Related papers: Orthogonal Matrix Retrieval in Cryo-Electron Micro…
Phase reconstruction is important in transmission electron microscopy for structural studies. We describe electron Fourier ptychography and its application to phase reconstruction of both radiation-resistant and beam-sensitive materials. We…
We introduce the first learning-based dense matching algorithm, termed Equirectangular Projection-Oriented Dense Kernelized Feature Matching (EDM), specifically designed for omnidirectional images. Equirectangular projection (ERP) images,…
Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting…
One of the challenges in single particle reconstruction in cryo-electron microscopy is to find a three-dimensional model of a molecule using its two-dimensional noisy projection-images. In this paper, we propose a robust "angular…
A novel orthogonalization-free method together with two specific algorithms are proposed to solve extreme eigenvalue problems. On top of gradient-based algorithms, the proposed algorithms modify the multi-column gradient such that earlier…
Symmetric orthogonalization via SVD, and closely related procedures, are well-known techniques for projecting matrices onto $O(n)$ or $SO(n)$. These tools have long been used for applications in computer vision, for example optimal 3D…
In this paper, we propose the SPR (sparse phase retrieval) method, which is a new phase retrieval method for coherent x-ray diffraction imaging (CXDI). Conventional phase retrieval methods effectively solve the problem for high…
Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure…
In the past decade, deep conditional generative models have revolutionized the generation of realistic images, extending their application from entertainment to scientific domains. Single-particle cryo-electron microscopy (cryo-EM) is…
Cryo-electron microscopy (cryo-EM) enables single-particle analysis of biological macromolecules under strict low-dose imaging conditions, but the resulting micrographs often exhibit extremely low signal-to-noise ratios and weak particle…
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…
Conventional 2-D scanning electron microscopy (SEM) is commonly used to rapidly and qualitatively evaluate membrane pore structure. Quantitative 2-D analyses of pore sizes can be extracted from SEM, but without information about 3-D spatial…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…
Ubiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically…
Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically…
We introduce a fast Eikonal Phase Retrieval (EPR) formulation that accelerates eikonal phase retrieval by more than two orders of magnitude while retaining controlled accuracy. The method is derived from a second-order asymptotic expansion…
Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and…
Ewald sphere curvature correction, which extends beyond the projection approximation, stretches the shallow depth of field in cryo-EM reconstructions of thick particles. Here we show that even for previously assumed thin particles,…