Deep neural networks in real-time coherent diffraction imaging
Abstract not provided.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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Results for “Bragg coherent diffraction imaging”
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Imaging extended single crystal lattice distortion fields with multi-peak Bragg ptychography
Recent advances in phase-retrieval-based x-ray imaging methods have demonstrated the ability to reconstruct 3D distortion vector fields within a nanocrystal by using coherent diffraction information from multiple crystal Bragg reflections. However, these works do not provide a solution to the challenges encountered in imaging lattice distortions in crystals with significant defect content that result in phase wrapping. Moreover, these methods only apply to isolated crystals smaller than the x-ray illumination, and therefore cannot be used for imaging of distortions in extended crystals. We introduce multi-peak Bragg ptychography which addresses both challenges via an optimization framework that combines stochastic gradient descent and phase unwrapping methods for robust image reconstruction of lattice distortions and defects in extended crystals. Our work uses modern automatic differentiation toolsets so that the method is easy to extend to other settings and easy to implement in high-performance computers. This work is particularly timely given the broad interest in using the increased coherent flux in fourth-generation synchrotrons for innovative material research.
36 MATERIALS SCIENCE↗
Enhanced Piezoelectric Response at Nanoscale Vortex Structures in Ferroelectrics
Not Available
42 ENGINEERING↗
Facet-dependent strain determination in electrochemically synthetized platinum model catalytic nanoparticles
Please check the README file for more information about the dataset.
Bragg Coherent X-ray Diffraction Imaging↗
Sub-pixel high-resolution imaging of high-energy x-rays inspired by sub-wavelength optical imaging
We have developed and demonstrated an image super-resolution method—XR-UNLOC: X-Ray UNsupervised particle LOCalization—for hard x-rays measured with fast-frame-rate detectors that is an adaptation of the principle of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), which enabled biological fluorescence imaging at sub-optical-wavelength scales. We demonstrate the approach on experimental coherent Bragg diffraction data measured with 52 keV x-rays from a nanocrystalline sample. From this sample, we resolve the fine fringe detail of a high-energy x-ray Bragg coherent diffraction pattern to an upsampling factor of 16 of the native pixel pitch of 30 μ m of a charge-integrating fastCCD detector. This was accomplished by analysis of individual photon locations in a series of “nearly-dark” instances of the diffraction pattern that each contain only a handful of photons. Central to our approach was the adaptation of the UNLOC photon fitting routine for PALM/STORM to the hard x-ray regime to handle much smaller point spread functions, which required a different statistical test for photon detection and for sub-pixel localization. A comparison to a photon-localization strategy used in the x-ray community (“droplet analysis”) showed that XR-UNLOC provides significant improvement in super-resolution. We also developed a metric by which to estimate the limit of reliable upsampling with XR-UNLOC under a given set of experimental conditions in terms of the signal-to-noise ratio of a photon detection event and the size of the point spread function for guiding future x-ray experiments in many disciplines where detector pixelation limits must be overcome.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Cepstral scanning transmission electron microscopy imaging of severe lattice distortions
The development of four-dimensional (4D) scanning transmission electron microscopy (STEM) using fast detectors has opened-up new avenues for addressing some of longstanding challenges in electron imaging. One of these challenges is how to image severely distorted crystal lattices, such as at a dislocation core. Here we develop a new 4D-STEM technique, called Cepstral STEM, for imaging disordered crystals using electron diffuse scattering. In contrast to analysis based on Bragg diffraction, which measures the average and periodic scattering potential, electron diffuse scattering can detect fluctuations caused by crystal disorder. Local fluctuations of diffuse scattering are captured by scanning electron nanodiffraction (SEND) using a coherent probe. The harmonic signals in electron diffuse scattering are detected through Cepstral analysis and used for imaging. By integrating Cepstral analysis with 4D-STEM, we demonstrate that information about the distortive part of electron scattering potential can be separated and imaged at nm spatial resolution. Here, we apply the technique to the analysis of a dislocation core in SiGe and lattice distortions in a high entropy alloy.
36 MATERIALS SCIENCE↗
Diffractive Image Reconstruction Utilizing Molecular Dynamics Enabling Near Atomic Resolution
We present a new algorithm for coherent x-ray imaging that combines error minimization and molecular dynamics. We show reconstructed atomic positions from Bragg peaks off simulated 2D nanocrystals and how these converge with atomic resolution.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Inversion of dynamical Bragg intensities to complex structure factors by iterated projections. For Ultramic. 2020. ("Pico" Festschrift, May 2021)
We discuss a method for recovering complex structure factors from many simultaneously excited Bragg beam intensities is described. The method is applied to simulated transmission electron diffraction data over a wide range of crystal thickness and beam energies. The method is based on iterated projections between structure and scattering matrices, which are related by a matrix unitary transformation, exponential, which we invert. The algorithm removes multiple-scattering perturbations from diffraction data and might be extended to other fields, including X-ray and neutron diffraction and cryo-electron microscopy. Because coherent multiple scattering involves interference between Bragg beams, the method also solves the phase problem. Unlike dynamical inversion from electron microscope images or ptychography data, the method, which starts with Bragg beam intensities, provides complex structure factors unaffected by focusing errors or resolution limitations imposed by lenses. We provide inversions from simulated data with 441 simultaneously excited Bragg beams over a range of thickness and beam energy. We discuss the retrieval of chirality information from enantiomorphs, the efficient incorporation of symmetry information using the irreducible representation of the group of structure matrices, and the effect of HOLZ lines to provide three-dimensional information.
97 MATHEMATICS AND COMPUTING↗
Reuniting crystallography with real space: Ab initio structure elucidation with 4D-STEM
Structure elucidation via single-crystal methods has historically lacked experimental access to real-space information, instead relying exclusively on diffraction-space measurements of Bragg reflections. Here we exploit the dual-space imaging power of 4D scanning transmission electron microscopy to meaningfully integrate real-space information into the crystallographic workflow. We show that virtual apertures assembled by segmentation of high-angle annular dark-field images enable i) pixel-by-pixel separation of coherent Bragg signal from clusters of closely spaced nanocrystals and ii) selective extraction of integrated intensities from thinner subregions of individual specimens, facilitating retroactive tuning of multiple scattering artifacts. This strategy empowers us to simply pick and choose whichever nanoscale regions of interest generate the highest-quality diffraction patterns, allowing us to solve several independent structures of the metal-organic framework UiO-66 from specimens whose agglomerated morphology proved intractable for conventional microcrystal electron diffraction. Our method is compatible with both rotational and serial approaches to data processing, ultimately divulging the first scanning nanobeam electron diffraction structures determined by direct methods at subangstrom resolution.
Saha, Ambarneil↗
Bragg grating inscription in photosensitive materials by an optical replication process
This paper examines the feasibility of producing multiplexed Bragg gratings for use as diffractive optical elements (DOEs) by coherent optical replication of a surface-relief phase grating into thick-film photosensitive materials. The use of such DOEs in light guide plates (LGPs) for optical imaging systems ensures energy-efficient light input into and output from LGPs and allows one to minimise their weight and size. We present simulation results for the interference structure fabrication process and recording of a series of multiplexed diffraction gratings in photosensitive materials. (paper)
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Enabling dynamic 3D coherent diffraction imaging via adaptive latent space tuning of generative autoencoders
Abstract Coherent diffraction imaging (CDI) is an advanced non-destructive 3D X-ray imaging technique for measuring a sample’s electron density. The main challenge of CDI is loss of phase information in diffraction intensity measurements, resulting in lengthy iterative reconstruction processes that can return non-unique solutions, which pose challenges for experiments attempting to track dynamic sample evolution through multiple states. As the increased brightness of fourth-generation light sources enables faster sample measurements and drives operando experiments with Bragg CDI, there is a growing need for faster reconstruction techniques that can keep pace. We have developed an adaptive generative autoencoder approach for uniquely tracking a sample’s electron density as it dynamically evolves. Our approach adaptively tunes the low-dimensional latent embedding of a generative autoencoder, enabling a computationally efficient manner to account for time-varying shifting distributions in real-time. Analytic proof of convergence is provided as well as numerical demonstration of sample tracking with noisy measurements.
97 MATHEMATICS AND COMPUTING↗
X‑ray Coherent Diffractive Imaging of Large Helium Nanodroplets Doped with Small Molecules
We report the first X-ray coherent diffractive imaging experiment on molecule-doped helium nanodroplets. It complements previous work, where we reported single-shot X-ray coherent diffractive imaging studies of Xe dopant clusters formed in 4He and 3He droplets. These noble gas clusters were used to visualize the impact of rotational excitation of the droplets on the spatial distribution of atomic dopants within the droplets, and to study the differences and connections between quantum and classical droplet rotational motion. Here, we expand our studies to the molecular dopants CF4, CHF3, CH3CN, and SF6, imaged with 1.5 keV photons. We find multiple Bragg spots in the diffraction patterns of molecule-doped droplets with radii of approximately 600 nm, which provide evidence that molecules form elongated clusters with preferential alignment along the angular momentum axis of the 4He droplets, in agreement with our previous results on the aggregation of Xe clusters on quantum vortices. Real-space reconstructions of molecular dopant cluster density profiles are obtained for droplets with smaller radii of approximately 300 nm. The diffuse images suggest the formation of low-density, potentially porous, molecular clusters upon aggregation at T = 0.4 K in 4He droplets. In the normal fluid 3He droplets, molecules aggregate into loose clusters on the droplets' equator, similar to previous observations for Xe atoms. Time-of-flight mass spectra reveal that the doped helium nanodroplet moieties fragment extensively into constituent atomic ions, producing only a small fraction of molecular fragment ions. The findings are discussed in the context of previously proposed schemes to use He droplets as potential tamper materials for ultrafast X-ray imaging experiments.
Feinberg, AlexandraJ↗
Imaging the Progression of Radiolytic Damage in Molecular Crystals with Scanning Nanobeam Electron Diffraction
Almost every electron microscopy experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive materials. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space movies of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting domains undergoes internal rearrangement as a function of accumulating electron fluence, causing the intensities of some associated Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the isotropic propagation of delocalized radiolytic damage well beyond the direct footprint of the incident beam. We refer to these expanding tides of amorphization as “impact craters.”
59 BASIC BIOLOGICAL SCIENCES↗
Quantitative agreement between dynamical rocking curves in ultrafast electron diffraction for x-ray lasers
Electron diffraction through a thin patterned silicon membrane can be used to create complex spatial modulations in electron distributions. By precisely varying parameters such as crystallographic orientation and wafer thickness, the intensity of reflections in the diffraction plane can be controlled and by placing an aperture to block all but one spot, we can form an image with different parts of the patterned membrane, as is done for bright-field imaging in microscopy. The patterned electron beams can then be used to control phase and amplitude of subsequent x-ray emission, enabling novel coherent x-ray methods. Furthermore, the electrons themselves can also be used for femtosecond time resolved diffraction and microscopy. As a first step toward patterned beams, we demonstrate experimentally and through simulation the ability to accurately predict and control diffraction spot intensities. We simulate MeV transmission electron diffraction patterns using the multislice method for various crystallographic orientations of a single crystal Si(001) membrane near beam normal. The resulting intensity maps of the Bragg reflections are compared to experimental results obtained at the Accelerator Structure Test Area Ultrafast Electron Diffraction (ASTA UED) facility at SLAC. Furthermore, the fraction of inelastic and elastic scattering of the initial charge is estimated along with the absorption of the membrane to determine the contrast that would be seen in a patterned version of the Si(001) membrane.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
High-luminosity meV-resolution single-shot hard X-ray spectrograph for cavity-based X-ray free-electron lasers
Cavity-based X-ray free-electron lasers (CBXFELs) represent a possible realization of fully coherent hard X-ray sources having high spectral brilliance along with a narrow spectral bandwidth of ∼1–50 meV, a high repetition pulse rate of ∼1 MHz, and good stability. A diagnostic tool is required to measure CBXFEL spectra with meV resolution and high luminosity on a shot-to-shot basis. We have designed a high-luminosity single-shot hard X-ray spectrograph that images 9.831 keV X-rays in a ∼200 meV spectral window with a spectral resolution of a few meV. The spectrograph is designed around angular dispersion of X-rays in Bragg diffraction from crystals. It operates close to design specifications, exhibiting a linear dispersion rate of ∼1.4 µm meV −1 and a ∼200 meV window of high-fidelity spectral imaging. The experimentally demonstrated spectral resolution is ∼20 meV; this resolution is twice as low as expected from theory primarily because the spectrograph is highly sensitive to crystal angular instabilities. The experiment was performed at the bending magnet X-ray optics testing beamline 1-BM at the Advanced Photon Source.
Bragg diffraction↗
Holographic Optical Data Storage
Although the basic idea may be traced back to the earlier X-ray diffraction studies of Sir W. L. Bragg, the holographic method as we know it was invented by D. Gabor in 1948 as a two-step lensless imaging technique to enhance the resolution of electron microscopy, for which he received the 1971 Nobel Prize in physics. The distinctive feature of holography is the recording of the object phase variations that carry the depth information, which is lost in conventional photography where only the intensity (= squared amplitude) distribution of an object is captured. Since all photosensitive media necessarily respond to the intensity incident upon them, an ingenious way had to be found to convert object phase into intensity variations, and Gabor achieved this by introducing a coherent reference wave along with the object wave during exposure. Gabor's in-line recording scheme, however, required the object in question to be largely transmissive, and could provide only marginal image quality due to unwanted terms simultaneously reconstructed along with the desired wavefront. Further handicapped by the lack of a strong coherent light source, optical holography thus seemed fated to remain just another scientific curiosity, until the field was revolutionized in the early 1960s by some major breakthroughs: the proposition and demonstration of the laser principle, the introduction of off-axis holography, and the invention of volume holography. Consequently, the remainder of that decade saw an exponential growth in research on theory, practice, and applications of holography. Today, holography not only boasts a wide variety of scientific and technical applications (e.g., holographic interferometry for strain, vibration, and flow analysis, microscopy and high-resolution imagery, imaging through distorting media, optical interconnects, holographic optical elements, optical neural networks, three-dimensional displays, data storage, etc.), but has become a prominent am advertising, and security medium as well. The evolution of holographic optical memories has followed a path not altogether different from holography itself, with several cycles of alternating interest over the past four decades. P. J. van Heerden is widely credited for being the first to elucidate the principles behind holographic data storage in a 1963 paper, predicting bit storage densities on the order of 1/lambda(sup 3) with source wavelength lambda - a fantastic capacity of nearly 1 TB/cu cm for visible light! The science and engineering of such a storage paradigm was heavily pursued thereafter, resulting in many novel hologram multiplexing techniques for dense data storage, as well as important advances in holographic recording materials. Ultimately, however, the lack of such enabling technologies as compact laser sources and high performance optical data I/O devices dampened the hopes for the development of a commercial product. After a period of relative dormancy, successful applications of holography in other arenas sparked a renewed interest in holographic data storage in the late 1980s and the early 1990s. Currently, with most of the critical optoelectronic device technologies in place and the quest for an ideal holographic recording medium intensified, holography is once again considered as one of several future data storage paradigms that may answer our constantly growing need for higher-capacity and faster-access memories.
Timucin, Dogan A.↗
Three-dimensional coherent X-ray diffraction imaging via deep convolutional neural networks
Abstract As a critical component of coherent X-ray diffraction imaging (CDI), phase retrieval has been extensively applied in X-ray structural science to recover the 3D morphological information inside measured particles. Despite meeting all the oversampling requirements of Sayre and Shannon, current phase retrieval approaches still have trouble achieving a unique inversion of experimental data in the presence of noise. Here, we propose to overcome this limitation by incorporating a 3D Machine Learning (ML) model combining (optional) supervised learning with transfer learning. The trained ML model can rapidly provide an immediate result with high accuracy which could benefit real-time experiments, and the predicted result can be further refined with transfer learning. More significantly, the proposed ML model can be used without any prior training to learn the missing phases of an image based on minimization of an appropriate ‘loss function’ alone. We demonstrate significantly improved performance with experimental Bragg CDI data over traditional iterative phase retrieval algorithms.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Extending the Takagi-Taupin equations for x-ray nanobeam Bragg coherent diffraction
We present an approach for simulating x-ray nanobeam Bragg coherent diffraction patterns based on the Takagi-Taupin equations. Compared to conventional methods, the current approach can be universally applied to any weakly strained system including semi-infinite crystals that diffract dynamically. It addresses issues such as the curved wave front and redivergence of the focused incident beam. In conclusion, we show excellent agreement with experimental data for a strained La 0.7 Sr 0.3 MnO 3 thin film on a SrTiO 3 substrate and a path to extracting physical information using automatic differentiation.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗