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The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together…

Computer Vision and Pattern Recognition · Computer Science 2017-04-25 Ke Ye , Lek-Heng Lim

Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…

Computer Vision and Pattern Recognition · Computer Science 2026-02-03 Bintao He , Yiran Cheng , Hongjia Li , Xiang Gao , Xin Gao , Fa Zhang , Renmin Han

Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at…

Applications · Statistics 2017-06-30 Tejal Bhamre , Zhizhen Zhao , Amit Singer

The core theme of X-ray crystallography is reconstructing the electron density distribution of crystals under the constraints of observed diffraction data. Nevertheless, the reconstruction of electron density distribution by straightforward…

Materials Science · Physics 2015-07-14 Hui Li , Meng He , Ze Zhang

Fourier ptychography microscopy (FPM), sharing its roots with synthetic aperture technique and phase retrieval method, is a recently developed computational microscopic super-resolution technique. By turning on the light-emitting diode…

Optics · Physics 2021-05-07 G. Zhou , S. Zhang , C. Zheng , T. Li , Y. Hu , Q. Hao

Single-particle cryo-electron microscopy (cryo-EM) has become a cornerstone of structural biology, enabling near-atomic resolution analysis of macromolecules through advanced computational methods. However, the development of cryo-EM…

Computer Vision and Pattern Recognition · Computer Science 2025-10-07 Runmin Jiang , Genpei Zhang , Yuntian Yang , Siqi Wu , Minhao Wu , Wanyue Feng , Yizhou Zhao , Xi Xiao , Xiao Wang , Tianyang Wang , Xingjian Li , Muyuan Chen , Min Xu

A barrier to realizing the potential of molecules for quantum information science applications is a lack of high-fidelity, single-molecule imaging techniques. Here, we present and theoretically analyze a general scheme for dispersive…

Scanning transmission electron microscopy (STEM) has been extensively used for imaging complex materials down to atomic resolution. The most commonly employed STEM modality, annular dark-field imaging, produces easily-interpretable…

Sequential registering of fluorescence signals in conventional Excitation-Emission Matrices (EEMs), followed by modeling based on multilinear properties of the data, requires stable fluorophore concentrations throughout the acquisition of…

Medical Physics · Physics 2025-02-28 Gabriel Siano , Sofia Mora , Agustina Schenone , Leonardo Giovanini

Quantitative phase imaging (QPI) recovers the exact wavefront of light from the intensity measured by a camera. Topographical maps of translucent microscopic bodies can be extracted from these quantified phase shifts. We demonstrate…

Quantum imaging is an advanced method for microscopy or investigating the optical properties of materials or bio-medical inspections with high accuracy, low noise, and extremely low photo-damage. In previous work, we proposed a quantum…

Optics · Physics 2025-05-09 Mousume Samad , Maki Shimizu , Yasuto Hijikata

Cryo Focused Ion-Beam Scanning Electron Microscopy (cryo FIB-SEM) enables three-dimensional and nanoscale imaging of biological specimens via a slice and view mechanism. The FIB-SEM experiments are, however, limited by a slow (typically,…

We propose and demonstrate a new phase retrieval method for imaging through random media. Although methods to recover the Fourier amplitude through random distortions are well established, recovery of the Fourier phase has been a more…

Optics · Physics 2021-05-14 Byungjae Hwang , Taeseong Woo , Cheolwoo Ahn , Jung-Hoon Park

Photonic quantum technologies utilize various degrees of freedom (DOFs) of light, such as polarization, frequency, and spatial modes, to encode quantum information. In the effort of further improving channel capacity of quantum…

Quantum Physics · Physics 2026-04-30 Roey Shafran , Ron Ziv , Mordechai Segev

The construction industry represents a major sector in terms of resource consumption. Recycled construction material has high reuse potential, but quality monitoring of the aggregates is typically still performed with manual methods.…

Computer Vision and Pattern Recognition · Computer Science 2025-08-06 Yu Zhou , Pelle Thielmann , Ayush Chamoli , Bruno Mirbach , Didier Stricker , Jason Rambach

We report a photoluminescence imaging system for locating single quantum emitters with respect to alignment features. Samples are interrogated in a 4~K closed-cycle cryostat by a high numerical aperture (NA=0.9, 100$\times$ magnification)…

Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream structural biology techniques because of its ability to determine high-resolution structures of dynamic bio-molecules. However, cryo-EM data acquisition…

Machine Learning · Computer Science 2022-04-18 Quanfu Fan , Yilai Li , Yuguang Yao , John Cohn , Sijia Liu , Seychelle M. Vos , Michael A. Cianfrocco

Iterative phase retrieval algorithms typically employ projections onto constraint subspaces to recover the unknown phases in the Fourier transform of an image, or, in the case of x-ray crystallography, the electron density of a molecule.…

Numerical Analysis · Mathematics 2025-10-20 Veit Elser

We demonstrate experimentally and theoretically that a coherent image of a pure phase object may be obtained by use of a spatially incoherent illumination beam. This is accomplished by employing a two-beam source of entangled photons…

Accurately recovering images from phaseless measurements is a challenging and long-standing problem. In this work, we present "deepECpr," which combines expectation-consistent (EC) approximation with deep denoising networks to surpass…

Computer Vision and Pattern Recognition · Computer Science 2024-11-27 Saurav K. Shastri , Philip Schniter