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Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…

Computer Vision and Pattern Recognition · Computer Science 2017-04-11 Roy R. Lederman , Amit Singer

Holography relies on the interference between a known reference and a signal of interest to reconstruct both the amplitude and phase of that signal. Commonly performed with photons and electrons, it finds numerous applications in imaging,…

Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to…

Machine Learning · Statistics 2015-01-29 Ali Punjani , Marcus A. Brubaker

Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each…

Data Analysis, Statistics and Probability · Physics 2015-06-17 Kartik Ayyer , Hugh T. Philipp , Mark W. Tate , Veit Elser , Sol M. Gruner

Direct detector device (DDD) cameras have revolutionized single particle electron cryomicroscopy (cryo-EM). In addition to an improved camera detective quantum efficiency, acquisition of DDD movies allows for correction of movement of the…

Quantitative Methods · Quantitative Biology 2015-11-23 John L. Rubinstein , Marcus A. Brubaker

A major challenge in single-particle cryo-electron microscopy (cryo-EM) is that the orientations adopted by the 3D particles prior to imaging are unknown; yet, this knowledge is essential for high-resolution reconstruction. We present a…

Machine Learning · Computer Science 2021-04-14 Jelena Banjac , Laurène Donati , Michaël Defferrard

Phase recovery from intensity-only measurements forms the heart of coherent imaging techniques and holography. Here we demonstrate that a neural network can learn to perform phase recovery and holographic image reconstruction after…

Computer Vision and Pattern Recognition · Computer Science 2017-12-13 Yair Rivenson , Yibo Zhang , Harun Gunaydin , Da Teng , Aydogan Ozcan

An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single…

For many complex materials systems, low-energy electron microscopy (LEEM) offers detailed insights into morphology and crystallography by naturally combining real-space and reciprocal-space information. Its unique strength, however, is that…

Fourier ptychographic microscopy (FPM) is a pivotal computational imaging technique that achieves phase and amplitude reconstruction with high resolution and wide field of view, using low numerical aperture objectives and LED array…

This paper introduces a new multiplane CGH computation method to reconstruct artefact-free high-quality holograms with natural-looking defocus blur. Our method introduces a new targeting scheme and a new loss function. While the targeting…

Computer Vision and Pattern Recognition · Computer Science 2023-02-08 Koray Kavaklı , Yuta Itoh , Hakan Urey , Kaan Akşit

We present energy-resolved photoelectron momentum maps for orbital tomography that have been collected with a novel and efficient time-of-flight momentum microscopy setup. This setup is combined with a 0.5 MHz table-top femtosecond…

We study the convolutional phase retrieval problem, of recovering an unknown signal $\mathbf x \in \mathbb C^n $ from $m$ measurements consisting of the magnitude of its cyclic convolution with a given kernel $\mathbf a \in \mathbb C^m $.…

Computation · Statistics 2019-10-08 Qing Qu , Yuqian Zhang , Yonina C. Eldar , John Wright

Objective: Quantitative technique based on In-line phase-contrast computed tomography with single scanning attracts more attention in application due to the flexibility of the implementation. However, the quantitative results usually suffer…

Medical Physics · Physics 2022-06-13 Suyu Liao , Shiwo Deng , Yining Zhu , Huitao Zhang , Peiping Zhu , Kai Zhang , Xing Zhao

In this study we explore the possibility to use deep learning for the reconstruction of phase images from 4D scanning transmission electron microscopy (4D-STEM) data. The process can be divided into two main steps. First, the complex…

Materials Science · Physics 2023-02-15 Thomas Friedrich , Chu-Ping Yu , Jo Verbeeck , Sandra Van Aert

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple…

Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As…

Computer Vision and Pattern Recognition · Computer Science 2018-08-06 Ayelet Heimowitz , Joakim Andén , Amit Singer

The manipulation and control of nanoscale magnetic spin textures is of rising interest as they are potential foundational units in next-generation computing paradigms. Achieving this requires a quantitative understanding of the spin texture…

Absorption imaging is a commonly adopted method to acquire, with high temporal resolution, spatial information on a partially transparent object. It relies on the interference between a probe beam and the coherent response of the object. In…