Rapid solution of the cryo-EM reconstruction problem by frequency marching
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Abstract: Determining the three-dimensional structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using "single particle" cryo-electron microscopy (cryo-EM) for this purpose. In cryo-EM, hundreds of thousands of two-dimensional images are obtained of individual copies of the same particle, each held in a thin sheet of ice at some unknown orientation. Each image corresponds to the noisy projection of the particle's electron-scattering density. The reconstruction of a high-resolution image from this data is typically formulated as a nonlinear, non-convex optimization problem for unknowns which encode the angular pose and lateral offset of each particle. Since there are hundreds of thousands of such parameters, this leads to a very CPU-intensive task---limiting both the number of particle images which can be processed and the number of independent reconstructions which can be carried out for the purpose of statistical validation. Here, we propose a deterministic method for high-resolution reconstruction that operates in an ab initio manner---that is, without the need for an initial guess. It requires a predictable and relatively modest amount of computational effort, by marching out radially in the Fourier domain from low to high frequency, increasing the resolution by a fixed increment at each step.
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Cites work
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- The exponentially convergent trapezoidal rule
- The kink phenomenon in Fejér and Clenshaw-Curtis quadrature
- The mathematics of computerized tomography
- Three-dimensional structure determination from common lines in cryo-EM by eigenvectors and semidefinite programming
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Cited in
(26)- Iterative hybrid regularization for extremely noisy full models in single particle analysis
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- An automatic particle picking method based on generative adversarial network
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- Hyper-molecules: on the representation and recovery of dynamical structures for applications in flexible macro-molecules in cryo-EM
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- The sample complexity of multireference alignment
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