Non-negative matrix factorization-aided phase unmixing and trace element quantification of STEM-EDXS data.

Energy-dispersive X-ray spectroscopy (EDXS) mapping with a scanning transmission electron microscope (STEM) is commonly used for chemical characterization of materials. However, STEM-EDXS quantification becomes challenging when the phases constituting the sample under investigation share common elements and overlap spatially. In this paper, we present a methodology to identify, segment, and unmix phases with a substantial spectral and spatial overlap in a semi-automated fashion through combining non-negative matrix factorization with a priori knowledge of the sample. We illustrate the methodology using a sample taken from an electron beam-sensitive mineral assemblage representing Earth's deep mantle. With it, we retrieve the true EDX spectra of the constituent phases and their corresponding phase abundance maps. It further enables us to achieve a reliable quantification for trace elements having concentration levels of ∼100 ppm. Our approach can be adapted to aid the analysis of many materials systems that produce STEM-EDXS datasets having phase overlap and/or limited signal-to-noise ratio (SNR) in spatially-integrated spectra.

espm: A Python library for the simulation of STEM-EDXS datasets.

We present two open-source Python packages: "electron spectro-microscopy" (espm) and "electron microscopy tables" (emtables). The espm software enables the simulation of scanning transmission electron microscopy energy-dispersive X-ray spectroscopy datacubes, based on user-defined chemical compositions and spatial abundance maps of constituent phases. The simulation process uses X-ray emission cross-sections generated via state-of-the-art calculations made with emtables. These tables are designed to be easily modifiable, either manually or using espm. The simulation framework is designed to test the application of decomposition algorithms for the analysis of STEM-EDX spectrum images with access to a known ground truth. We validate our approach using the case of a complex geology-related sample, comparing raw simulated and experimental datasets and the outputs of their non-negative matrix factorization. In addition to testing machine learning algorithms, our packages will also help experimental design, for instance, predicting dataset characteristics or establishing minimum counts needed to measure nanoscale features.

3D reconstruction of curvilinear structures with stereo matching deep convolutional neural networks.

Curvilinear structures frequently appear in microscopy imaging as the object of interest. Crystallographic defects, i.e dislocations, are one of the curvilinear structures that have been repeatedly investigated under transmission electron microscopy (TEM) and their 3D structural information is of great importance for understanding the properties of materials. 3D information of dislocations is often obtained by tomography which is a cumbersome process since it is required to acquire many images with different tilt angles and similar imaging conditions. Although, alternative stereoscopy methods lower the number of required images to two, they still require human intervention and shape priors for accurate 3D estimation. We propose a fully automated pipeline for both detection and matching of curvilinear structures in stereo pairs by utilizing deep convolutional neural networks (CNNs) without making any prior assumption on 3D shapes. In this work, we mainly focus on 3D reconstruction of dislocations from stereo pairs of TEM images.

Investigating Magma Ocean Solidification on Earth Through Laser-Heated Diamond Anvil Cell Experiments.

We carried out a series of silicate fractional crystallization experiments at lower mantle pressures using the laser-heated diamond anvil cell. Phase relations and the compositional evolution of the cotectic melt and equilibrium solids along the liquid line of descent were determined and used to assemble the melting phase diagram. In a pyrolitic magma ocean, the first mineral to crystallize in the deep mantle is iron-depleted calcium-bearing bridgmanite. From the phase diagram, we estimate that the initial 33%-36% of the magma ocean will crystallize to form such a buoyant bridgmanite. Substantial calcium solubility in bridgmanite is observed up to 129 GPa, and significantly delays the crystallization of the calcium silicate perovskite phase during magma ocean solidification. Residual melts are strongly iron-enriched as crystallization proceeds, making them denser than any of the coexisting solids at deep mantle conditions, thus supporting the terrestrial basal magma ocean hypothesis (Labrosse et al., 2007).

3D Ordering at the Liquid-Solid Polar Interface of Nanowires.

The nature of the liquid-solid interface determines the characteristics of a variety of physical phenomena, including catalysis, electrochemistry, lubrication, and crystal growth. Most of the established models for crystal growth are based on macroscopic thermodynamics, neglecting the atomistic nature of the liquid-solid interface. Here, experimental observations and molecular dynamics simulations are employed to identify the 3D nature of an atomic-scale ordering of liquid Ga in contact with solid GaAs in a nanowire growth configuration. An interplay between the liquid ordering and the formation of a new bilayer is revealed, which, contrary to the established theories, suggests that the preference for a certain polarity and polytypism is influenced by the atomic structure of the interface. The conclusions of this work open new avenues for the understanding of crystal growth, as well as other processes and systems involving a liquid-solid interface.

A large planetary body inferred from diamond inclusions in a ureilite meteorite.

Planetary formation models show that terrestrial planets are formed by the accretion of tens of Moon- to Mars-sized planetary embryos through energetic giant impacts. However, relics of these large proto-planets are yet to be found. Ureilites are one of the main families of achondritic meteorites and their parent body is believed to have been catastrophically disrupted by an impact during the first 10 million years of the solar system. Here we studied a section of the Almahata Sitta ureilite using transmission electron microscopy, where large diamonds were formed at high pressure inside the parent body. We discovered chromite, phosphate, and (Fe,Ni)-sulfide inclusions embedded in diamond. The composition and morphology of the inclusions can only be explained if the formation pressure was higher than 20 GPa. Such pressures suggest that the ureilite parent body was a Mercury- to Mars-sized planetary embryo.

Stereo-vision three-dimensional reconstruction of curvilinear structures imaged with a TEM.

Deriving accurate three-dimensional (3-D) structural information of materials at the nanometre level is often crucial for understanding their properties. Tomography in transmission electron microscopy (TEM) is a powerful technique that provides such information. It is however demanding and sometimes inapplicable, as it requires the acquisition of multiple images within a large tilt arc and hence prolonged exposure to electrons. In some cases, prior knowledge about the structure can tremendously simplify the 3-D reconstruction if incorporated adequately. Here, a novel algorithm is presented that is able to produce a full 3-D reconstruction of curvilinear structures from stereo pair of TEM images acquired within a small tilt range that spans from only a few to tens of degrees. Reliability of the algorithm is demonstrated through reconstruction of a model 3-D object from its simulated projections, and is compared with that of conventional tomography. This method is experimentally demonstrated for the 3-D visualization of dislocation arrangements in a deformed metallic micro-pillar.

Tilt-less 3-D electron imaging and reconstruction of complex curvilinear structures.

The ability to obtain three-dimensional (3-D) information about morphologies of nanostructures elucidates many interesting properties of materials in both physical and biological sciences. Here we demonstrate a novel method in scanning transmission electron microscopy (STEM) that gives a fast and reliable assessment of the 3-D configuration of curvilinear nanostructures, all without needing to tilt the sample through an arc. Using one-dimensional crystalline defects known as dislocations as a prototypical example of a complex curvilinear object, we demonstrate their 3-D reconstruction two orders of magnitude faster than by standard tilt-arc TEM tomographic techniques, from data recorded by selecting different ray paths of the convergent STEM probe. Due to its speed and immunity to problems associated with a tilt arc, the tilt-less 3-D imaging offers important advantages for investigations of radiation-sensitive, polycrystalline, or magnetic materials. Further, by using a segmented detector, the total electron dose is reduced to a single STEM raster scan acquisition; our tilt-less approach will therefore open new avenues for real-time 3-D electron imaging of dynamic processes.

Direct Imaging of Dopant Distribution in Polycrystalline ZnO Films.

Two fundamental requirements of transparent conductive oxides are high conductivity and low optical absorptance, properties strongly dependent on the free-carrier concentration of the film. The free-carrier concentration is usually tuned by the addition of dopant atoms; which are commonly assumed to be uniformly distributed in the films or partially segregated at grain boundaries. Here, the combination of secondary ion mass spectroscopy at the nanometric scale (NanoSIMS) and Kelvin probe force microscopy (KPFM) allows direct imaging of boron-dopant distribution in polycrystalline zinc oxide (ZnO) films. This work demonstrates that the boron atoms have a bimodal spatial distribution within each grain of the ZnO films. NanoSIMS analysis shows that boron atoms are preferentially incorporated into one of the two sides of each ZnO grain. KPFM measurements confirm that boron atoms are electrically active, locally increasing the free-carrier concentration in the film. The proposed cause of this nonuniform dopant distribution is the different sticking coefficient of Zn adatoms on the two distinct surface terminations of the ZnO grains. The higher sticking coefficient of Zn on the c+ surface restricts the boron incorporation on this side of the grains, resulting in preferential boron incorporation on the c- side and causing the bimodal distribution.

Spin and valence dependence of iron partitioning in Earth's deep mantle.

We performed laser-heated diamond anvil cell experiments combined with state-of-the-art electron microanalysis (focused ion beam and aberration-corrected transmission electron microscopy) to study the distribution and valence of iron in Earth's lower mantle as a function of depth and composition. Our data reconcile the apparently discrepant existing dataset, by clarifying the effects of spin (high/low) and valence (ferrous/ferric) states on iron partitioning in the deep mantle. In aluminum-bearing compositions relevant to Earth's mantle, iron concentration in silicates drops above 70 GPa before increasing up to 110 GPa with a minimum at 85 GPa; it then dramatically drops in the postperovskite stability field above 116 GPa. This compositional variation should strengthen the lowermost mantle between 1,800 km depth and 2,000 km depth, and weaken it between 2,000 km depth and the D" layer. The succession of layers could dynamically decouple the mantle above 2,000 km from the lowermost mantle, and provide a rheological basis for the stabilization and nonentrainment of large low-shear-velocity provinces below that depth.

Direct visualization of dispersed lipid bicontinuous cubic phases by cryo-electron tomography.

Bulk and dispersed cubic liquid crystalline phases (cubosomes), present in the body and in living cell membranes, are believed to play an essential role in biological phenomena. Moreover, their biocompatibility is attractive for nutrient or drug delivery system applications. Here the three-dimensional organization of dispersed cubic lipid self-assembled phases is fully revealed by cryo-electron tomography and compared with simulated structures. It is demonstrated that the interior is constituted of a perfect bicontinuous cubic phase, while the outside shows interlamellar attachments, which represent a transition state between the liquid crystalline interior phase and the outside vesicular structure. Therefore, compositional gradients within cubosomes are inferred, with a lipid bilayer separating at least one water channel set from the external aqueous phase. This is crucial to understand and enhance controlled release of target molecules and calls for a revision of postulated transport mechanisms from cubosomes to the aqueous phase.

Height-resolved quantification of microstructure and texture in polycrystalline thin films using TEM orientation mapping.

A method is presented for the quantitative investigation of microstructure and texture evolution in polycrystalline thin films based on in-plane automated crystal orientation mapping in transmission electron microscopy, from the substrate up. To demonstrate the method we apply it to the example of low pressure metal-organic chemical vapor deposited ZnO layers. First, orientation mapping is applied to standard cross-section and plan-view transmission electron microscopy samples of films, illustrating how plan-view samples both reduce the occurrence of grain overlap that is detrimental to reliable orientation mapping and also improve sampling statistics compared to cross-sections. Motivated by this, orientation mapping has been combined with a double-wedge method for specimen preparation developed by Spiecker et al. (2007) [1], which creates a large area plan-view sample that traverses the film thickness. By measuring >10,000 grains in the film, the resulting data give access to grain size, orientation and misorientation distributions in function of height above the substrate within the film, which are, in turn, the inputs necessary for quantitative assessment of growth models and simulations. The orientation data are directly related to microstructural images, allowing correlation of orientations with in-plane and out-of-plane grain sizes and shapes. The spatial correlation of the entire data set gives insights into previously unnoticed growth mechanisms such as the presence of renucleation or preferred misorientations. Finally, the data set can be used to guide targeted, local studies by other transmission electron microscopy techniques. This is demonstrated by the site-specific application of nano-beam diffraction to validate the presence of coherent [21̄1̄0]/(011̄3) twin boundaries first suggested by the orientation mapping.

Gentle quantitative measurement of helium density in nanobubbles in silicon by spectrum imaging.

We propose an original method for the determination of the physical properties of nanometer sized helium bubbles using spectrum imaging in an energy-filtered transmission electron microscope. Helium bubbles synthesized by high fluence implantation and thermal annealing in silicon are investigated. The acquisition parameters are determined to optimize both signal/noise ratio and time. The limitations to the extent of observable areas on a typical sample are explained. The necessary data correction and helium K-edge position measurement procedures are detailed and the accuracy of the method is discussed. Finally helium density maps are obtained and discussed.

Enhanced quantification for 3D energy dispersive spectrometry: going beyond the limitation of large volume of X-ray emission.

This paper presents a method developed to quantify three-dimensional energy dispersive spectrometry (3D EDS) data with voxel size smaller than the volume from which X-rays are emitted. The influence of the neighboring voxels is corrected by applying recursively a complex quantification, improving thereby the accuracy of the quantification of critically small features. The enhanced quantification method is applied to simulated and measured data. A systematic improvement is obtained compared with classical quantification, proving the concept and the prospect of this method.

Measurements of local chemistry and structure in Ni(O)-YSZ composites during reduction using energy-filtered environmental TEM.

Energy-filtered transmission electron microscopy images are acquired during the reduction of a NiO-YSZ composite in H2 up to 600 °C. Temperature-resolved quantitative information about both chemistry and structure is extracted with nm spatial resolution from the data, paving the way for the development of detailed reduction models.

Identifying champion nanostructures for solar water-splitting.

Charge transport in nanoparticle-based materials underlies many emerging energy-conversion technologies, yet assessing the impact of nanometre-scale structure on charge transport across micrometre-scale distances remains a challenge. Here we develop an approach for correlating the spatial distribution of crystalline and current-carrying domains in entire nanoparticle aggregates. We apply this approach to nanoparticle-based α-Fe2O3 electrodes that are of interest in solar-to-hydrogen energy conversion. In correlating structure and charge transport with nanometre resolution across micrometre-scale distances, we have identified the existence of champion nanoparticle aggregates that are most responsible for the high photoelectrochemical activity of the present electrodes. Indeed, when electrodes are fabricated with a high proportion of these champion nanostructures, the electrodes achieve the highest photocurrent of any metal oxide photoanode for photoelectrochemical water-splitting under 100 mW cm(-2) air mass 1.5 global sunlight.

Silicon filaments in silicon oxide for next-generation photovoltaics.

Nanometer wide silicon filaments embedded in an amorphous silicon oxide matrix are grown at low temperatures over a large area. The optical and electrical properties of these mixed-phase nanomaterials can be tuned independently, allowing for advanced light management in high efficiency thin-film silicon solar cells and for band-gap tuning via quantum confinement in third-generation photovoltaics.

Electronic interactions between "pea" and "pod": the case of oligothiophenes encapsulated in carbon nanotubes.

One of the most challenging strategies to achieve tunable nanophotonic devices is to build robust nanohybrids with variable emission in the visible spectral range, while keeping the merits of pristine single-walled carbon nanotubes (SWNTs). This goal is realized by filling SWNTs ("pods") with a series of oligothiophene molecules ("peas"). The physical properties of these peapods are depicted by using aberration-corrected high-resolution transmission electron microscopy, Raman spectroscopy, and other optical methods including steady-state and time-resolved measurements. Visible photoluminescence with quantum yields up to 30% is observed for all the hybrids. The underlying electronic structure is investigated by density functional theory calculations for a series of peapods with different molecular lengths and tube diameters, which demonstrate that van der Waals interactions are the bonding mechanism between the encapsulated molecule and the tube.

Magnetic circular dichroism in EELS: towards 10 nm resolution.

We describe a new experimental setup for the detection of magnetic circular dichroism with fast electrons (EMCD). As compared to earlier findings the signal is an order of magnitude higher, while the probed area could be significantly reduced, allowing a spatial resolution of better than 40 nm. A simplified analysis of the experimental results is based on the decomposition of the mixed dynamic form factor S(q-->,q-->('),E) into a real part related to the scalar product and an imaginary part related to the vector product of the scattering vectors q--> and q-->('). Following the recent detection of chiral electronic transitions in the electron microscope the present experiment is a crucial demonstration of the potential of EMCD for nanoscale investigations.