Non-rigid alignment in electron tomography in materials science.

Electron tomography is a key technique that enables the visualization of an object in three dimensions with a resolution of about a nanometre. High-quality 3D reconstruction is possible thanks to the latest compressed sensing algorithms and/or better alignment and preprocessing of the 2D projections. Rigid alignment of 2D projections is routine in electron tomography. However, it cannot correct misalignments induced by (i) deformations of the sample due to radiation damage or (ii) drifting of the sample during the acquisition of an image in scanning transmission electron microscope mode. In both cases, those misalignments can give rise to artefacts in the reconstruction. We propose a simple-to-implement non-rigid alignment technique to correct those artefacts. This technique is particularly suited for needle-shaped samples in materials science. It is initiated by a rigid alignment of the projections and it is then followed by several rigid alignments of different parts of the projections. Piecewise linear deformations are applied to each projection to force them to simultaneously satisfy the rigid alignments of the different parts. The efficiency of this technique is demonstrated on three samples, an intermetallic sample with deformation misalignments due to a high electron dose typical to spectroscopic electron tomography, a porous silicon sample with an extremely thin end particularly sensitive to electron beam and another porous silicon sample that was drifting during image acquisitions.

State-of-the-Art Three-Dimensional Chemical Characterization of Solid Oxide Fuel Cell Using Focused Ion Beam Time-of-Flight Secondary Ion Mass Spectrometry Tomography.

In this paper the potential of time-of-flight secondary ion mass spectroscopy combined with focused ion beam technology to characterize the composition of a solid oxide fuel cell (SOFC) in three-dimension is demonstrated. The very high sensitivity of this method allows even very small amounts of elements/compounds to be detected and localized. Therefore, interlayer diffusion of elements between porous electrodes and presence of pollutants can be analyzed with a spatial resolution of the order of 100 nm. However, proper element recognition and mass interference still remain important issues. Here, we present a complete elemental analysis of the SOFC as well as techniques that help to validate the reliability of obtained results. A discussion on origins of probable artifacts is provided.

Selenium segregation in femtosecond-laser hyperdoped silicon revealed by electron tomography.

Doping of silicon with chalcogens (S, Se, Te) by femtosecond laser irradiation to concentrations well above the solubility limit leads to near-unity optical absorptance in the visible and infrared (IR) range and is a promising route toward silicon-based IR optoelectronics. However, open questions remain about the nature of the IR absorptance and in particular about the impact of the dopant distribution and possible role of dopant diffusion. Here we use electron tomography using a high-angle annular dark-field (HAADF) detector in a scanning transmission electron microscope (STEM) to extract information about the three-dimensional distribution of selenium dopants in silicon and correlate these findings with the optical properties of selenium-doped silicon. We quantify the tomography results to extract information about the size distribution and density of selenium precipitates. Our results show correlation between nanoscale distribution of dopants and the observed sub-band gap optical absorptance and demonstrate the feasibility of HAADF-STEM tomography for the investigation of dopant distribution in highly-doped semiconductors.

Status of the hard X-ray microprobe beamline ID22 of the European Synchrotron Radiation Facility.

The ESRF synchrotron beamline ID22, dedicated to hard X-ray microanalysis and consisting of the combination of X-ray fluorescence, X-ray absorption spectroscopy, diffraction and 2D/3D X-ray imaging techniques, is one of the most versatile instruments in hard X-ray microscopy science. This paper describes the present beamline characteristics, recent technical developments, as well as a few scientific examples from recent years of the beamline operation. The upgrade plans to adapt the beamline to the growing needs of the user community are briefly discussed.

Probing the structure of heterogeneous diluted materials by diffraction tomography.

The advent of nanosciences calls for the development of local structural probes, in particular to characterize ill-ordered or heterogeneous materials. Furthermore, because materials properties are often related to their heterogeneity and the hierarchical arrangement of their structure, different structural probes covering a wide range of scales are required. X-ray diffraction is one of the prime structural methods but suffers from a relatively poor detection limit, whereas transmission electron analysis involves destructive sample preparation. Here we show the potential of coupling pencil-beam tomography with X-ray diffraction to examine unidentified phases in nanomaterials and polycrystalline materials. The demonstration is carried out on a high-pressure pellet containing several carbon phases and on a heterogeneous powder containing chalcedony and iron pigments. The present method enables a non-invasive structural refinement with a weight sensitivity of one part per thousand. It enables the extraction of the scattering patterns of amorphous and crystalline compounds with similar atomic densities and compositions. Furthermore, such a diffraction-tomography experiment can be carried out simultaneously with X-ray fluorescence, Compton and absorption tomographies, enabling a multimodal analysis of prime importance in materials science, chemistry, geology, environmental science, medical science, palaeontology and cultural heritage.

Mechanical and structural characterisation of completely degradable polylactic acid/calcium phosphate glass scaffolds.

This study involves the mechanical and structural characterisation of completely degradable scaffolds for tissue engineering applications. The scaffolds are a composite of polylactic acid (PLA) and a soluble calcium phosphate glass, and are thus completely degradable. A factorial experimental design was applied to optimise scaffold composition prior to simultaneous microtomography and micromechanical testing. Synchrotron X-ray microtomography combined with in situ micromechanical testing was performed to obtain three-dimensional (3D) images of the scaffolds under compression. The 3D reconstruction was converted into a finite element mesh which was validated by simulating a compression test and comparing it with experimental results. The experimental design reveals that larger glass particle and pore sizes reduce the stiffness of the scaffolds, and that the porosity is largely unaffected by changes in pore sizes or glass weight content. The porosity ranges between 93% and 96.5%, and the stiffness ranges between 50 and 200 kPa. X-ray projections show a homogeneous distribution of the glass particles within the PLA matrix, and illustrate pore-wall breakage under strain. The 3D reconstructions are used qualitatively to visualise the distribution of the phases of the composite material, and to follow pore deformation under compression. Quantitatively, scaffold porosity, pore interconnectivity and surface/volume ratios have been calculated. Finite element analysis revealed the stress and strain distribution in the scaffold under compression, and could be used in the future to characterise the mechanical properties of the scaffolds.

2D/3D Microanalysis by Energy Dispersive X-ray Absorption Spectroscopy Tomography.

X-ray spectroscopic techniques have proven to be particularly useful in elucidating the molecular and electronic structural information of chemically heterogeneous and complex micro- and nano-structured materials. However, spatially resolved chemical characterization at the micrometre scale remains a challenge. Here, we report the novel hyperspectral technique of micro Energy Dispersive X-ray Absorption Spectroscopy (µED-XAS) tomography which can resolve in both 2D and 3D the spatial distribution of chemical species through the reconstruction of XANES spectra. To document the capability of the technique in resolving chemical species, we first analyse a sample containing 2-30 µm grains of various ferrous- and ferric-iron containing minerals, including hypersthene, magnetite and hematite, distributed in a light matrix of a resin. We accurately obtain the XANES spectra at the Fe K-edge of these four standards, with spatial resolution of 3 µm. Subsequently, a sample of ~1.9 billion-year-old microfossil from the Gunflint Formation in Canada is investigated, and for the first time ever, we are able to locally identify the oxidation state of iron compounds encrusting the 5 to 10 µm microfossils. Our results highlight the potential for attaining new insights into Precambrian ecosystems and the composition of Earth's earliest life forms.

Self-adapting denoising, alignment and reconstruction in electron tomography in materials science.

An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson-Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography.

X-ray micro Laue diffraction tomography analysis of a solid oxide fuel cell.

The relevance of micro Laue diffraction tomography (µ-LT) to investigate heterogeneous polycrystalline materials has been studied. For this purpose, a multiphase solid oxide fuel cell (SOFC) electrode composite made of yttria-stabilized zirconia and nickel oxide phases, with grains of about a few micrometres in size, has been analyzed. In order to calibrate the Laue data and to test the technique's sensitivity limits, a monocrystalline germanium sample of about 8 × 4 µm in cross-section size has also been studied through µ-LT. The SOFC and germanium Laue diffraction pattern analyses are compared and discussed. The indexing procedure has been successfully applied for the analysis of the germanium Laue data, and the depth-resolved two-dimensional cartographies of the full deviatoric strain tensor components were obtained. The development and application of an original geometrical approach to analyze the SOFC Laue data allowed the authors to resolve grains with sizes of about 3 µm and to identify their individual Laue patterns; by indexing those Laue patterns, the crystalline phases and orientations of most of the grains identified through the geometrical approach could be resolved.

3D spatial resolution improvement by dual-axis electron tomography: application to tri-gate transistors.

The performance of semiconductor devices can be linked to geometry and variations of the structure. For transistors in particular, the geometry of the gate stack is essential. In this work we investigate the gate stack of a tri-gate transistor using dual-axis electron tomography. This allows the reconstruction of all surfaces of the gate of the transistor with high resolution and measurement of the local thickness of the gate oxide. While previously, dual-axis electron tomography was employed for reducing missing wedge artifacts, our work demonstrates the potential of dual-axis tomography for improving the resolution of a tomographic reconstruction, even for structures not affected by missing wedge artifacts. By simulations and experiments we show the value of dual-axis tomography for characterization of nanoscale devices as an approach that requires no prior information and that can be easily extended even to more than two tilt axes.

A hard x-ray nanoprobe for scanning and projection nanotomography.

To fabricate and qualify nanodevices, characterization tools must be developed to provide a large panel of information over spatial scales spanning from the millimeter down to the nanometer. Synchrotron x-ray-based tomography techniques are getting increasing interest since they can provide fully three-dimensional (3D) images of morphology, elemental distribution, and crystallinity of a sample. Here we show that by combining suitable scanning schemes together with high brilliance x-ray nanobeams, such multispectral 3D volumes can be obtained during a single analysis in a very efficient and nondestructive way. We also show that, unlike other techniques, hard x-ray nanotomography allows reconstructing the elemental distribution over a wide range of atomic number and offers truly depth resolution capabilities. The sensitivity, 3D resolution, and complementarity of our approach make hard x-ray nanotomography an essential characterization tool for a large panel of scientific domains.

Cobalt distribution in keratinocyte cells indicates nuclear and perinuclear accumulation and interaction with magnesium and zinc homeostasis.

Cobalt is known to be toxic at high concentration, to induce contact dermatosis, and occupational radiation skin damage because of its use in nuclear industry. We investigated the intracellular distribution of cobalt in HaCaT human keratinocytes as a model of skin cells, and its interaction with endogenous trace elements. Direct micro-chemical imaging based on ion beam techniques was applied to determine the quantitative distribution of cobalt in HaCaT cells. In addition, synchrotron radiation X-ray fluorescence microanalysis in tomography mode was performed, for the first time on a single cell, to determine the 3D intracellular distribution of cobalt. Results obtained with these micro-chemical techniques were compared to a more classical method based on cellular fractionation followed by inductively coupled plasma atomic emission spectrometry (ICP-AES) measurements. Cobalt was found to accumulate in the cell nucleus and in perinuclear structures indicating the possible direct interaction with genomic DNA, and nuclear proteins. The perinuclear accumulation in the cytosol suggests that cobalt could be stored in the endoplasmic reticulum or the Golgi apparatus. The multi-elemental analysis revealed that cobalt exposure significantly decreased magnesium and zinc content, with a likely competition of cobalt for magnesium and zinc binding sites in proteins. Overall, these data suggest a multiform toxicity of cobalt related to interactions with genomic DNA and nuclear proteins, and to the alteration of zinc and magnesium homeostasis.

Comet 81P/Wild 2 under a microscope.

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.

Elemental compositions of comet 81P/Wild 2 samples collected by Stardust.

We measured the elemental compositions of material from 23 particles in aerogel and from residue in seven craters in aluminum foil that was collected during passage of the Stardust spacecraft through the coma of comet 81P/Wild 2. These particles are chemically heterogeneous at the largest size scale analyzed ( approximately 180 ng). The mean elemental composition of this Wild 2 material is consistent with the CI meteorite composition, which is thought to represent the bulk composition of the solar system, for the elements Mg, Si, Mn, Fe, and Ni to 35%, and for Ca and Ti to 60%. The elements Cu, Zn, and Ga appear enriched in this Wild 2 material, which suggests that the CI meteorites may not represent the solar system composition for these moderately volatile minor elements.