Related papers: Cryo-EM as a Stochastic Inverse Problem
An efficient computational approach for optimal reconstruction of binary-type images suitable for models in various applications including biomedical imaging is developed and validated. The methodology includes derivative-free optimization…
We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain $2n \times n$ matrix storing properly-scaled basis vectors for the…
We report a multiscale approach of broad applicability to stochastic reconstruction of multiphase materials, including porous ones. The approach devised uses an optimization method, such as the simulated annealing (SA) and the so-called…
We introduce the EMC algorithm for reconstructing a particle's 3D diffraction intensity from very many photon shot-noise limited 2D measurements, when the particle orientation in each measurement is unknown. The algorithm combines a…
Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron…
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single-particle nature, it has the potential to provide…
We present a geometry-aware method for heterogeneous single-particle cryogenic electron microscopy (cryo-EM) reconstruction that predicts atomic backbone conformations. To incorporate protein-structure priors, we represent the backbone as a…
We introduce a probabilistic approach to ptychographic reconstruction in computational imaging. Ptychography is an imaging method where the complex amplitude of an object is estimated from a sequence of diffraction measurements. We…
A multi-scale approach to the inverse reconstruction of a pattern's microstructure is reported. Instead of a correlation function, a pair of entropic descriptors (EDs) is proposed for stochastic optimization method. The first of them…
Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological…
The Expectation Maximization (EM) algorithm is a key reference for inference in latent variable models; unfortunately, its computational cost is prohibitive in the large scale learning setting. In this paper, we propose an extension of the…
The Expectation Maximization (EM) algorithm is of key importance for inference in latent variable models including mixture of regressors and experts, missing observations. This paper introduces a novel EM algorithm, called…
We propose a framework to jointly determine the deformation parameters and reconstruct the unknown volume in electron cryotomography (CryoET). CryoET aims to reconstruct three-dimensional biological samples from two-dimensional projections.…
Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…
Nowadays, modern electron microscopes deliver images at atomic scale. The precise atomic structure encodes information about material properties. Thus, an important ingredient in the image analysis is to locate the centers of the atoms…
Electron microscopy has enabled many scientific breakthroughs across multiple fields. A key challenge is the tuning of microscope parameters based on images to overcome optical aberrations that deteriorate image quality. This calibration…
Computational image reconstruction algorithms generally produce a single image without any measure of uncertainty or confidence. Regularized Maximum Likelihood (RML) and feed-forward deep learning approaches for inverse problems typically…
In this paper, we describe and study a mathematical framework for cryo-elecron microscopy. The main result, is a a proof of the admissability (correctness) and the numerical stability of the intrinsic reconstitution algorithm which was…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
Background: Single-particle cryo-electron microscopy (cryo-EM) has become a popular tool for structural determination of biological macromolecular complexes. High-resolution cryo-EM reconstruction often requires hundreds of thousands of…