Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

X-ray free electron lasers (XFEL) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges both in terms of experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classification tasks using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering (FXS) algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. We envision skopi as a resource to aid the development of on-the-fly feedback during non-crystalline experiments at XFEL facilities, which will provide critical insights into biomolecular structure and function.

Resolution Enhancement in Coherent Diffraction Imaging Using High Dynamic Range Image

In a coherent diffraction imaging (CDI) system, the information of the sample is retrieved from the diffraction patterns recorded by the image sensor via multiple iterations. The limited dynamic range of the image sensor restricts the resolution of the reconstructed sample information. To alleviate this problem, the high dynamic range imaging technology is adopted to increase the signal-to-noise ratio of the diffraction patterns. A sequence of raw diffraction images with differently exposure time are recorded by the image sensor. Then, they are fused to generate a high quality diffraction pattern based on the response function of the image sensor. With the fused diffraction patterns, the resolution of the coherent diffraction imaging can be effectively improved. The experiments on USAF resolution card is carried out to verify the effectiveness of our proposed method, in which the spatial resolution is improved by 1.8 times using the high dynamic range imaging technology.

A convolutional neural network for defect classification in Bragg coherent X-ray diffraction

Coherent diffraction imaging enables the imaging of individual defects, such as dislocations or stacking faults, in materials. These defects and their surrounding elastic strain fields have a critical influence on the macroscopic properties and functionality of materials. However, their identification in Bragg coherent diffraction imaging remains a challenge and requires significant data mining. The ability to identify defects from the diffraction pattern alone would be a significant advantage when targeting specific defect types and accelerates experiment design and execution. Here, we exploit a computational tool based on a three-dimensional (3D) parametric atomistic model and a convolutional neural network to predict dislocations in a crystal from its 3D coherent diffraction pattern. Simulated diffraction patterns from several thousands of relaxed atomistic configurations of nanocrystals are used to train the neural network and to predict the presence or absence of dislocations as well as their type (screw or edge). Our study paves the way for defect-recognition in 3D coherent diffraction patterns for material science.

Development and application of a tender X-ray ptychographic coherent diffraction imaging system on BL27SU at SPring-8

Ptychographic coherent diffraction imaging (CDI) allows the visualization of both the structure and chemical state of materials on the nanoscale, and has been developed for use in the soft and hard X-ray regions. In this study, a ptychographic CDI system with pinhole or Fresnel zone-plate optics for use in the tender X-ray region (2–5 keV) was developed on beamline BL27SU at SPring-8, in which high-precision pinholes optimized for the tender energy range were used to obtain diffraction intensity patterns with a low background, and a temperature stabilization system was developed to reduce the drift of the sample position. A ptychography measurement of a 200 nm thick tantalum test chart was performed at an incident X-ray energy of 2.500 keV, and the phase image of the test chart was successfully reconstructed with approximately 50 nm resolution. As an application to practical materials, a sulfur polymer material was measured in the range of 2.465 to 2.500 keV including the sulfur K absorption edge, and the phase and absorption images were successfully reconstructed and the nanoscale absorption/phase spectra were derived from images at multiple energies. In 3 GeV synchrotron radiation facilities with a low-emittance storage ring, the use of the present system will allow the visualization on the nanoscale of the chemical states of various light elements that play important roles in materials science, biology and environmental science.