Structural variability from noisy tomographic projections

Joakim Andén, Amit Singer

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


In cryo-electron microscopy, the three-dimensional (3D) electric potentials of an ensemble of molecules are projected along arbitrary viewing directions to yield noisy two-dimensional 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 (Fomrula presented), where the condition number k is empirically in the range 10-200. Its efficiency relies on the observation that the normal equations are equivalent to a deconvolution problem in six dimensions. 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 the 3D covariance from noisy projections. It also compares favorably in runtime with respect to previously proposed nonconsistent estimators. Motivated by the recent success of eigenvalue shrinkage procedures for high-dimensional covariance matrix estimation, we incorporate 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.

Original languageEnglish (US)
Pages (from-to)1441-1492
Number of pages52
JournalSIAM Journal on Imaging Sciences
Issue number2
StatePublished - 2018

All Science Journal Classification (ASJC) codes

  • Applied Mathematics
  • Mathematics(all)


  • Conjugate gradient
  • Cryo-electron microscopy
  • Deconvolution
  • Heterogeneity
  • Principal component analysis
  • Shift invariance
  • Single-particle reconstruction
  • Toeplitz matrices


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