Free log-likelihood as an unbiased metric for coherent diffraction imaging

Using convolutional neural network denoising to reduce ambiguity in X-ray coherent diffraction imaging

The inherent ambiguity in reconstructed images from coherent diffraction imaging (CDI) poses an intrinsic challenge, as images derived from the same dataset under varying initial conditions often display inconsistencies. This study introduces a method that employs the Noise2Noise approach combined with neural networks to effectively mitigate these ambiguities. We applied this methodology to hundreds of ambiguous reconstructed images retrieved from a single diffraction pattern using a conventional retrieval algorithm. Our results demonstrate that ambiguous features in these reconstructions are effectively treated as inter-reconstruction noise and are significantly reduced. The post-Noise2Noise treated images closely approximate the average and singular value decomposition analysis of various reconstructions, providing consistent and reliable reconstructions.

Correcting angular distortions in Bragg coherent X-ray diffraction imaging

Bragg coherent X-ray diffraction imaging (BCDI) has emerged as a powerful technique for strain imaging and morphology reconstruction of nanometre-scale crystals. However, BCDI often suffers from angular distortions that appear during data acquisition, caused by radiation pressure, heating or imperfect scanning stages. This limits the applicability of BCDI, in particular for small crystals and high-flux X-ray beams. Here, we present a pre-processing algorithm that recovers the 3D datasets from the BCDI dataset measured under the impact of large angular distortions. We systematically investigate the performance of this method for different levels of distortion and find that the algorithm recovers the correct angles for distortions up to 16.4× (1640%) the angular step size dθ = 0.004°. We also show that the angles in a continuous scan can be recovered with high accuracy. As expected, the correction provides marked improvements in the subsequent phase retrieval.

Capturing Catalyst Strain Dynamics during Operando CO Oxidation

Understanding the strain dynamic behavior of catalysts is crucial for the development of cost-effective, efficient, stable, and long-lasting catalysts. Using time-resolved Bragg coherent diffraction imaging at the fourth generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS), we achieved subsecond time resolution during operando chemical reactions. Upon investigation of Pt nanoparticles during CO oxidation, the three-dimensional strain profile highlights significant changes in the surface and subsurface regions, where localized strain is probed along the [111] direction. Notably, a rapid increase in tensile strain was observed at the top and bottom Pt {111} facets during CO adsorption. Moreover, we detected oscillatory strain changes (6.4 s period) linked to CO adsorption during oxidation, where a time resolution of 0.25 s was achieved. This approach allows for the study of adsorption dynamics of catalytic nanomaterials at the single-particle level under operando conditions, which provides insight into nanoscale catalytic mechanisms.

Unveiling Core-Shell Structure Formation in a Ni3Fe Nanoparticle with In Situ Multi-Bragg Coherent Diffraction Imaging

Solid-state reactions play a key role in materials science. The evolution of the structure of a single 350 nm Ni3Fe nanoparticle, i.e., its morphology (facets) as well as its deformation field, has been followed by applying multireflection Bragg coherent diffraction imaging. Through this approach, we unveiled a demixing process that occurs at high temperatures (600 °C) under an Ar atmosphere. This process leads to the gradual emergence of a highly strained core-shell structure, distinguished by two distinct lattice parameters with a difference of 0.4%. Concurrently, this transformation causes the facets to vanish, ultimately yielding a rounded core-shell nanoparticle. This final structure comprises a Ni3Fe core surrounded by a 40 nm Ni-rich outer shell due to preferential iron oxidation. Providing in situ 3D imaging of the lattice parameters at the nanometer scale while varying the temperature, this study─with the support of atomistic simulations─not only showcases the power of in situ multireflection BCDI but also provides valuable insights into the mechanisms at work during a solid-state reaction characterized by a core-shell transition.

Similarity score for screening phase-retrieved maps in X-ray diffraction imaging - characterization in reciprocal space

X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.

Protocol using similarity score and improved shrink-wrap algorithm for better convergence of phase-retrieval calculation in X-ray diffraction imaging

In X-ray diffraction imaging (XDI), electron density maps of a targeted particle are reconstructed computationally from the diffraction pattern alone using phase-retrieval (PR) algorithms. However, the PR calculations sometimes fail to yield realistic electron density maps that approximate the structure of the particle. This occurs due to the absence of structure amplitudes at and near the zero-scattering angle and the presence of Poisson noise in weak diffraction patterns. Consequently, the PR calculation becomes a bottleneck for XDI structure analyses. Here, a protocol to efficiently yield realistic maps is proposed. The protocol is based on the empirical observation that realistic maps tend to yield low similarity scores, as suggested in our prior study [Sekiguchi et al. (2017), J. Synchrotron Rad. 24, 1024-1038]. Among independently and concurrently executed PR calculations, the protocol modifies all maps using the electron-density maps exhibiting low similarity scores. This approach, along with a new protocol for estimating particle shape, improved the probability of obtaining realistic maps for diffraction patterns from various aggregates of colloidal gold particles, as compared with PR calculations performed without the protocol. Consequently, the protocol has the potential to reduce computational costs in PR calculations and enable efficient XDI structure analysis of non-crystalline particles using synchrotron X-rays and X-ray free-electron laser pulses.

Unraveling the synergistic effects of Cu-Ag tandem catalysts during electrochemical CO2 reduction using nanofocused X-ray probes

Controlling the selectivity of the electrocatalytic reduction of carbon dioxide into value-added chemicals continues to be a major challenge. Bulk and surface lattice strain in nanostructured electrocatalysts affect catalytic activity and selectivity. Here, we unravel the complex dynamics of synergistic lattice strain and stability effects of Cu-Ag tandem catalysts through a previously unexplored combination of in situ nanofocused X-ray absorption spectroscopy and Bragg coherent diffraction imaging. Three-dimensional strain maps reveal the lattice dynamics inside individual nanoparticles as a function of applied potential and product yields. Dynamic relations between strain, redox state, catalytic activity and selectivity are derived. Moderate Ag contents effectively reduce the competing evolution of H2 and, concomitantly, lead to an enhanced corrosion stability. Findings from this study evidence the power of advanced nanofocused spectroscopy techniques to provide new insights into the chemistry and structure of nanostructured catalysts.

Bragg coherent diffraction imaging with the CITIUS charge-integrating detector

The CITIUS detector is a next-generation high-speed X-ray imaging detector. It has integrating-type pixels and is designed to show a consistent linear response at a frame rate of 17.4 kHz, which results in a saturation count rate of over 30 Mcps pixel-1 when operating at an acquisition duty cycle close to 100%, and up to 20 times higher with special extended acquisition modes. Here, its application for Bragg coherent diffraction imaging is demonstrated by taking advantage of the fourth-generation Extremely Brilliant Source of the European Synchrotron (ESRF-EBS, Grenoble, France). The CITIUS detector outperformed a photon-counting detector, similar spatial resolution being achieved (20 ± 6 nm versus 22 ± 9 nm) with greatly reduced acquisition times (23 s versus 200 s). It is also shown how the CITIUS detector can be expected to perform during dynamic Bragg coherent diffraction imaging measurements. Finally, the current limitations of the CITIUS detector and further optimizations for coherent imaging techniques are discussed.

Imaging the strain evolution of a platinum nanoparticle under electrochemical control

Surface strain is widely employed in gas phase catalysis and electrocatalysis to control the binding energies of adsorbates on active sites. However, in situ or operando strain measurements are experimentally challenging, especially on nanomaterials. Here we exploit coherent diffraction at the new fourth-generation Extremely Brilliant Source of the European Synchrotron Radiation Facility to map and quantify strain within individual Pt catalyst nanoparticles under electrochemical control. Three-dimensional nanoresolution strain microscopy, together with density functional theory and atomistic simulations, show evidence of heterogeneous and potential-dependent strain distribution between highly coordinated ({100} and {111} facets) and undercoordinated atoms (edges and corners), as well as evidence of strain propagation from the surface to the bulk of the nanoparticle. These dynamic structural relationships directly inform the design of strain-engineered nanocatalysts for energy storage and conversion applications.

Gwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imaging

In a world where data are steadily made more available, Gwaihir is a tool that overcomes multiple issues by bridging remote access, cluster computing and a user-friendly interface, consequentially improving the link between synchrotrons and their users for Bragg coherent diffraction imaging.

Bragg coherent X-ray diffraction is a nondestructive method for probing material structure in three dimensions at the nanoscale, with unprecedented resolution in displacement and strain fields. This work presents Gwaihir, a user-friendly and open-source tool to process and analyze Bragg coherent X-ray diffraction data. It integrates the functionalities of the existing packages bcdi and PyNX in the same toolbox, creating a natural workflow and promoting data reproducibility. Its graphical interface, based on Jupyter Notebook widgets, combines an interactive approach for data analysis with a powerful environment designed to link large-scale facilities and scientists.

Bragg coherent diffraction imaging of single 20 nm Pt particles at the ID01-EBS beamline of ESRF

Electronic or catalytic properties can be modified at the nanoscale level. Engineering efficient and specific nanomaterials requires the ability to study their complex structure-property relationships. Here, Bragg coherent diffraction imaging was used to measure the three-dimensional shape and strain of platinum nanoparticles with a diameter smaller than 30 nm, i.e. significantly smaller than any previous study. This was made possible by the realization of the Extremely Brilliant Source of ESRF, The European Synchrotron. This work demonstrates the feasibility of imaging the complex structure of very small particles in three dimensions and paves the way towards the observation of realistic catalytic particles.

Imaging the facet surface strain state of supported multi-faceted Pt nanoparticles during reaction

Nanostructures with specific crystallographic planes display distinctive physico-chemical properties because of their unique atomic arrangements, resulting in widespread applications in catalysis, energy conversion or sensing. Understanding strain dynamics and their relationship with crystallographic facets have been largely unexplored. Here, we reveal in situ, in three-dimensions and at the nanoscale, the volume, surface and interface strain evolution of single supported platinum nanocrystals during reaction using coherent x-ray diffractive imaging. Interestingly, identical {hkl} facets show equivalent catalytic response during non-stoichiometric cycles. Periodic strain variations are rationalised in terms of O₂ adsorption or desorption during O₂ exposure or CO oxidation under reducing conditions, respectively. During stoichiometric CO oxidation, the strain evolution is, however, no longer facet dependent. Large strain variations are observed in localised areas, in particular in the vicinity of the substrate/particle interface, suggesting a significant influence of the substrate on the reactivity. These findings will improve the understanding of dynamic properties in catalysis and related fields.

Understanding strain dynamics and their relationship with crystallographic facets have been largely unexplored. Here the authors demonstrate how the 3D lattice displacement and strain evolution depend on the crystallographic facets of Pt nanoparticles during CO oxidation reaction, providing new insights in the relationship between facet-related surface strain and chemistry.

X-ray Diffraction Imaging of Deformations in Thin Films and Nano-Objects

The quantification and localization of elastic strains and defects in crystals are necessary to control and predict the functioning of materials. The X-ray imaging of strains has made very impressive progress in recent years. On the one hand, progress in optical elements for focusing X-rays now makes it possible to carry out X-ray diffraction mapping with a resolution in the 50-100 nm range, while lensless imaging techniques reach a typical resolution of 5-10 nm. This continuous evolution is also a consequence of the development of new two-dimensional detectors with hybrid pixels whose dynamics, reading speed and low noise level have revolutionized measurement strategies. In addition, a new accelerator ring concept (HMBA network: hybrid multi-bend achromat lattice) is allowing a very significant increase (a factor of 100) in the brilliance and coherent flux of synchrotron radiation facilities, thanks to the reduction in the horizontal size of the source. This review is intended as a progress report in a rapidly evolving field. The next ten years should allow the emergence of three-dimensional imaging methods of strains that are fast enough to follow, in situ, the evolution of a material under stress or during a transition. Handling massive amounts of data will not be the least of the challenges.

Twin boundary migration in an individual platinum nanocrystal during catalytic CO oxidation

At the nanoscale, elastic strain and crystal defects largely influence the properties and functionalities of materials. The ability to predict the structural evolution of catalytic nanocrystals during the reaction is of primary importance for catalyst design. However, to date, imaging and characterising the structure of defects inside a nanocrystal in three-dimensions and in situ during reaction has remained a challenge. We report here an unusual twin boundary migration process in a single platinum nanoparticle during CO oxidation using Bragg coherent diffraction imaging as the characterisation tool. Density functional theory calculations show that twin migration can be correlated with the relative change in the interfacial energies of the free surfaces exposed to CO. The x-ray technique also reveals particle reshaping during the reaction. In situ and non-invasive structural characterisation of defects during reaction opens new avenues for understanding defect behaviour in confined crystals and paves the way for strain and defect engineering.

Exploring the 3D structure and defects of a self-assembled gold mesocrystal by coherent X-ray diffraction imaging

Mesocrystals are nanostructured materials consisting of individual nanocrystals having a preferred crystallographic orientation. On mesoscopic length scales, the properties of mesocrystals are strongly affected by structural heterogeneity. Here, we report the detailed structural characterization of a faceted mesocrystal grain self-assembled from 60 nm sized gold nanocubes. Using coherent X-ray diffraction imaging, we determined the structure of the mesocrystal with the resolution sufficient to resolve each gold nanoparticle. The reconstructed electron density of the gold mesocrystal reveals its intrinsic structural heterogeneity, including local deviations of lattice parameters, and the presence of internal defects. The strain distribution shows that the average superlattice obtained by angular X-ray cross-correlation analysis and the real, "multidomain" structure of a mesocrystal are very close to each other, with a deviation less than 10%. These results will provide an important impact to understanding the fundamental principles of structuring and self-assembly including ensuing properties of mesocrystals.

Facet-Dependent Strain Determination in Electrochemically Synthetized Platinum Model Catalytic Nanoparticles

Studying model nanoparticles is one approach to better understand the structural evolution of a catalyst during reactions. These nanoparticles feature well-defined faceting, offering the possibility to extract structural information as a function of facet orientation and compare it to theoretical simulations. Using Bragg Coherent X-ray Diffraction Imaging, the uniformity of electrochemically synthesized model catalysts is studied, here high-index faceted tetrahexahedral (THH) platinum nanoparticles at ambient conditions. 3D images of an individual nanoparticle are obtained, assessing not only its shape but also the specific components of the displacement and strain fields both at the surface of the nanocrystal and inside. The study reveals structural diversity of shapes and defects, and shows that the THH platinum nanoparticles present strain build-up close to facets and edges. A facet recognition algorithm is further applied to the imaged nanoparticles and provides facet-dependent structural information for all measured nanoparticles. In the context of strain engineering for model catalysts, this study provides insight into the shape-controlled synthesis of platinum nanoparticles with high-index facets.

Three-Dimensional Coherent Bragg Imaging of Rotating Nanoparticles

Bragg coherent diffraction imaging is a powerful strain imaging tool, often limited by beam-induced sample instability for small particles and high power densities. Here, we devise and validate an adapted diffraction volume assembly algorithm, capable of recovering three-dimensional datasets from particles undergoing uncontrolled and unknown rotations. We apply the method to gold nanoparticles which rotate under the influence of a focused coherent x-ray beam, retrieving their three-dimensional shapes and strain fields. The results show that the sample instability problem can be overcome, enabling the use of fourth generation synchrotron sources for Bragg coherent diffraction imaging to their full potential.

PyNX: high-performance computing toolkit for coherent X-ray imaging based on operators

The open-source PyNX toolkit has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical processing units (GPUs) to achieve high-performance computing speeds. The toolkit can be used for coherent diffraction imaging (CDI), ptychography and wavefront propagation, in the far- or near-field regime. Moreover, all imaging operations (propagation, projections, algorithm cycles…) can be implemented in Python as simple mathematical operators, an approach which can be used to easily combine basic algorithms in a tailored chain. Calculations can also be distributed to multiple GPUs, e.g. for large ptychography data sets. Command-line scripts are available for on-line CDI and ptychography analysis, either from raw beamline data sets or using the coherent X-ray imaging data format.

Continuous scanning for Bragg coherent X-ray imaging

We explore the use of continuous scanning during data acquisition for Bragg coherent diffraction imaging, i.e., where the sample is in continuous motion. The fidelity of continuous scanning Bragg coherent diffraction imaging is demonstrated on a single Pt nanoparticle in a flow reactor at \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$400\,^\circ \hbox {C}$$\end{document}400∘C in an Ar-based gas flowed at 50 ml/min. We show a reduction of 30% in total scan time compared to conventional step-by-step scanning. The reconstructed Bragg electron density, phase, displacement and strain fields are in excellent agreement with the results obtained from conventional step-by-step scanning. Continuous scanning will allow to minimise sample instability under the beam and will become increasingly important at diffraction-limited storage ring light sources.

Towards a quantitative determination of strain in Bragg Coherent X-ray Diffraction Imaging: artefacts and sign convention in reconstructions

Bragg coherent X-ray diffraction imaging (BCDI) has emerged as a powerful technique to image the local displacement field and strain in nanocrystals, in three dimensions with nanometric spatial resolution. However, BCDI relies on both dataset collection and phase retrieval algorithms that can induce artefacts in the reconstruction. Phase retrieval algorithms are based on the fast Fourier transform (FFT). We demonstrate how to calculate the displacement field inside a nanocrystal from its reconstructed phase depending on the mathematical convention used for the FFT. We use numerical simulations to quantify the influence of experimentally unavoidable detector deficiencies such as blind areas or limited dynamic range as well as post-processing filtering on the reconstruction. We also propose a criterion for the isosurface determination of the object, based on the histogram of the reconstructed modulus. Finally, we study the capability of the phasing algorithm to quantitatively retrieve the surface strain (i.e., the strain of the surface voxels). This work emphasizes many aspects that have been neglected so far in BCDI, which need to be understood for a quantitative analysis of displacement and strain based on this technique. It concludes with the optimization of experimental parameters to improve throughput and to establish BCDI as a reliable 3D nano-imaging technique.