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We consider the problem of estimating an unbiased and reference-free ab-inito model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment…

Quantitative Methods · Quantitative Biology 2018-10-30 Ido Greenberg , Yoel Shkolnisky

This work is concerned with fan- and cone-beam computed tomography with circular source trajectory, where the reconstruction inverse problem requires an accurate knowledge of source, detector and rotational axis relative positions and…

Numerical Analysis · Mathematics 2024-05-09 Patricio Guerrero , Simon Bellens , Ricardo Santander , Wim Dewulf

Topo-Tomography (TT) is a synchrotron-based X-ray diffraction imaging technique used to characterize grain shape and crystal orientation in polycrystalline samples. This work aims to provide a decisive and fundamental understanding of 3D…

Computational Physics · Physics 2025-10-13 Zheheng Liu , Nicola Vigano , Henry Proudhon , Wolfgang Ludwig

This paper addresses the deconvolution of an image that has been obtained by superimposing many copies of an underlying unknown image of interest. The superposition is assumed to not be exact due to noise, and is described using an error…

Numerical Analysis · Mathematics 2007-10-04 Wooram Park , Daniel N. Rockmore , Dean Madden , Gregory S. Chirikjian

We introduce a new rotationally invariant viewing angle classification method for identifying, among a large number of Cryo-EM projection images, similar views without prior knowledge of the molecule. Our rotationally invariant features are…

Biomolecules · Quantitative Biology 2014-03-19 Zhizhen Zhao , Amit Singer

Accurate pose estimation and shift correction are key challenges in cryo-EM due to the very low SNR, which directly impacts the fidelity of 3D reconstructions. We present an approach for pose estimation in cryo-EM that leverages…

Computer Vision and Pattern Recognition · Computer Science 2025-07-22 Kaishva Chintan Shah , Virajith Boddapati , Karthik S. Gurumoorthy , Sandip Kaledhonkar , Ajit Rajwade

Both a good understanding of geometrical concepts and a broad familiarity with objects lead to our excellent perception of moving objects. The human ability to detect and segment moving objects works in the presence of multiple objects,…

Computer Vision and Pattern Recognition · Computer Science 2022-03-02 Pia Bideau , Erik Learned-Miller , Cordelia Schmid , Karteek Alahari

Single particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution 3-D structure of biological macromolecules from many noisy and randomly oriented projection images. One notable…

Biomolecules · Quantitative Biology 2024-01-30 Andy Zhang , Oscar Mickelin , Joe Kileel , Eric J. Verbeke , Nicholas F. Marshall , Marc Aurèle Gilles , Amit Singer

Coherent diffraction imaging (CDI) for visualizing objects at atomic resolution has been realized as a promising tool for imaging single molecules. Drawbacks of CDI are associated with the difficulty of the numerical phase retrieval from…

We study diffraction of twisted matter waves (electrons and light ions carrying orbital angular momentum $\ell/\hbar=0,\pm1,\pm2,\ldots$ by circular and triangular apertures. Within the scalar Kirchhoff-Fresnel framework, circular apertures…

Quantum Physics · Physics 2026-04-22 Maksim Maksimov , Nikita Borodin , Daria Kargina , Dmitry Naumov , Dmitry Karlovets

Diffraction tomography aims to recover an object's scattering potential from measured wave fields. In the classical setting, the object is illuminated by plane waves from many directions, and the Fourier diffraction theorem provides a…

Numerical Analysis · Mathematics 2026-03-11 Peter Elbau , Noemi Naujoks

Rotational symmetry is a defining feature of many tomography systems, including computed tomography (CT) and emission computed tomography (ECT), where detectors are arranged in a circular or periodically rotating configuration. This study…

Medical Physics · Physics 2025-02-05 Yaogong Zhang , Fang-Fang Yin , Lei Zhang

Shape reconstruction techniques using structured light have been widely researched and developed due to their robustness, high precision, and density. Because the techniques are based on decoding a pattern to find correspondences, it…

Computer Vision and Pattern Recognition · Computer Science 2017-10-03 Ryo Furukawa , Ryusuke Sagawa , Hiroshi Kawasaki

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

Optical diffraction tomography is an indispensable tool for studying objects in three-dimensions due to its ability to accurately reconstruct scattering objects. Until now this technique has been limited to coherent light because spatial…

The propagation of light in moving media is dragged by atomic motion. The light-drag effect can be dramatically enhanced by reducing the group velocity with electro-magnetically induced transparency (EIT). We develop a systematic procedure…

Atomic Physics · Physics 2022-05-24 Yuzhuo Wang , Jian Zhao , Xing Huang , Liyang Qiu , Lingjing Ji , Yudi Ma , Yizun He , James P. Sobol , Saijun Wu

Magnetic Resonance Imaging (MRI) is highly susceptible to motion artifacts due to the extended acquisition times required for k-space sampling. These artifacts can compromise diagnostic utility, particularly for dynamic imaging. We propose…

Image and Video Processing · Electrical Eng. & Systems 2025-07-04 Frederic Wang , Jonathan I. Tamir

Most motion deblurring algorithms rely on spatial-domain convolution models, which struggle with the complex, non-linear blur arising from camera shake and object motion. In contrast, we propose a novel single-image deblurring approach that…

Image and Video Processing · Electrical Eng. & Systems 2025-01-23 Wang Pang , Zhihao Zhan , Xiang Zhu , Yechao Bai

A main task in cryo-electron microscopy single particle reconstruction is to find a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm for…

Computational Physics · Physics 2022-11-11 Adi Shasha Geva , Yoel Shkolnisky

The non-linear transformations incurred by the rays in an optical system can be suitably described by matrices to any desired order of approximation. In systems composed of uniform refractive index elements, each individual ray refraction…

Optics · Physics 2009-11-10 Jose B. Almeida