Structural variability from noisy tomographic projections

DOI10.1137/17M1153509MaRDI QIDQ4689767zbMATH OpenDBLPWikidataFDO

Authors Joakim Andén, A. Singer

Publication date 17 October 2018

Published in SIAM Journal on Imaging Sciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1710.09791

zbMATH Keywords

conjugate gradientcryo-electron microscopydeconvolutionheterogeneityprincipal component analysisshift invariancesingle-particle reconstructionToeplitz matrices

Mathematics Subject Classification ID

Radon transform (44A12) Nonparametric estimation (62G05) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Numerical methods for inverse problems for integral equations (65R32) Computing methodologies for image processing (68U10) Biomedical imaging and signal processing (92C55)

Abstract: In cryo-electron microscopy, the 3D electric potentials of an ensemble of molecules are projected along arbitrary viewing directions to yield noisy 2D images. The volume maps representing these potentials typically exhibit a great deal of structural variability, which is described by their 3D covariance matrix. Typically, this covariance matrix is approximately low-rank and can be used to cluster the volumes or estimate the intrinsic geometry of the conformation space. We formulate the estimation of this covariance matrix as a linear inverse problem, yielding a consistent least-squares estimator. For $n$ images of size $N$-by-$N$ pixels, we propose an algorithm for calculating this covariance estimator with computational complexity $mathcalO(n{N}^4+sqrtkappa{N}^{6}logN)$, where the condition number $kappa$ is empirically in the range $10$--$200$. Its efficiency relies on the observation that the normal equations are equivalent to a deconvolution problem in 6D. This is then solved by the conjugate gradient method with an appropriate circulant preconditioner. The result is the first computationally efficient algorithm for consistent estimation of 3D covariance from noisy projections. It also compares favorably in runtime with respect to previously proposed non-consistent estimators. Motivated by the recent success of eigenvalue shrinkage procedures for high-dimensional covariance matrices, we introduce a shrinkage procedure that improves accuracy at lower signal-to-noise ratios. We evaluate our methods on simulated datasets and achieve classification results comparable to state-of-the-art methods in shorter running time. We also present results on clustering volumes in an experimental dataset, illustrating the power of the proposed algorithm for practical determination of structural variability.

Recommendations

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Cited in

(15)

• On the choice of high-dimensional regression parameters in Gaussian random tomography
• A max-cut approach to heterogeneity in cryo-electron microscopy
• Method of moments for 3D single particle \textit{ab initio} modeling with non-uniform distribution of viewing angles
• Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM
• Multitaper estimation on arbitrary domains
• Matrix denoising for weighted loss functions and heterogeneous signals
• Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes
• Covariance matrix estimation for the cryo-EM heterogeneity problem
• Spectral decomposition of atomic structures in heterogeneous cryo-EM
• Estimation under group actions: recovering orbits from invariants
• Deep neural-network prior for orbit recovery from method of moments
• Geometric shape matching for recovering protein conformations from single-particle cryo-EM data
• Computerized tomography and reproducing kernels
• A transversality theorem for semi-algebraic sets with application to signal recovery from the second moment and cryo-EM
• Sparse approximations of protein structure from noisy random projections

Describes a project that uses

Uses Software

• cryoSPARC
• RELION
• FREALIGN
• mftoolbox

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