Novel fabrication tools for dynamic compression targets with engineered voids using photolithography methods.

Mesoscale imperfections, such as pores and voids, can strongly modify the properties and the mechanical response of materials under extreme conditions. Tracking the material response and microstructure evolution during void collapse is crucial for understanding its performance. In particular, imperfections in the ablator materials, such as voids, can limit the efficiency of the fusion reaction and ultimately hinder ignition. To characterize how voids influence the response of materials during dynamic loading and seed hydrodynamic instabilities, we have developed a tailored fabrication procedure for designer targets with voids at specific locations. Our procedure uses SU-8 as a proxy for the ablator materials and hollow silica microspheres as a proxy for voids and pores. By using photolithography to design the targets' geometry, we demonstrate precise and highly reproducible placement of a single void within the sample, which is key for a detailed understanding of its behavior under shock compression. This fabrication technique will benefit high-repetition rate experiments at x-ray and laser facilities. Insight from shock compression experiments will provide benchmarks for the next generation of microphysics modeling.

Ring artifact and Poisson noise attenuation via volumetric multiscale nonlocal collaborative filtering of spatially correlated noise.

X-ray micro-tomography systems often suffer from high levels of noise. In particular, severe ring artifacts are common in reconstructed images, caused by defects in the detector, calibration errors, and fluctuations producing streak noise in the raw sinogram data. Furthermore, the projections commonly contain high levels of Poissonian noise arising from the photon-counting detector. This work presents a 3-D multiscale framework for streak attenuation through a purposely designed collaborative filtering of correlated noise in volumetric data. A distinct multiscale denoising step for attenuation of the Poissonian noise is further proposed. By utilizing the volumetric structure of the projection data, the proposed fully automatic procedure offers improved feature preservation compared with 2-D denoising and avoids artifacts which arise from individual filtering of sinograms.

Sizes of pure and doped helium droplets from single shot x-ray imaging.

Advancements in x-ray free-electron lasers on producing ultrashort, ultrabright, and coherent x-ray pulses enable single-shot imaging of fragile nanostructures, such as superfluid helium droplets. This imaging technique gives unique access to the sizes and shapes of individual droplets. In the past, such droplet characteristics have only been indirectly inferred by ensemble averaging techniques. Here, we report on the size distributions of both pure and doped droplets collected from single-shot x-ray imaging and produced from the free-jet expansion of helium through a 5 µm diameter nozzle at 20 bars and nozzle temperatures ranging from 4.2 to 9 K. This work extends the measurement of large helium nanodroplets containing 109-1011 atoms, which are shown to follow an exponential size distribution. Additionally, we demonstrate that the size distributions of the doped droplets follow those of the pure droplets at the same stagnation condition but with smaller average sizes.

Ring artifact reduction via multiscale nonlocal collaborative filtering of spatially correlated noise.

X-ray micro-tomography systems often suffer severe ring artifacts in reconstructed images. These artifacts are caused by defects in the detector, calibration errors, and fluctuations producing streak noise in the raw sinogram data. In this work, these streaks are modeled in the sinogram domain as additive stationary correlated noise upon logarithmic transformation. Based on this model, a streak removal procedure is proposed where the Block-Matching and 3-D (BM3D) filtering algorithm is applied across multiple scales, achieving state-of-the-art performance in both real and simulated data. Specifically, the proposed fully automatic procedure allows for attenuation of streak noise and the corresponding ring artifacts without creating major distortions common to other streak removal algorithms.

An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials.

The analysis of chemical states and morphology in nanomaterials is central to many areas of science. We address this need with an ultrahigh-resolution scanning transmission soft x-ray microscope. Our instrument provides multiple analysis tools in a compact assembly and can achieve few-nanometer spatial resolution and high chemical sensitivity via x-ray ptychography and conventional scanning microscopy. A novel scanning mechanism, coupled to advanced x-ray detectors, a high-brightness x-ray source, and high-performance computing for analysis provide a revolutionary step forward in terms of imaging speed and resolution. We present x-ray microscopy with 8-nm full-period spatial resolution and use this capability in conjunction with operando sample environments and cryogenic imaging, which are now routinely available. Our multimodal approach will find wide use across many fields of science and facilitate correlative analysis of materials with other types of probes.

Iterative X-ray spectroscopic ptychography.

Spectroscopic ptychography is a powerful technique to determine the chemical composition of a sample with high spatial resolution. In spectro-ptychography, a sample is rastered through a focused X-ray beam with varying photon energy so that a series of phaseless diffraction data are recorded. Each chemical component in the material under investigation has a characteristic absorption and phase contrast as a function of photon energy. Using a dictionary formed by the set of contrast functions of each energy for each chemical component, it is possible to obtain the chemical composition of the material from high-resolution multi-spectral images. This paper presents SPA (spectroscopic ptychography with alternating direction method of multipliers), a novel algorithm to iteratively solve the spectroscopic blind ptychography problem. First, a nonlinear spectro-ptychography model based on Poisson maximum likelihood is designed, and then the proposed method is constructed on the basis of fast iterative splitting operators. SPA can be used to retrieve spectral contrast when considering either a known or an incomplete (partially known) dictionary of reference spectra. By coupling the redundancy across different spectral measurements, the proposed algorithm can achieve higher reconstruction quality when compared with standard state-of-the-art two-step methods. It is demonstrated how SPA can recover accurate chemical maps from Poisson-noised measurements, and its enhanced robustness when reconstructing reduced-redundancy ptychography data using large scanning step sizes is shown.

Advanced denoising for X-ray ptychography.

The success of ptychographic imaging experiments strongly depends on achieving high signal-to-noise ratio. This is particularly important in nanoscale imaging experiments when diffraction signals are very weak and the experiments are accompanied by significant parasitic scattering (background), outliers or correlated noise sources. It is also critical when rare events, such as cosmic rays, or bad frames caused by electronic glitches or shutter timing malfunction take place. In this paper, we propose a novel iterative algorithm with rigorous analysis that exploits the direct forward model for parasitic noise and sample smoothness to achieve a thorough characterization and removal of structured and random noise. We present a formal description of the proposed algorithm and prove its convergence under mild conditions. Numerical experiments from simulations and real data (both soft and hard X-ray beamlines) demonstrate that the proposed algorithms produce better results when compared to state-of-the-art methods.

Shaping coherent x-rays with binary optics.

Diffractive lenses fabricated by lithographic methods are one of the most popular image forming optics in the x-ray regime. Most commonly, binary diffractive optics, such as Fresnel zone plates, are used due to their ability to focus at high resolution and to manipulate the x-ray wavefront. We report here a binary zone plate design strategy to form arbitrary illuminations for coherent multiplexing, structured illumination, and wavefront shaping experiments. Given a desired illumination, we adjust the duty cycle, harmonic order, and zone placement to vary both the amplitude and phase of the wavefront at the lens. This enables the binary lithographic pattern to generate arbitrary structured illumination optimized for a variety of applications such as holography, interferometry, ptychography, imaging, and others.

Denoising Poisson phaseless measurements via orthogonal dictionary learning.

Phaseless diffraction measurements recorded by CCD detectors are often affected by Poisson noise. In this paper, we propose a dictionary learning model by employing patches based sparsity in order to denoise such Poisson phaseless measurements. The model consists of three terms: (i) A representation term by an orthogonal dictionary, (ii) an L0 pseudo norm of the coefficient matrix, and (iii) a Kullback-Leibler divergence term to fit phaseless Poisson data. Fast alternating minimization method (AMM) and proximal alternating linearized minimization (PALM) are adopted to solve the proposed model, and especially the theoretical guarantee of the convergence of PALM is provided. The subproblems for these two algorithms both have fast solvers, and indeed, the solutions for the sparse coding and dictionary updating both have closed forms due to the orthogonality of learned dictionaries. Numerical experiments for phase retrieval using coded diffraction and ptychographic patterns are conducted to show the efficiency and robustness of proposed methods, which, by preserving texture features, produce visually and quantitatively improved restored images compared with other phase retrieval algorithms without regularization and local sparsity promoting algorithms.

Xi-cam: a versatile interface for data visualization and analysis.

Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. With Xi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data. Xi-cam's plugin-based architecture targets cross-facility and cross-technique collaborative development, in support of multi-modal analysis. Xi-cam is open-source and cross-platform, and available for download on GitHub.

Partially coherent ptychography by gradient decomposition of the probe.

Coherent ptychographic imaging experiments often discard the majority of the flux from a light source to define the coherence of the illumination. Even when the coherent flux is sufficient, the stability required during an exposure is another important limiting factor. Partial coherence analysis can considerably reduce these limitations. A partially coherent illumination can often be written as the superposition of a single coherent illumination convolved with a separable translational kernel. This article proposes the gradient decomposition of the probe (GDP), a model that exploits translational kernel separability, coupling the variances of the kernel with the transverse coherence. An efficient first-order splitting algorithm (GDP-ADMM) for solving the proposed nonlinear optimization problem is described. Numerical experiments demonstrate the effectiveness of the proposed method with Gaussian and binary kernel functions in fly-scan measurements. Remarkably, GDP-ADMM using nanoprobes produces satisfactory results even when the ratio between the kernel width and the beam size is more than one, or when the distance between successive acquisitions is twice as large as the beam width.

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography.

Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.

Nanosurveyor: a framework for real-time data processing.

BACKGROUND: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. RESULTS: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis. CONCLUSIONS: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the microscope operators.

Measuring spectroscopy and magnetism of extracted and intracellular magnetosomes using soft X-ray ptychography.

Characterizing the chemistry and magnetism of magnetotactic bacteria (MTB) is an important aspect of understanding the biomineralization mechanism and function of the chains of magnetosomes (Fe3O4 nanoparticles) found in such species. Images and X-ray absorption spectra (XAS) of magnetosomes extracted from, and magnetosomes in, whole Magnetovibrio blakemorei strain MV-1 cells have been recorded using soft X-ray ptychography at the Fe 2p edge. A spatial resolution of 7 nm is demonstrated. Precursor-like and immature magnetosome phases in a whole MV-1 cell were visualized, and their Fe 2p spectra were measured. Based on these results, a model for the pathway of magnetosome biomineralization for MV-1 is proposed. Fe 2p X-ray magnetic circular dichroism (XMCD) spectra have been derived from ptychography image sequences recorded using left and right circular polarization. The shape of the XAS and XMCD signals in the ptychographic absorption spectra of both sample types is identical to the shape and signals measured with conventional bright-field scanning transmission X-ray microscope. A weaker and inverted XMCD signal was observed in the ptychographic phase spectra of the extracted magnetosomes. The XMCD ptychographic phase spectrum of the intracellular magnetosomes differed from the ptychographic phase spectrum of the extracted magnetosomes. These results demonstrate that spectro-ptychography offers a superior means of characterizing the chemical and magnetic properties of MTB at the individual magnetosome level.

Effects of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO4 Porous Electrodes.

High-resolution X-ray microscopy is used to investigate the sequence of lithiation in LiFePO4 porous electrodes. For electrodes with homogeneous interparticle electronic connectivity via the carbon black network, the smaller particles lithiate first. For electrodes with heterogeneous connectivity, the better-connected particles preferentially lithiate. Correlative electron and X-ray microscopy also reveal the presence of incoherent nanodomains that lithiate as if they are separate particles.

Dependence on Crystal Size of the Nanoscale Chemical Phase Distribution and Fracture in LixFePO4.

The performance of battery electrode materials is strongly affected by inefficiencies in utilization kinetics and cycle life as well as size effects. Observations of phase transformations in these materials with high chemical and spatial resolution can elucidate the relationship between chemical processes and mechanical degradation. Soft X-ray ptychographic microscopy combined with X-ray absorption spectroscopy and electron microscopy creates a powerful suite of tools that we use to assess the chemical and morphological changes in lithium iron phosphate (LiFePO4) micro- and nanocrystals that occur upon delithiation. All sizes of partly delithiated crystals were found to contain two phases with a complex correlation between crystallographic orientation and phase distribution. However, the lattice mismatch between LiFePO4 and FePO4 led to severe fracturing on microcrystals, whereas no mechanical damage was observed in nanoplates, indicating that mechanics are a principal driver in the outstanding electrode performance of LiFePO4 nanoparticles. These results demonstrate the importance of engineering the active electrode material in next generation electrical energy storage systems, which will achieve theoretical limits of energy density and extended stability. This work establishes soft X-ray ptychographic chemical imaging as an essential tool to build comprehensive relationships between mechanics and chemistry that guide this engineering design.

Quantitative phase-contrast confocal microscope.

We present a quantitative phase-contrast confocal microscope (QPCCM) by combining a line-scanning confocal system with digital holography (DH). This combination can merge the merits of these two different imaging modalities. High-contrast intensity images with low coherent noise, and the optical sectioning capability are made available due to the confocality. Phase profiles of the samples become accessible thanks to DH. QPCCM is able to quantitatively measure the phase variations of optical sections of the opaque samples and has the potential to take high-quality intensity and phase images of non-opaque samples such as many biological samples. Because each line scan is recorded by a hologram that may contain the optical aberrations of the system, it opens avenues for a variety of numerical aberration compensation methods and development of full digital adaptive optics confocal system to emulate current hardware-based adaptive optics system for biomedical imaging, especially ophthalmic imaging. Preliminary experiments with a microscope objective of NA 0.65 and 40 × on opaque samples are presented to demonstrate this idea. The measured lateral and axial resolutions of the intensity images from the current system are ~0.64µm and ~2.70µm respectively. The noise level of the phase profile by QPCCM is ~2.4nm which is better than the result by DH.

Helium superfluidity. Shapes and vorticities of superfluid helium nanodroplets.

Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~10(8) to 10(11) atoms. The formation of quantum vortex lattices inside the droplets is confirmed by observing characteristic Bragg patterns from xenon clusters trapped in the vortex cores. The vortex densities are up to five orders of magnitude larger than those observed in bulk liquid helium. The droplets exhibit large centrifugal deformations but retain axially symmetric shapes at angular velocities well beyond the stability range of viscous classical droplets.

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

Sensing the wavefront of x-ray free-electron lasers using aerosol spheres.

Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 10(21) W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.