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With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
Knowledge gained through X-ray crystallography fostered structural determination of materials and greatly facilitated the development of modern science and technology in the past century. Atomic details of sample structures is achievable by…
Building on top of our recent work [arXiv:2502.08511], we introduce a new strategy to solve the problem of detecting atoms in high-resolution images of microtrap arrays. By alternating estimation and detection steps, we get rid of the need…
An image super-resolution method from multiple observation of low-resolution images is proposed. The method is based on sub-pixel accuracy block matching for estimating relative displacements of observed images, and sparse signal…
Dual-energy X-ray tomography is considered in a context where the target under imaging consists of two distinct materials. The materials are assumed to be possibly intertwined in space, but at any given location there is only one material…
A basic principle in crystal structure determination is that there should be proper distances between adjacent atoms. Therefore, detection of atom bumping is of fundamental significance in structure determination, especially in the direct…
In this paper we propose a global optimization-based approach to jointly matching a set of images. The estimated correspondences simultaneously maximize pairwise feature affinities and cycle consistency across multiple images. Unlike…
This work is concerned with applying iterative image reconstruction, based on constrained total-variation minimization, to low-intensity X-ray CT systems that have a high sampling rate. Such systems pose a challenge for iterative image…
Fluorescence microscopy is essential in biological and medical research, providing critical insights into cellular structures. However, limited by optical diffraction and background noise, a substantial amount of hidden information is still…
In this work, we introduce an original self-consistent scheme based on the one-body reduced density matrix ($\gamma$) formalism. A significant feature of this methodology is the utilization of an optimal unitary transformation of the…
Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing of hundreds of thousands (or more) of images that contain very few x-rays. Each low-flux image of the diffraction pattern is…
The local arrangement of atoms is one of the most important predictors of mechanical and functional properties of materials. However, algorithms for identifying the geometrical arrangements of atoms in complex materials systems are lacking.…
A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. chemical…
In the context of assessing and characterizing structures in X-ray images, we compare different approaches. Most often the intensity level is very low and necessitates a special treatment of Poisson statistics. The method based on wavelet…
The missing phase problem in X-ray crystallography is commonly solved using the technique of molecular replacement, which borrows phases from a previously solved homologous structure, and appends them to the measured Fourier magnitudes of…
Serial crystallography experiments routinely produce thousands of diffraction patterns from crystals in random orientations. To turn this stream of images into a usable dataset, each pattern must be indexed before integration and merging…
Conservative mass limits are often imposed on the dark matter halo catalogues extracted from N-body simulations. By comparing simulations with different mass resolutions, at $z=0$ we find that even for halos resolved by 100 particles, the…
The projected gravitational potential of galaxy clusters is reflected in both their X-ray emission and their imprint on the images of background sources due to their gravitational lensing effects. Since these projections of the potential…
Volumetric crystal structure indexing and orientation mapping are key data processing steps for virtually any quantitative study of spatial correlations between the local chemistry and the microstructure of a material. For electron and…
A novel method, termed Reduced Dimensionality Cluster Identification, RDCI, is presented, for the identification and quantitative description of clusters formed by N objects in three dimensional space. The method consists of finding a path,…