Young's double-slit interference with single hard X-ray photons.

Double-slit interference experiments using monochromatic hard X-rays with the energy of 25 keV are presented. The experiments were performed at a synchrotron source with a distance of 110 m between the interferometer and the detector to produce an interference pattern with a sufficiently broad period that could be adequately sampled by a photon-counting detector with 75 micrometre pixels. In the single-particle version of the experiment, over one million image frames with a single registered photon in each one were collected.

Signal-to-noise and spatial resolution in in-line imaging. 1. Basic theory, numerical simulations and planar experimental images.

Signal-to-noise ratio and spatial resolution are quantitatively analysed in the context of in-line (propagation based) X-ray phase-contrast imaging. It is known that free-space propagation of a coherent X-ray beam from the imaged object to the detector plane, followed by phase retrieval in accordance with Paganin's method, can increase the signal-to-noise in the resultant images without deteriorating the spatial resolution. This results in violation of the noise-resolution uncertainty principle and demonstrates `unreasonable' effectiveness of the method.

Propagation-based phase-contrast imaging of the breast: image quality and the effect of X-ray energy and radiation dose.

Objectives: Propagation-based phase-contrast computed tomography (PB-CT) is a new imaging technique that exploits refractive and absorption properties of X-rays to enhance soft tissue contrast and improve image quality. This study compares image quality of PB-CT and absorption-based CT (AB-CT) for breast imaging while exploring X-ray energy and radiation dose.

Methods: Thirty-nine mastectomy samples were scanned at energy levels of 28-34keV using a flat panel detector at radiation dose levels of 4mGy and 2mGy.

Unified fast reconstruction algorithm for conventional, phase-contrast, and diffraction tomography.

A unified method for three-dimensional reconstruction of objects from transmission images collected at multiple illumination directions is described. The method may be applicable to experimental conditions relevant to absorption-based, phase-contrast, or diffraction imaging using x rays, electrons, and other forms of penetrating radiation or matter waves. Both the phase retrieval (also known as contrast transfer function correction) and the effect of Ewald sphere curvature (in the cases with a shallow depth of field and significant in-object diffraction) are incorporated in the proposed algorithm and can be taken into account.

Method for virtual optical sectioning and tomography utilizing shallow depth of field.

A method is proposed for high-resolution, three-dimensional reconstruction of internal structures of objects from planar transmission images. The described approach can be used with any form of radiation or matter waves, in principle, provided that the depth of field is smaller than the thickness of the sample. The physical optics basis for the method is elucidated, and the reconstruction algorithm is presented in detail.

Imaging Breast Microcalcifications Using Dark-Field Signal in Propagation-Based Phase-Contrast Tomography.

Breast microcalcifications are an important primary radiological indicator of breast cancer. However, microcalcification classification and diagnosis may be still challenging for radiologists due to limitations of the standard 2D mammography technique, including spatial and contrast resolution. In this study, we propose an approach to improve the detection of microcalcifications in propagation-based phase-contrast X-ray computed tomography of breast tissues.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood.

A Method for High-Resolution Three-Dimensional Reconstruction with Ewald Sphere Curvature Correction from Transmission Electron Images.

A method for three-dimensional reconstruction of objects from defocused images collected at multiple illumination directions in high-resolution transmission electron microscopy is presented. The method effectively corrects for the Ewald sphere curvature by taking into account the in-particle propagation of the electron beam. Numerical simulations demonstrate that the proposed method is capable of accurately reconstructing biological molecules or nanoparticles from high-resolution defocused images under conditions achievable in single-particle electron cryo-microscopy or electron tomography with realistic radiation doses, non-trivial aberrations, multiple scattering, and other experimentally relevant factors.

Effect of x-ray energy on the radiological image quality in propagation-based phase-contrast computed tomography of the breast.

Breast cancer is the most common cancer in women in developing and developed countries and is responsible for 15% of women's cancer deaths worldwide. Conventional absorption-based breast imaging techniques lack sufficient contrast for comprehensive diagnosis. Propagation-based phase-contrast computed tomography (PB-CT) is a developing technique that exploits a more contrast-sensitive property of x-rays: x-ray refraction.

Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons, Part II: Differential Holographic Tomography.

It has been argued that in atomic-resolution transmission electron microscopy (TEM) of sparse weakly scattering structures, such as small biological molecules, multiple electron scattering usually has only a small effect, while the in-molecule Fresnel diffraction can be significant due to the intrinsically shallow depth of focus. These facts suggest that the three-dimensional reconstruction of such structures from defocus image series collected at multiple rotational orientations of a molecule can be effectively performed for each atom separately, using the incoherent first Born approximation. The corresponding reconstruction method, termed here Differential Holographic Tomography, is developed theoretically and demonstrated computationally on several numerical models of biological molecules.

: a software suite for ptychographic X-ray speckle tracking.

In recent years, X-ray speckle-tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to their simple experimental setup, high angular sensitivity and compatibility with low-coherence sources, these methods have been actively developed for use with synchrotron and laboratory light sources.

Effect of radiation damage and illumination variability on signal-to-noise ratio in X-ray free-electron laser single-particle imaging.

The deterioration of both the signal-to-noise ratio and the spatial resolution in the electron-density distribution reconstructed from diffraction intensities collected at different orientations of a sample is analysed theoretically with respect to the radiation damage to the sample and the variations in the X-ray intensities illuminating different copies of the sample. The simple analytical expressions and numerical estimates obtained for models of radiation damage and incident X-ray pulses may be helpful in planning X-ray free-electron laser (XFEL) imaging experiments and in analysis of experimental data. This approach to the analysis of partially coherent X-ray imaging configurations can potentially be used for analysis of other forms of imaging where the temporal behaviour of the sample and the incident intensity during exposure may affect the inverse problem of sample reconstruction.

Relative roles of multiple scattering and Fresnel diffraction in the imaging of small molecules using electrons.

The relative roles of multiple electron scattering and in-molecule Fresnel diffraction in atomic-resolution transmission electron microscopy of small molecules are discussed. It is argued that, while multiple scattering tends to have only a moderate effect, the in-molecule Fresnel diffraction can be significant due to the shallow depth of focus in high-resolution electron microscopy. When the depth of focus is smaller than the size of molecule along the trajectory of the electrons, the projection approximation breaks down and pairs of images at orientations of the molecule rotated by 180 degrees are not the same.

Dark-field signal extraction in propagation-based phase-contrast imaging.

A method for extracting the dark-field signal in propagation-based phase-contrast imaging is proposed. In the case of objects consisting predominantly of a single material, or several different materials with similar ratios of the real decrement to the imaginary part of the complex refractive index, the proposed method requires a single image for extraction of the dark-field signal in two-dimensional projection imaging. In the case of three-dimensional tomographic imaging, the method needs only one image to be collected at each projection angle.

Ptychographic X-ray speckle tracking.

A method is presented for the measurement of the phase gradient of a wavefront by tracking the relative motion of speckles in projection holograms as a sample is scanned across the wavefront. By removing the need to obtain an undistorted reference image of the sample, this method is suitable for the metrology of highly divergent wavefields. Such wavefields allow for large magnification factors that, according to current imaging capabilities, will allow for nanoradian angular sensitivity and nanoscale sample projection imaging.

Noise-resolution uncertainty principle in classical and quantum systems.

We show that the width of an arbitrary function and the width of the distribution of its values cannot be made arbitrarily small simultaneously. In the case of ergodic stochastic processes, an ensuing uncertainty relationship is then demonstrated for the product of correlation length and variance. A closely related uncertainty principle is also established for the average degree of fourth-order coherence and the spatial width of modes of bosonic quantum fields.

BERTHA: Implementation of a four-component Dirac-Kohn-Sham relativistic framework.

In this paper, we present and review the most recent computational advances in the BERTHA code. BERTHA can be regarded as the state of the art in fully relativistic four-component Dirac-Kohn-Sham (DKS) software. Thanks to the implementation of various parallelization and memory open-ended distribution schemes in combination with efficient "density fitting" algorithms, it greatly reduces the computational burden of four-component DKS calculations.

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs.

PyBERTHART: A Relativistic Real-Time Four-Component TDDFT Implementation Using Prototyping Techniques Based on Python.

We present a real-time time-dependent four-component Dirac-Kohn-Sham (RT-TDDKS) implementation based on the BERTHA code. This new implementation takes advantage of modern software engineering, including the prototyping techniques. The software design follows a three step approach: (i) the prototype implementation of a time-propagation algorithm in nonrelativistic real-time TDDFT within the Psi4NumPy framework, which provides a suitable environment for the creation of a clear, readable, and easy to test reference code in Python, (ii) the design of an original Python application programming interface for the relativistic four-component code BERTHA (PyBERTHA), which has an efficient computational kernel for relativistic integrals written in FORTRAN, and (iii) the porting of the time-propagation scheme enveloped within the Psi4NumPy framework to PyBERTHA.

Comparison of propagation-based CT using synchrotron radiation and conventional cone-beam CT for breast imaging.

Objectives: To evaluate and compare the image quality of propagation-based phase-contrast computed tomography (PB-CT) using synchrotron radiation and conventional cone-beam breast computed tomography (CBBCT) based on various radiological image quality criteria.

Methods: Eight excised breast tissue samples of various sizes and containing different lesion types were scanned using PB-CT at a synchrotron facility and using CBBCT at a university-affiliated breast imaging centre. PB-CT scans were performed at two different mean glandular dose (MGD) levels: standard (5.

Propagation-based x-ray phase-contrast tomography of mastectomy samples using synchrotron radiation.

Purpose: Propagation-based phase-contrast computed tomography (PB-CT) is a method for three-dimensional x-ray imaging that utilizes refraction, as well as absorption, of x rays in the tissues to increase the signal-to-noise ratio (SNR) in the resultant images, in comparison with equivalent conventional absorption-only x-ray tomography (CT). Importantly, the higher SNR is achieved without sacrificing spatial resolution or increasing the radiation dose delivered to the imaged tissues. The present work has been carried out in the context of the current development of a breast CT imaging facility at the Australian Synchrotron.

A fast and adaptable method for high accuracy integration of the time-dependent Schrödinger equation.

We present an adaptable, fast, and robust method for integrating the time-dependent Schrödinger equation. We apply the method to calculations of High Harmonic (HHG) and Above Threshold Ionisation (ATI) spectra for a single atomic electron in an intense laser field. Our approach implements the stabilized bi-conjugate gradient method (BiCG-STAB) for solving a sparse linear system to evolve the electronic wavefunction in time.

Signal-to-noise, spatial resolution and information capacity of coherent diffraction imaging.

It is shown that the average signal-to-noise ratio (SNR) in the three-dimensional electron-density distribution of a sample reconstructed by coherent diffractive imaging cannot exceed twice the square root of the ratio of the mean total number of scattered photons detected during the scan and the number of spatially resolved voxels in the reconstructed volume. This result leads to an upper bound on Shannon's information capacity of this imaging method by specifying the maximum number of distinguishable density distributions within the reconstructed volume when the radiation dose delivered to the sample and the spatial resolution are both fixed. If the spatially averaged SNR in the reconstructed electron density is fixed instead, the radiation dose is shown to be proportional to the third or fourth power of the spatial resolution, depending on the sampling of the three-dimensional diffraction space and the scattering power of the sample.