Strain in a silicon-on-insulator nanostructure revealed by 3D x-ray Bragg ptychography

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.

Fast nanoscale imaging of strain in a multi-segment heterostructured nanowire with 2D Bragg ptychography

Developing semiconductor devices requires a fast and reliable source of strain information with high spatial resolution and strain sensitivity. This work investigates the strain in an axially heterostructured 180 nm-diameter GaInP nanowire with InP segments of varying lengths down to 9 nm, simultaneously probing both materials. Scanning X-ray diffraction (XRD) is compared with Bragg projection ptychography (BPP), a fast single-projection method. BPP offers a sufficient spatial resolution to reveal fine details within the largest segments, unlike scanning XRD. The spatial resolution affects the quantitative accuracy of the strain maps, where BPP shows much-improved agreement with an elastic 3D finite element model compared with scanning XRD. The sensitivity of BPP to small deviations from the Bragg condition is systematically investigated. The experimental confirmation of the model suggests that the large lattice mismatch of 1.52% is accommodated without defects.

Optical ptychography for biomedical imaging: recent progress and future directions [Invited]

Ptychography is an enabling microscopy technique for both fundamental and applied sciences. In the past decade, it has become an indispensable imaging tool in most X-ray synchrotrons and national laboratories worldwide. However, ptychography's limited resolution and throughput in the visible light regime have prevented its wide adoption in biomedical research. Recent developments in this technique have resolved these issues and offer turnkey solutions for high-throughput optical imaging with minimum hardware modifications. The demonstrated imaging throughput is now greater than that of a high-end whole slide scanner. In this review, we discuss the basic principle of ptychography and summarize the main milestones of its development. Different ptychographic implementations are categorized into four groups based on their lensless/lens-based configurations and coded-illumination/coded-detection operations. We also highlight the related biomedical applications, including digital pathology, drug screening, urinalysis, blood analysis, cytometric analysis, rare cell screening, cell culture monitoring, cell and tissue imaging in 2D and 3D, polarimetric analysis, among others. Ptychography for high-throughput optical imaging, currently in its early stages, will continue to improve in performance and expand in its applications. We conclude this review article by pointing out several directions for its future development.

4th generation synchrotron source boosts crystalline imaging at the nanoscale

New 4^th-generation synchrotron sources, with their increased brilliance, promise to greatly improve the performances of coherent X-ray microscopy. This perspective is of major interest for crystal microscopy, which aims at revealing the 3D crystalline structure of matter at the nanoscale, an approach strongly limited by the available coherent flux. Our results, based on Bragg ptychography experiments performed at the first 4^th-generation synchrotron source, demonstrate the possibility of retrieving a high-quality image of the crystalline sample, with unprecedented quality. Importantly, the larger available coherent flux produces datasets with enough information to overcome experimental limitations, such as strongly deteriorated scanning conditions. We show this achievement would not be possible with 3^rd-generation sources, a limit that has inhibited the development of this otherwise powerful microscopy method, so far. Hence, the advent of next-generation synchrotron sources not only makes Bragg ptychography suitable for high throughput studies but also strongly relaxes the associated experimental constraints, making it compatible with a wider range of experimental set-ups at the new synchrotrons.

Revealing nano-scale lattice distortions in implanted material with 3D Bragg ptychography

Small ion-irradiation-induced defects can dramatically alter material properties and speed up degradation. Unfortunately, most of the defects irradiation creates are below the visibility limit of state-of-the-art microscopy. As such, our understanding of their impact is largely based on simulations with major unknowns. Here we present an x-ray crystalline microscopy approach, able to image with high sensitivity, nano-scale 3D resolution and extended field of view, the lattice strains and tilts in crystalline materials. Using this enhanced Bragg ptychography tool, we study the damage helium-ion-irradiation produces in tungsten, revealing a series of crystalline details in the 3D sample. Our results lead to the conclusions that few-atom-large 'invisible' defects are likely isotropic in orientation and homogeneously distributed. A partially defect-denuded region is observed close to a grain boundary. These findings open up exciting perspectives for the modelling of irradiation damage and the detailed analysis of crystalline properties in complex materials.

Geometrical-optics formalism to model contrast in dark-field X-ray microscopy

Dark-field X-ray microscopy, DFXM, is a new full-field imaging technique that non-destructively maps the structure and local strain inside deeply embedded crystalline elements in three dimensions. In DFXM an objective lens is placed along the diffracted beam to generate a magnified projection image of the local diffracted volume. In this work, a general formalism based on geometrical optics is provided for the diffraction imaging, valid for any crystallographic space group. This allows the simulation of DFXM images based on micro-mechanical models. Example simulations are presented with the formalism, demonstrating how this may be used to design new experiments or to interpret existing ones. In particular, it is shown how modifications to the experimental design may tailor the reciprocal-space resolution function to map specific components of the deformation-gradient tensor. The formalism supports multi-length-scale experiments, as it enables DFXM to be interfaced with 3D X-ray diffraction. To illustrate the use of the formalism, DFXM images are simulated from different contrast mechanisms on the basis of the strain field around a straight dislocation.

On the use of the scattering amplitude in coherent X-ray Bragg diffraction imaging

Lens-less imaging of crystals with coherent X-ray diffraction offers some unique possibilities for strain-field characterization. It relies on numerically retrieving the phase of the scattering amplitude from a crystal illuminated with coherent X-rays. In practice, the algorithms encode this amplitude as a discrete Fourier transform of an effective or Bragg electron density. This short article suggests a detailed route from the classical expression of the (continuous) scattering amplitude to this discrete function. The case of a heterogeneous incident field is specifically detailed. Six assumptions are listed and quantitatively discussed when no such analysis was found in the literature. Details are provided for two of them: the fact that the structure factor varies in the vicinity of the probed reciprocal lattice vector, and the polarization factor, which is heterogeneous along the measured diffraction patterns. With progress in X-ray sources, data acquisition and analysis, it is believed that some approximations will prove inappropriate in the near future.

Removal of spurious data in Bragg coherent diffraction imaging: an algorithm for automated data preprocessing

Bragg coherent diffraction imaging (BCDI) provides a powerful tool for obtaining high-resolution structural information from nanocrystalline materials. Here a BCDI sample consisting of a large number of randomly oriented nanoscale crystals is considered. Ideally, only one crystal is oriented to produce a Bragg peak on the detector. However, diffraction from other crystals often produces additional signals on the detector. Before the measured diffraction patterns can be processed into structural images, scientists routinely need to manually identify and remove the `alien' intensities from sources other than the intended crystal. With the development of modern high-coherence storage rings, such as the upgraded Advanced Photon Source (APS), the already slow process of manual preprocessing will be untenable for the large volumes of data that will be produced. An automated method of identifying and deleting alien intensities is proposed. This method exploits the fact that BCDI of a perfect crystal produces diffraction data with inversion symmetry around the Bragg peak. This approach uses the machine learning clustering method DBSCAN to distinguish between diffraction from multiple sources, and then calculates cluster size and inversion symmetry to assess whether clusters of intensity belong to desired data or alien signals. This approach can dramatically reduce the amount of time spent manually processing data, allowing BCDI data processing capabilities to keep pace with the technological advances of fourth-generation synchrotron light sources.

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.

Strain mapping inside an individual processed vertical nanowire transistor using scanning X-ray nanodiffraction

Semiconductor nanowires in wrapped, gate-all-around transistor geometry are highly favorable for future electronics. The advanced nanodevice processing results in strain due to the deposited dielectric and metal layers surrounding the nanowires, significantly affecting their performance. Therefore, non-destructive nanoscale characterization of complete devices is of utmost importance due to the small feature sizes and three-dimensional buried structure. Direct strain mapping inside heterostructured GaSb-InAs nanowire tunnel field-effect transistor embedded in dielectric HfO2, W metal gate layers, and an organic spacer is performed using fast scanning X-ray nanodiffraction. The effect of 10 nm W gate on a single embedded nanowire with segment diameters down to 40 nm is retrieved. The tensile strain values reach 0.26% in the p-type GaSb segment of the transistor. Supported by the finite element method simulation, we establish a connection between the Ar pressure used during the W layer deposition and the nanowire strain state. Thus, we can benchmark our models for further improvements in device engineering. Our study indicates, how the significant increase in X-ray brightness at 4th generation synchrotron, makes high-throughput measurements on realistic nanoelectronic devices viable.

Confocal Bragg ptychography for bulk specimens: a numerical demonstration

We report on a new X-ray imaging method, which generalizes Bragg ptychography to 3D mapping of embedded crystalline volumes within thick specimens. The sample is probed by a pencil X-ray beam. The diffracted beam is magnified by an objective and passes through a slit in the image plane to be monitored by a 2D detector in the far-field of the image plane. The dimensions of the incoming beam and the slit opening define a confocal Bragg volume. Scanning the sample with respect to this probe volume, an iterative oversampling routine is used to reconstruct the shape and projected displacement field of extended internal volumes. This routine takes into account the pupil function and known aberrations of the lens. We demonstrate the method by a numerical study of a 3.5 µm grain comprising a wall of edge dislocations. With a probe volume of ∼0.12 µm³ and a compound refractive lens with a numerical aperture of 0.49×10^-3 as the objective, the dislocations are fully resolved with a displacement sensitivity of ∼10 pm. The spatial resolution is 26×27×123 nm³ (rms), with the poor resolution along the optical axis being limited by the probe size. With a four times larger numerical aperture, the resolution becomes 16×8×123 nm³ (rms). The lens aberrations are found to be not critical.

Using automatic differentiation as a general framework for ptychographic reconstruction

Coherent diffraction imaging methods enable imaging beyond lens-imposed resolution limits. In these methods, the object can be recovered by minimizing an error metric that quantifies the difference between diffraction patterns as observed, and those calculated from a present guess of the object. Efficient minimization methods require analytical calculation of the derivatives of the error metric, which is not always straightforward. This limits our ability to explore variations of basic imaging approaches. In this paper, we propose to substitute analytical derivative expressions with the automatic differentiation method, whereby we can achieve object reconstruction by specifying only the physics-based experimental forward model. We demonstrate the generality of the proposed method through straightforward object reconstruction for a variety of complex ptychographic experimental models.

Influence of the elastic deformations on the form factor of polyhedral nanocrystals: the illustrative example of the pseudomorphic inclusion

Using an analytically tractable example, the pseudomorphic inclusion, this article examines the influence of elastic deformations on the form factor of polyhedral nanocrystals. A control parameter, the total amplitude of the variation of the complex density phase, is identified and it is shown that for low enough deformations the characteristic asymptotic behaviours as a function of the scattering vector associated with the polyhedral crystal shape are preserved, leading to a strong contrast in the dependence of the form factor on orientation. Using the sections method, it is explained why these results can be generalized to more realistic elastic situations.

Three-Dimensional Imaging of Phase Ordering in an Fe-Al Alloy by Bragg Ptychography

We show three-dimensional images of phase ordering in a Fe_{55}Al_{45} alloy obtained by coherent x-ray diffraction Bragg ptychography. Fe-Al alloys display ordered phases where the atoms organize on sublattices resulting in the emergence of otherwise forbidden superlattice reflections. The degeneracy of the ordering results in antiphase domain boundaries that, in addition to the general lattice strain, provide phase shifts of the diffracted beam depending on the reflection. The reconstructed phase images can be separated into components originating from B2 phase domains and lattice strain by performing Bragg ptychography on both the (002) fundamental and the (001) superlattice reflections.

Numerical study of Bragg CDI on thick polycrystalline specimens

Bragg coherent diffraction imaging (BCDI) is a powerful X-ray imaging technique for crystalline materials, providing high resolution maps of structure and strain. The technique is typically used to study a small isolated object, and is in general not compatible with a bulk polycrystalline sample, due to overlap of diffraction signals from various crystalline elements. In this paper, we present an imaging method for bulk samples, based on the use of a coherent source. The diffracted X-ray beam from a grain or domain of choice is magnified by an objective before being monitored by a 2D detector in the far field. The reconstruction principle is similar to the case of BCDI, while taking the magnification and pupil function into account. The concept is demonstrated using numerical simulations and reconstructions. We find that by using an object-lens distance shorter than the focal length, the numerical aperture is larger than in a traditional imaging geometry, and at the same time the setup is insensitive to small phase errors by lens imperfections. According to our simulations, we expect to be able to achieve a spatial resolution smaller than 20 nm when using the objective lens in this configuration.

Towards in situ determination of 3D strain and reorientation in the interpenetrating nanofibre networks of cuticle

Determining the in situ 3D nano- and microscale strain and reorientation fields in hierarchical nanocomposite materials is technically very challenging. Such a determination is important to understand the mechanisms enabling their functional optimization. An example of functional specialization to high dynamic mechanical resistance is the crustacean stomatopod cuticle. Here we develop a new 3D X-ray nanostrain reconstruction method combining analytical modelling of the diffraction signal, fibre-composite theory and in situ deformation, to determine the hitherto unknown nano- and microscale deformation mechanisms in stomatopod tergite cuticle. Stomatopod cuticle at the nanoscale consists of mineralized chitin fibres and calcified protein matrix, which form (at the microscale) plywood (Bouligand) layers with interpenetrating pore-canal fibres. We uncover anisotropic deformation patterns inside Bouligand lamellae, accompanied by load-induced fibre reorientation and pore-canal fibre compression. Lamination theory was used to decouple in-plane fibre reorientation from diffraction intensity changes induced by 3D lamellae tilting. Our method enables separation of deformation dynamics at multiple hierarchical levels, a critical consideration in the cooperative mechanics characteristic of biological and bioinspired materials. The nanostrain reconstruction technique is general, depending only on molecular-level fibre symmetry and can be applied to the in situ dynamics of advanced nanostructured materials with 3D hierarchical design.

X-ray Bragg Ptychography on a Single InGaN/GaN Core-Shell Nanowire

The future of solid-state lighting can be potentially driven by applications of InGaN/GaN core-shell nanowires. These heterostructures provide the possibility for fine-tuning of functional properties by controlling a strain state between mismatched layers. We present a nondestructive study of a single 400 nm-thick InGaN/GaN core-shell nanowire using two-dimensional (2D) X-ray Bragg ptychography (XBP) with a nanofocused X-ray beam. The XBP reconstruction enabled the determination of a detailed three-dimensional (3D) distribution of the strain in the particular nanowire using a model based on finite element method. We observed the strain induced by the lattice mismatch between the GaN core and InGaN shell to be in the range from -0.1% to 0.15% for an In concentration of 30%. The maximum value of the strain component normal to the facets was concentrated at the transition region between the main part of the nanowire and the GaN tip. In addition, a variation in misfit strain relaxation between the axial growth and in-plane directions was revealed.

Deterministic Bragg Coherent Diffraction Imaging

A deterministic variant of Bragg Coherent Diffraction Imaging is introduced in its kinematical approximation, for X-ray scattering from an imperfect crystal whose imperfections span no more than half of the volume of the crystal. This approach provides a unique analytical reconstruction of the object's structure factor and displacement fields from the 3D diffracted intensity distribution centred around any particular reciprocal lattice vector. The simple closed-form reconstruction algorithm, which requires only one multiplication and one Fourier transformation, is not restricted by assumptions of smallness of the displacement field. The algorithm performs well in simulations incorporating a variety of conditions, including both realistic levels of noise and departures from ideality in the reference (i.e. imperfection-free) part of the crystal.

High-resolution three-dimensional structural microscopy by single-angle Bragg ptychography

Coherent X-ray microscopy by phase retrieval of Bragg diffraction intensities enables lattice distortions within a crystal to be imaged at nanometre-scale spatial resolutions in three dimensions. While this capability can be used to resolve structure-property relationships at the nanoscale under working conditions, strict data measurement requirements can limit the application of current approaches. Here, we introduce an efficient method of imaging three-dimensional (3D) nanoscale lattice behaviour and strain fields in crystalline materials with a methodology that we call 3D Bragg projection ptychography (3DBPP). This method enables 3D image reconstruction of a crystal volume from a series of two-dimensional X-ray Bragg coherent intensity diffraction patterns measured at a single incident beam angle. Structural information about the sample is encoded along two reciprocal-space directions normal to the Bragg diffracted exit beam, and along the third dimension in real space by the scanning beam. We present our approach with an analytical derivation, a numerical demonstration, and an experimental reconstruction of lattice distortions in a component of a nanoelectronic prototype device.

A computational framework for ptychographic reconstructions

Ptychography is now a well-established X-ray microscopy tool for synchrotron end-stations equipped with a scanning stage and a pixelated detector. Ptychographic phasing algorithms use information from coherent diffraction to deliver quantitative images of the specimen at a resolution higher than the scanning resolution. These algorithms have traditionally been implemented in software on a per-instrument basis in various degrees of user-friendliness and sophistication. Here, we present Ptypy, a ptychography software written with the intention to serve as a framework across the diverse sets of available instruments and usage cases. A distinctive feature of the software is its formalism, which provides a convenient abstraction of the physical model, thus allowing for concise algorithmic implementations and portability across set-up geometries. We give an overview of the supported usage cases, explain the abstraction layer and design principles, and provide a step-by-step guide describing how an algorithm may be realized in a concise and readable manner. The software capabilities are illustrated with reconstructions from visible light and X-ray data.

PyNX.Ptycho: a computing library for X-ray coherent diffraction imaging of nanostructures

X-ray imaging techniques have undergone a remarkable development during the past decade, taking advantage of coherent X-ray sources. Among these techniques, ptychography allows reconstruction of the specimen and the illumination probe from a series of diffraction patterns without any prior knowledge about the sample. However, the reconstruction of the ptychographic data remains challenging and the reconstruction software is often not publicly available. Presented here is an open-source library for the reconstruction of two-dimensional ptychographic data, written in Python. This library implements existing algorithms, with examples of data reconstruction on both simulated and experimental (Bragg ptychography on heterogeneous strained InAs/GaAs nanowires) data sets. It can be used for educational (simulation) purposes or experimental data analysis, and also features an OpenCL version of the ptychography algorithm for high-performance computing.

Imperfection and radiation damage in protein crystals studied with coherent radiation

Fringes and speckles occur within diffraction spots when a crystal is illuminated with coherent radiation during X-ray diffraction. The additional information in these features provides insight into the imperfections in the crystal at the sub-micrometre scale. In addition, these features can provide more accurate intensity measurements (e.g. by model-based profile fitting), detwinning (by distinguishing the various components), phasing (by exploiting sampling of the molecular transform) and refinement (by distinguishing regions with different unit-cell parameters). In order to exploit these potential benefits, the features due to coherent diffraction have to be recorded and any change due to radiation damage properly modelled. Initial results from recording coherent diffraction at cryotemperatures from polyhedrin crystals of approximately 2 µm in size are described. These measurements allowed information about the type of crystal imperfections to be obtained at the sub-micrometre level, together with the changes due to radiation damage.

Ptychography in anisotropic media

This letter describes ptychography in the context of polarized light probing anisotropic specimen (i.e., showing properties of birefringence and/or diattenuation). We established an optimization strategy using a vectorial formalism. We propose a measurement scheme using a set of linearly polarized probes and linear polarization analyzers, which allows the retrieval of the full anisotropy map of the specimen.