References
- D.P. Bertsekas. Nonlinear Programming. Athena Scientific, Belmont, 1999.
- J.F. Cai, R. Chan and Z. Shen. A framelet-based image inpainting algorithm. Appl. Comput. Harmon. Anal., 24(2):131–149, 2008. http://dx.doi.org/10.1016/j.acha.2007.10.002.
- J.F. Cai, H. Ji, C. Liu and Z. Shen. Blind motion deblurring from a single image using sparse approximation. In Computer Vision and Pattern Recognition, 2009, pp. 104–111, 2009.
- J.F. Cai, S. Osher and Z. Shen. Split bregman methods and frame based image restoration. Multiscale Model. Simul. SIAM Interdiscip. J., 8(2):337–369, 2009. http://dx.doi.org/10.1137/090753504.
- R.A. Crowther. Procedures for three-dimensional reconstruction of spherical viruses by fourier synthesis from electron micrographs. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 261(837):221–230, 1971. http://dx.doi.org/10.1098/rstb.1971.0054.
- R.A. Crowther, D.J. DeRosier and A. Klug. The reconstruction of a three- dimensional structure from projections and its application to electron microscopy. Proc. Roy. Soc., Ser. A, 317(1530):319–340, 1970. http://dx.doi.org/10.1098/rspa.1970.0119.
- I. Daubechies, M. Defrise and C. DeMol. An iterative thresholding algorithm for linear inverse problems with a sparsity constraint. Comm. Pure Appl. Math, 57(11):1413–1457, 2004. http://dx.doi.org/10.1002/cpa.20042.
- D.J. DeRosier and A. Klug. Reconstruction of three dimensional structures from electron micrographs. Nature, 217(5124):130–134, 1968. http://dx.doi.org/10.1038/217130a0.
- B. Dong, A. Chien, Z. Shen and S. Osher. A new multiscale representation for shapes and its application to blood vessel recovery. SIAM J. Sci. Comput., 32(4):1724–1739, 2010. http://dx.doi.org/10.1137/09076043X.
- B. Dong, H. Ji, J. Li, Z. Shen and Y. Xu. Wavelet frame based blind image inpainting. Appl. Comput. Harmon. Anal., 32(2):268–279, 2012. http://dx.doi.org/10.1016/j.acha.2011.06.001.
- B. Dong, J. Li and Z. Shen. X-ray CT image reconstruction via wavelet frame based regularization and radon domain inpainting. J. Sci. Comput., 54(2-3):333–349, 2013. http://dx.doi.org/10.1007/s10915-012-9579-6.
- J. Frank. Electron Tomography Methods for Three-Dimensional Visualization of Structures in the Cell. Springer, New York, second edition, 2006.
- J. Frank. Three-dimensional electron microscopy of macromolecular assemblies. Oxford University Press, New York, 2006.
- S.D. Fuller, S.J Butcher, R.H. Cheng and T.S. Baker. Three-dimensional reconstruction of icosahedral particles—the uncommon line. J. Struct. Biol., 116(1):48–55, 1996. http://dx.doi.org/10.1006/jsbi.1996.0009.
- N. Grigorieff. Frealign: High-resolution refinement of single particle structures. J. Struct. Biol., 157(1):117–125, 2007. http://dx.doi.org/10.1016/j.jsb.2006.05.004.
- M.V. Heel. Angular reconstruction: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy, 21(2):111–124, 1987. http://dx.doi.org/10.1016/0304-3991(87)90078-7.
- M.V. Heel, B. Gowen, R. Matadeen, E.V. Orlova, R. Finn, T. Pape, D. Cohen, H. Stark, R. Schmidt, M. Schatz and A. Patwardhan. Single-particle electron cryo-microscopy: towards atomic resolution. Q. Rev. Biophys., 33(4):307–369, 2000. http://dx.doi.org/10.1017/S0033583500003644.
- W.C. Lau and J.L. Rubinstein. Subnanometre-resolution structure of the intact Thermus thermophilus H + -driven ATP synthase. nature, 481(7380):214–219, 2012.
- M. Li, Z. Fan, H. Ji and Z. Shen. Wavelet frame based algorithm for 3d reconstruction in electron microscopy. SIAM J. Sci. Comput., 36(1):B45–B69, 2014. http://dx.doi.org/10.1137/130914474.
- M. Li, G. Xu, C. O.S. Sorzano, F. Sun and C. L. Bajaj. Single-particle reconstruction using L2-gradient flow. J. Struct. Biol., 176:259–267, 2011. http://dx.doi.org/10.1016/j.jsb.2011.08.005.
- S.J. Ludtke, P.R. Baldwin and W. Chiu. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol., 128(1):82–97, 1999. http://dx.doi.org/10.1006/jsbi.1999.4174.
- J.A. Nelder and R. Mead. A simplex method for function minimization. Comput. J., 7:308–313, 1965. http://dx.doi.org/10.1093/comjnl/7.4.308.
- P.A. Penczek, R.A. Grasucci and J. Frank. The ribosome at improved resolution: New techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy, 53(3):251–270, 1994.
- H.R. Saibil. Macromolecular structure determination by cryo-electron microscopy. Acta Cryst. D, 56(1):1215–1222, 2000. http://dx.doi.org/10.1107/S0907444900010787.
- C.O.S. Sorzano, R. Marabini, J. Velázquez-Muriel, J.R. Bilbao-Castro, S.H.W. Scheres, J.M. Carazo and A. Pascual-Montano. Xmipp: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol., 148(2):194–204, 2004. http://dx.doi.org/10.1016/j.jsb.2004.06.006.