Autocorrelation analysis for cryo-EM with sparsity constraints: Improved sample complexity and projection-based algorithms.

The number of noisy images required for molecular reconstruction in single-particle cryoelectron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly oriented, noisy projection images. In this work, we consider the effect of imposing sparsity priors on the molecule. We use techniques from signal processing, optimization, and applied algebraic geometry to obtain theoretical and computational contributions for this challenging nonlinear inverse problem with sparsity constraints. We prove that molecular structures modeled as sums of Gaussians are uniquely determined by the second-order autocorrelation of their projection images, implying that the sample complexity is proportional to the square of the variance of the noise. This theory improves upon the nonsparse case, where the third-order autocorrelation is required for uniformly oriented particle images and the sample complexity scales with the cube of the noise variance. Furthermore, we build a computational framework to reconstruct molecular structures which are sparse in the wavelet basis. This method combines the sparse representation for the molecule with projection-based techniques used for phase retrieval in X-ray crystallography.

Detecting Non-Overlapping Signals with Dynamic Programming.

This paper studies the classical problem of detecting the locations of signal occurrences in a one-dimensional noisy measurement. Assuming the signal occurrences do not overlap, we formulate the detection task as a constrained likelihood optimization problem and design a computationally efficient dynamic program that attains its optimal solution. Our proposed framework is scalable, simple to implement, and robust to model uncertainties. We show by extensive numerical experiments that our algorithm accurately estimates the locations in dense and noisy environments, and outperforms alternative methods.

An approximate expectation-maximization for two-dimensional multi-target detection.

We consider the two-dimensional multi-target detection (MTD) problem of estimating a target image from a noisy measurement that contains multiple copies of the image, each randomly rotated and translated. The MTD model serves as a mathematical abstraction of the structure reconstruction problem in single-particle cryo-electron microscopy, the chief motivation of this study. We focus on high noise regimes, where accurate detection of image occurrences within a measurement is impossible. To estimate the image, we develop an expectation-maximization framework that aims to maximize an approximation of the likelihood function. We demonstrate image recovery in highly noisy environments, and show that our framework outperforms the previously studied autocorrelation analysis in a wide range of parameters.

Single-particle cryo-electron microscopy: Mathematical theory, computational challenges, and opportunities.

In recent years, an abundance of new molecular structures have been elucidated using cryo-electron microscopy (cryo-EM), largely due to advances in hardware technology and data processing techniques. Owing to these new exciting developments, cryo-EM was selected by Nature Methods as Method of the Year 2015, and the Nobel Prize in Chemistry 2017 was awarded to three pioneers in the field. The main goal of this article is to introduce the challenging and exciting computational tasks involved in reconstructing 3-D molecular structures by cryo-EM. Determining molecular structures requires a wide range of computational tools in a variety of fields, including signal processing, estimation and detection theory, high-dimensional statistics, convex and non-convex optimization, spectral algorithms, dimensionality reduction, and machine learning. The tools from these fields must be adapted to work under exceptionally challenging conditions, including extreme noise levels, the presence of missing data, and massively large datasets as large as several Terabytes. In addition, we present two statistical models: multi-reference alignment and multi-target detection, that abstract away much of the intricacies of cryo-EM, while retaining some of its essential features. Based on these abstractions, we discuss some recent intriguing results in the mathematical theory of cryo-EM, and delineate relations with group theory, invariant theory, and information theory.

Multi-target Detection with an Arbitrary Spacing Distribution.

Motivated by the structure reconstruction problem in single-particle cryo-electron microscopy, we consider the multi-target detection model, where multiple copies of a target signal occur at unknown locations in a long measurement, further corrupted by additive Gaussian noise. At low noise levels, one can easily detect the signal occurrences and estimate the signal by averaging. However, in the presence of high noise, which is the focus of this paper, detection is impossible. Here, we propose two approaches-autocorrelation analysis and an approximate expectation maximization algorithm-to reconstruct the signal without the need to detect signal occurrences in the measurement. In particular, our methods apply to an arbitrary spacing distribution of signal occurrences. We demonstrate reconstructions with synthetic data and empirically show that the sample complexity of both methods scales as SNR-3 in the low SNR regime.

Bispectrum Inversion with Application to Multireference Alignment.

We consider the problem of estimating a signal from noisy circularly-translated versions of itself, called multireference alignment (MRA). One natural approach to MRA could be to estimate the shifts of the observations first, and infer the signal by aligning and averaging the data. In contrast, we consider a method based on estimating the signal directly, using features of the signal that are invariant under translations. Specifically, we estimate the power spectrum and the bispectrum of the signal from the observations. Under mild assumptions, these invariant features contain enough information to infer the signal. In particular, the bispectrum can be used to estimate the Fourier phases. To this end, we propose and analyze a few algorithms. Our main methods consist of non-convex optimization over the smooth manifold of phases. Empirically, in the absence of noise, these non-convex algorithms appear to converge to the target signal with random initialization. The algorithms are also robust to noise. We then suggest three additional methods. These methods are based on frequency marching, semidefinite relaxation and integer programming. The first two methods provably recover the phases exactly in the absence of noise. In the high noise level regime, the invariant features approach for MRA results in stable estimation if the number of measurements scales like the cube of the noise variance, which is the information-theoretic rate. Additionally, it requires only one pass over the data which is important at low signal-to-noise ratio when the number of observations must be large.

Sparse sampling in helical cone-beam CT perfect reconstruction algorithms.

In the current paper we consider the Helical Cone Beam CT. This scanning method exposes the patient to large quantities of radiation and results in very large amounts of data being collected and stored. Both these facts are prime motivators for the development of an efficient, reduced rate, sampling pattern. We calculate bounds on the support in the frequency domain of the collected data and use these to suggest an efficient sampling pattern. A reduction of up to a factor of 2 in sampling rate is suggested. Indeed, we show that reconstruction quality is not affected by this reduction of sampling rates.

Self Fourier shell correlation: properties and application to cryo-ET.

The Fourier shell correlation (FSC) is a measure of the similarity between two signals computed over corresponding shells in the frequency domain and has broad applications in microscopy. In structural biology, the FSC is ubiquitous in methods for validation, resolution determination, and signal enhancement. Computing the FSC usually requires two independent measurements of the same underlying signal, which can be limiting for some applications. Here, we analyze and extend on an approach to estimate the FSC from a single measurement. In particular, we derive the necessary conditions required to estimate the FSC from downsampled versions of a single noisy measurement. These conditions reveal additional corrections which we implement to increase the applicability of the method. We then illustrate two applications of our approach, first as an estimate of the global resolution from a single 3-D structure and second as a data-driven method for denoising tomographic reconstructions in electron cryo-tomography. These results provide general guidelines for computing the FSC from a single measurement and suggest new applications of the FSC in microscopy.

Signal enhancement for two-dimensional cryo-EM data processing.

Different tasks in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM) require enhancing the quality of the highly noisy raw images. To this end, we develop an efficient algorithm for signal enhancement of cryo-EM images. The enhanced images can be used for a variety of downstream tasks, such as two-dimensional classification, removing uninformative images, constructing ab initio models, generating templates for particle picking, providing a quick assessment of the data set, dimensionality reduction, and symmetry detection. The algorithm includes built-in quality measures to assess its performance and alleviate the risk of model bias. We demonstrate the effectiveness of the proposed algorithm on several experimental data sets. In particular, we show that the quality of the resulting images is high enough to produce ab initio models of Å resolution. The algorithm is accompanied by a publicly available, documented, and easy-to-use code.

Self Fourier shell correlation: properties and application to cryo-ET.

The Fourier shell correlation (FSC) is a measure of the similarity between two signals computed over corresponding shells in the frequency domain and has broad applications in microscopy. In structural biology, the FSC is ubiquitous in methods for validation, resolution determination, and signal enhancement. Computing the FSC usually requires two independent measurements of the same underlying signal, which can be limiting for some applications. Here, we analyze and extend on an approach proposed by Koho et al. [1] to estimate the FSC from a single measurement. In particular, we derive the necessary conditions required to estimate the FSC from downsampled versions of a single noisy measurement. These conditions reveal additional corrections which we implement to increase the applicability of the method. We then illustrate two applications of our approach, first as an estimate of the global resolution from a single 3-D structure and second as a data-driven method for denoising tomographic reconstructions in electron cryo-tomography. These results provide general guidelines for computing the FSC from a single measurement and suggest new applications of the FSC in microscopy.

Super-resolution multi-reference alignment.

We study super-resolution multi-reference alignment, the problem of estimating a signal from many circularly shifted, down-sampled and noisy observations. We focus on the low SNR regime, and show that a signal in ℝ M is uniquely determined when the number L of samples per observation is of the order of the square root of the signal's length ( L = O ( M ) ). Phrased more informally, one can square the resolution. This result holds if the number of observations is proportional to 1/SNR3. In contrast, with fewer observations recovery is impossible even when the observations are not down-sampled (L = M). The analysis combines tools from statistical signal processing and invariant theory. We design an expectation-maximization algorithm and demonstrate that it can super-resolve the signal in challenging SNR regimes.

Heterogeneous multireference alignment for images with application to 2-D classification in single particle reconstruction.

Motivated by the task of 2-D classification in single particle reconstruction by cryo-electron microscopy (cryo-EM), we consider the problem of heterogeneous multireference alignment of images. In this problem, the goal is to estimate a (typically small) set of target images from a (typically large) collection of observations. Each observation is a rotated, noisy version of one of the target images. For each individual observation, neither the rotation nor which target image has been rotated are known. As the noise level in cryo-EM data is high, clustering the observations and estimating individual rotations is challenging. We propose a framework to estimate the target images directly from the observations, completely bypassing the need to cluster or register the images. The framework consists of two steps. First, we estimate rotation-invariant features of the images, such as the bispectrum. These features can be estimated to any desired accuracy, at any noise level, provided sufficiently many observations are collected. Then, we estimate the images from the invariant features. Numerical experiments on synthetic cryo-EM datasets demonstrate the effectiveness of the method. Ultimately, we outline future developments required to apply this method to experimental data.