–543 (2006). doi:10.1016/j.cplett.2005.11.031
Arslan, I, Walmsley, JC, Rytter, E, Bergene, E, Midgley, PA: Toward three-dimensional nanoengineering of heterogeneous catalysts. J. Am. Chem. Soc. 130(17), 5716–5719 (2008). doi:10.1021/ja710299h
Gilbert, PFC: The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. ii. direct methods. Proc. R. Soc. B. 182(1066), 89–102 (1972). doi:10.1098/rspb.1972.0068
Batenburg, KJ, Bals, S, Sijbers, J, Kübel, C, Midgley, PA, Hernandez, JC, Kaiser, U, Encina, ER, Coronado, EA, Tendeloo, GV: 3d imaging of nanomaterials by discrete tomography. Ultramicroscopy. 109(6), 730–740 (2009). doi:10.1016/j.ultramic.2009.01.009
Goris, B, den Broek, WV, Batenburg, KJ, Mezerji, HH, Bals, S: Electron tomography based on a total variation minimization reconstruction technique. Ultramicroscopy. 113, 120–130 (2012). doi:10.1016/j.ultramic.2011.11.004
Leary, R, Saghi, Z, Midgley, PA, Holland, DJ: Compressed sensing electron tomography. Ultramicroscopy. 131, 70–91 (2013). doi:10.1016/j.ultramic.2013.03.019
Shepp, LA, Logan, BF: The fourier reconstruction of a head section. IEEE Trans. Nucl. Sci. 21(3), 21–43 (1974). doi:10.1109/TNS.1974.6499235
Thévenaz, P: An ImageJ Plugin for the Creation of the Shepp-Logan Phantom. http://bigwww.epfl.ch/thevenaz/shepplogan/
Farrell, D: Radon Transform Plugin for ImageJ. http://imagej.net/plugins/radon-transform.html
Schindelin, J, Arganda-Carreras, I, Frise, E, Kaynig, V, Longair, M, Pietzsch, T, Preibisch, S, Rueden, C, Saalfeld, S, Schmid, B, Tinevez, J-Y, White, DJ, Hartenstein, V, Eliceiri, K, Tomancak, P, Cardona, A: Fiji: an open-source platform for biological-image analysis. Nat Meth. 9(7), 676–682 (2012).
Tosa, Y: Multi Otsu Threshold Plugin for ImageJ. http://imagej.net/plugins/multi-otsu-threshold.html
Liao, P, Chew, T, Chung, P: A fast algorithm for multilevel thresholding. J. Inf. Sci. Eng. 17(5), 713–727 (2001).
Otsu, N: Threshold selection method from gray-level histograms. IEEE Trans. Syst. Man, Cybern. 9(1), 62–66 (1979).
Fernández, J-J, Li, S: An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms. J. Struct. Biol. 144(1-2), 152–161 (2003). doi:10.1016/j.jsb.2003.09.010
Narasimha, R, Aganj, I, Bennett, AE, Borgnia, MJ, Zabransky, D, Sapiro, G, McLaughlin, SW, Milne, JLS, Subramaniam, S: Evaluation of denoising algorithms for biological electron tomography. J. Struct. Biol. 164(1), 7–17 (2008). doi:10.1016/j.jsb.2008.04.006.
Frangakis, AS, Hegerl, R: Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135(3), 239–250 (2001). doi:10.1006/jsbi.2001.4406
Batenburg, KJ, Sijbers, J: Optimal threshold selection for tomogram segmentation by projection distance minimization. IEEE Trans. Med. Imaging. 28(5), 676–686 (2009). doi:10.1109/TMI.2008.2010437
Kawase, N, Kato, M, Nishioka, H, Jinnai, H: Transmission electron microtomography without the “missing wedge” for quantitative structural analysis. Ultramicroscopy. 107(1), 8–15 (2007). doi:10.1016/j.ultramic.2006.04.007
Witten, IH, Frank, E: Data Mining: Practical Machine Learning Tools and Techniques. 2nd edn. Morgan Kaufman, Burlington, Massachusetts, US (2005).
Hall, M, Frank, E, Holmes, G, Pfahringer, B, Reutemann, P, Witten, IH: The WEKA Data Mining Software: An Update. SIGKDD Explor. 11(1), 10–18 (2009).
Sommer, C, Straehle, C, Koethe, U, Hamprecht, FA: Ilastik: Interactive learning and segmentation toolkit. In: Biomedical Imaging: From Nano to Macro, 2011, p. 230,233. IEEE International Symposium on (2011). doi: doi: http://dx.doi.org/10.1109/ISBI.2011.5872394
Breiman, L: Random forests. Mach. Learn. 45(1), 5–32 (2001). doi:10.1023/A:1010933404324
Meyer, F: Topographic distance and watershed lines. Signal Process. 38(1), 113–125 (1994). doi:10.1016/0165-1684(94)90060-4