zbMATH — the first resource for mathematics

Rapid solution of the cryo-EM reconstruction problem by frequency marching. (English) Zbl 1380.92036

MSC:
 92C55 Biomedical imaging and signal processing 94A08 Image processing (compression, reconstruction, etc.) in information and communication theory 65K10 Numerical optimization and variational techniques
Software:
EMan; FREALIGN; RELION; SIMPLE; SPARX; SPIDER
Full Text:
References:
 [1] G. Bao, P. Li, J. Lin, and F. Triki, Inverse scattering problems with multi-frequencies, Inverse Problems, 31 (2015), 093001. · Zbl 1332.78019 [2] J. M. Bell, M. Chen, P. R. Baldwin, and S. J. Ludtke, High resolution single particle refinement in EMAN2.1, Methods, 100 (2016), pp. 25–34. [3] H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, The protein data bank, Nucleic Acids Res., 28 (2000), pp. 235–242, . [4] C. Borges, A. Gillman, and L. Greengard, High resolution inverse scattering in two dimensions using recursive linearization, SIAM J. Imaging Sci., 10 (2017), pp. 641–664, . · Zbl 1371.35027 [5] M. A. Brubaker, A. Punjani, and D. J. Fleet, Building proteins in a day: Efficient 3D molecular reconstruction, IEEE Trans. Pattern Anal. Mach. Intel., 39 (2017), pp. 706–718. [6] Y. Chen, Recursive Linearization for Inverse Scattering, Yale Research Report/DCS/RR-1088, Department of Computer Science, Yale University, New Haven, CT, 1995. [7] Y. Chen, Inverse scattering via Heisenberg’s uncertainty principle, Inverse Problems, 13 (1997), pp. 253–282. · Zbl 0872.35123 [8] Y. Cheng, N. Grigorieff, P. A. Penczek, and T. Walz, A primer to single-particle cryo-electron microscopy, Cell, 161 (2015), pp. 439–449. [9] R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, Reference free structure determination through eigenvectors of center of mass operators, Appl. Comput. Harmon. Anal., 47 (2010), pp. 296–312. · Zbl 1188.81188 [10] Y. Cong, J. A. Kovacs, and W. Wriggers, 2D fast rotational matching for image processing of biophysical data, J. Struct. Biol., 144 (2003), pp. 51–60. [11] N. C. Dvornek, F. J. Sigworth, and H. D. Tagare, SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction, J. Struct. Biol., 190 (2015), pp. 200–214. [12] D. Elmlund and H. Elmlund, SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles, J. Struct. Biol., 180 (2012), pp. 420–427. [13] J. Frank, B. Shimkin, and H. Dowse, SPIDER—a modular software system for electron image processing, Ultramicroscopy, 6 (1981), pp. 343–358. [14] A. B. Goncharov, Methods of integral geometry and the determination of the mutual orientation of identical particles arbitrarily arranged in a plane from their projections on a line, Dokl. Akad. Nauk SSSR, 293 (1987), pp. 355–358 (in Russian). [15] A. B. Goncharov and M. S. Gelfand, Determination of mutual orientation of identical particles from their projections by the moments method, Ultramicroscopy, 25 (1988), pp. 317–328. [16] L. Greengard and J.-Y. Lee, Accelerating the nonuniform fast Fourier transform, SIAM Rev., 46 (2004), pp. 443–454, . · Zbl 1064.65156 [17] N. Grigorieff, FREALIGN: High-resolution refinement of single particle structures, J. Struct. Biol., 157 (2007), pp. 117–125. [18] N. Grigorieff, Frealign: An exploratory tool for single-particle cryo-EM, in The Resolution Revolution: Recent Advances in cryoEM, Methods in Enzymology 579, R. A. Crowther, ed., Academic Press, New York, 2016, pp. 191–226. [19] R. Henderson, Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise, Proc. Natl. Acad. Sci. U.S.A., 110 (2013), pp. 18037–18041. [20] R. Henderson, A. Sali, M. L. Baker, B. Carragher, B. Devkota, K. H. Downing, E. H. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. J. Ludtke, O. Medalia, P. A. Penczek, P. B. Rosenthal, M. G. Rossmann, M. F. Schmid, G. F. Schröder, A. C. Steven, D. L. Stokes, J. D. Westbrook, W. Wriggers, H. Yang, J. Young, H. M. Berman, W. Chiu, G. J. Kleywegt, and C. L. Lawson, Outcome of the first electron microscopy validation task force meeting, Structure, 20 (2012), pp. 205–214. [21] J. B. Heymann, Validation of 3D EM reconstructions: The phantom in the noise, AIMS Biophys., 2 (2015), pp. 21–35. [22] M. Hohn, G. Tang, G. Goodyear, P. Baldwin, Z. Huang, P. Penczek, C. Yang, R. Glaeser, P. Adams, and S. Ludtke, Sparx, a new environment for cryo-em image processing, J. Struct. Biol., 157 (2007), pp. 47–55. [23] P. Joubert and M. Habeck, Bayesian inference of initial models in cryo-electron microscopy using pseudo-atoms, Biophysical Journal, 108 (2015), pp. 1165–1175. [24] L. Joyeux and P. A. Penczek, Efficiency of 2D alignment methods, Ultramicroscopy, 92 (2002), pp. 33–46. [25] D. Kimanius, B. O. Forsberg, S. H. Scheres, and E. Lindehl, Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-\textup2, eLife, 5 (2016), e18722. [26] D. Lyumkis, A. F. Brilot, D. L. Theobald, and N. Grigorieff, Likelihood-based classification of cryo-EM images using FREALIGN, J. Struct. Biol., 183 (2013), pp. 377–388. [27] J. L. S. Milne, M. J. Borgnia, A. Bartesaghi, E. E. H. Tran, L. A. Earl, D. M. Schauder, J. Lengyel, J. Pierson, A. Patwardhan, and S. Subramaniam, Cryo-electron microscopy—a primer for the non-microscopist, FEBS J., 280 (2013), pp. 28–45. [28] J. A. Mindell and N. Grigorieff, Accurate determination of local defocus and specimen tilt in electron microscopy, J. Struct. Biol., 142 (2003), pp. 334–347. [29] F. Natterer, The Mathematics of Computerized Tomography, Classics Appl. Math. 21, SIAM, Philadelphia, 2001, . · Zbl 0973.92020 [30] E. Nogales, The development of cryo-EM into a mainstream structural biology technique, Nature Methods, 13 (2016), pp. 24–27. [31] P. Penczek, M. Radermacher, and J. Frank, Three-dimensional reconstruction of single particles embedded in ice, Ultramicroscopy, 40 (1992), pp. 33–53. [32] P. A. Penczek, Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State, Oxford University Press, Oxford, UK, 2006. [33] P. A. Penczek, Resolution measures in molecular electron microscopy, Methods Enzymol., 482 (2010), pp. 73–100. [34] P. A. Penczek, R. A. Grassucci, 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 (1994), pp. 251–270. [35] P. A. Penczek, J. Zhu, and J. Frank, A common-lines based method for determining orientations for $$N>3$$ particle projections simultaneously, Ultramicroscopy, 63 (1996), pp. 205–218. [36] S. W. Provencher and R. H. Vogel, Three-dimensional reconstruction from electron micrographs of disordered specimens I. Method, Ultramicroscopy, 25 (1988), pp. 209–221. [37] P. B. Rosenthal and J. L. Rubinstein, Validating maps from single particle electron cryomicroscopy, Current Opinion Struct. Biol., 34 (2015), pp. 135–144. [38] E. Sanz-García, A. B. Stewart, and D. M. Belnap, The random-model method enables ab initio three-dimensional reconstruction of asymmetric particles and determination of particle symmetry, J. Struct. Biol., 171 (2010), pp. 216–222. [39] S. H. W. Scheres, A Bayesian view on cryo-EM structure determination, J. Mol. Biol., 415 (2012), pp. 406–418. [40] S. H. W. Scheres, RELION: Implementation of a Bayesian approach to cryo-EM structure determination, J. Struct. Biol., 180 (2012), pp. 519–530. [41] S. H. W. Scheres, M. Valle, P. Grob, E. Nogales, and J.-M. Carazo, Maximum likelihood refinement of electron microscopy data with normalization errors, J. Struct. Biol., 166 (2009), pp. 234–240. [42] Y. Shkolnisky and A. Singer, Viewing direction estimation in cryo-EM using synchronization, SIAM J. Imaging Sci., 5 (2012), pp. 1088–1110, . · Zbl 1254.92058 [43] F. J. Sigworth, A maximum-likelihood approach to single-particle image refinement, J. Struct. Biol., 122 (1998), pp. 328–339. [44] F. J. Sigworth, P. C. Doerschuk, J.-M. Carazo, and S. H. W. Scheres, An introduction to maximum-likelihood methods in cryo-EM, in Cryo-EM, Part B: 3D Reconstruction, Methods in Enzymology 482, G. J. Jensen, Academic Press, New York, 2010, pp. 263–294. [45] A. Singer, R. R. Coifman, F. J. Sigworth, D. W. Chester, and Y. Shkolnisky, Detecting consistent common lines in cryo-EM by voting, J. Struct. Biol., 169 (2009), pp. 312–322. [46] A. Singer and Y. Shkolnisky, Three-dimensional structure determination from common lines in cryo-EM by eigenvectors and semidefinite programming, SIAM J. Imaging Sci., 4 (2011), pp. 543–572, . · Zbl 1216.92045 [47] G. Tang, L. Peng, P. Baldwin, D. Mann, W. Jiang, I. Rees, and S. Ludtke, EMAN2: An extensible image processing suite for electron microscopy, J. Struct. Biol., 157 (2007), pp. 38–46. [48] L. N. Trefethen and J. A. C. Weideman, The exponentially convergent trapezoidal rule, SIAM Rev., 56 (2014), pp. 385–458, . · Zbl 1307.65031 [49] B. Vainshtein and A. Goncharov, Determination of the spatial orientation of arbitrary arranged identical particles of an unknown structure from their projections, in Proceedings of the 11th International Congress on Electron Microscopy, Kyoto, Japan, 1986, pp. 459–460. [50] M. van Heel, Angular reconstruction: A posteriori assignment of projection directions for 3D reconstruction, Ultramicroscopy, 21 (1987), pp. 111–123. [51] M. van Heel, E. V. Orlova, G. Harauz, H. Stark, P. Dube, F. Zemlin, and M. Schatz, Angular reconstitution in three-dimensional electron microscopy: Historical and theoretical aspects, Scanning Microscopy, 11 (1997), pp. 195–210. [52] K. R. Vinothkumar and R. Henderson, Single particle electron cryomicroscopy: Trends, issues and future perspective, Quart. Rev. Biophys., 49 (2016), e13. [53] R. H. Vogel and S. W. Provencher, Three-dimensional reconstruction from electron micrographs of disordered specimens II. Implementation and results, Ultramicroscopy, 25 (1988), pp. 223–240. [54] R. H. Wade, A brief look at imaging and contrast transfer, Ultramicroscopy, 46 (1992), pp. 145–156. [55] L. Wang, A. Singer, and Z. Wen, Orientation determination of cryo-EM images using least unsquared deviations, SIAM J. Imaging Sci., 6 (2013), pp. 2450–2483, . · Zbl 1402.92449 [56] J. A. C. Weideman and L. N. Trefethen, The kink phenomenon in Fejér and Clenshaw–Curtis quadrature, Numer. Math., 107 (2007), pp. 707–727. · Zbl 1142.41010
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.