Scanning Transmission X-ray Microscopy Images Research Articles

Current status of the TwinMic beamline at Elettra: asoft X-ray transmission and emission microscopy station.

The current status of the TwinMic beamline at Elettra synchrotron light source, that hosts the European twin X-ray microscopy station, is reported. The X-ray source, provided by a short hybrid undulator with source size and divergence intermediate between bending magnets and conventional undulators, is energy-tailored using a collimated plane-grating monochromator. The TwinMic spectromicroscopy experimental station combines scanning and full-field imaging in a single instrument, with contrast modes such as absorption, differential phase, interference and darkfield. The implementation of coherent diffractive imaging modalities and ptychography is ongoing. Typically, scanning transmission X-ray microscopy images are simultaneously collected in transmission and differential phase contrast and can be complemented by chemical and elemental analysis using across-absorption-edge imaging, X-ray absorption near-edge structure or low-energy X-ray fluorescence. The lateral resolutions depend on the particular imaging and contrast mode chosen. The TwinMic range of applications covers diverse research fields such as biology, biochemistry, medicine, pharmacology, environment, geochemistry, food, agriculture and materials science. They will be illustrated in the paper with representative results.

Imaging the surface morphology, chemistry and conductivity of LiNi1/3Fe1/3Mn4/3O4 crystalline facets using scanning transmission X-ray microscopy.

Scanning transmission X-ray microscopy (STXM) using the X-ray fluorescence mode has been employed to elucidate the chemical structures at Ni, Fe, Mn and O sites from the (111) and (100) facets of micron-sized LiNi1/3Fe1/3Mn4/3O4 energy material particles. Furthermore, STXM imaging using electron yield mode has mapped out the surface conductivity of the crystalline particles. This study presents a novel approach that visualizes local element segregation, chemistry and conductivity variation among different crystal facets, which will assist further tailoring of the morphology and surface structure of this high voltage spinel lithium ion battery cathode material.

Transmission Electron Microscopy and Scanning Transmission X-Ray Microscopy Studies on the Bioaccumulation and Tissue Level Absorption of TiO2 Nanoparticles in Daphnia magna.

In this study, bioaccumulation and tissue-level absorption of TiO2 nanoparticles (NPs) in freshwater invertebrates were investigated using transmission electron microscopy (TEM) and scanning transmission X-ray microscopy (STXM). The TiO2 NPs were used to test impacts of core sizes (i.e., 5 ± 2 nm and 23 ± 7 nm for TiO2(SYN) and TiO2(P25), respectively) and agglomerations (i.e., well dispersed vs. highly agglomerated) on the uptake of TiO2 NPs in Daphnia magna (D. magna). Highly agglomerated TiO2 NPs, regardless of their core sizes, were heavily taken up into the digestive tract of D. magna and no detectable penetration of both TiO2 NPs into the gut epithelial cells of D. magna was observed in TEM and STXM images. However, significant damages involving morphological changes in the microvilli and gut epithelial cells (e.g., irregular shaped microvilli, epithelial cell protrusion, and dilatation of cytoplasmic inclusion) were observed only with the commercial TiO2 NPs (TiO2(P25)) with larger core size and mixed crystalline phase, while the laboratory synthesized TiO2 NPs (TiO2(Syn)) with smaller core size and single crystalline phase showed slight morphological changes in the gut microvilli and epithelial cells. In the case of D. magna exposed to the well dispersed synthetic TiO2 NP ((Cit)TiO2(Syn)), only a negligible amount of TiO2 NPs were found within the digestive tract of the D. magna without any significant damages in the gut microvilli and epithelial cells and any detectable penetrations of TiO2 NPs into epithelial cells of D. magna gut. These TEM and STXM observations confirmed us that uptake of NP into D. magna are strongly dependent on their agglomeration (i.e., hydrodynamic sizes), rather than their core sizes, while direct penetration of NPs into tissues of digestive tract seems unlikely without significant morphological changes (e.g., collapse of the epithelial tissue) caused by high toxicity of NPs or released metal ions.

Differential expression of extracellular thiol groups of moderately thermophilic Sulfobacillus thermosulfidooxidans and extremely thermophilic Acidianus manzaensis grown on S(0) and Fe (2.).

Bio-oxidation of elemental sulfur (S(0)) is very important in bioleaching and sulfur cycle. S(0) was proposed to be first activated by reacting with reactive thiol groups (-SH) of outer membrane proteins, forming -S n H (n≥2) complexes. The differential expression of -SH of moderately thermophilic Sulfobacillus thermosulfidooxidans and extremely thermophilic Acidianus manzaensis grown on Fe(2+) and S(0) was investigated by synchrotron radiation-based scanning transmission X-ray microscopy (STXM) imaging and micro-beam X-ray fluorescence (μ-XRF) mapping. The STXM imaging and μ-XRF mapping of extracellular -SH were based on the analysis of Ca(2+) bound on the cell. By comparing Ca(2+) of the cells with and without labeling by Ca(2+), the distribution and content of thiol groups were obtained. The results showed that, for both S. thermosulfidooxidans and A. manzaensis, the expression of extracellular -SH of S(0)-grown cells was higher than that of Fe(2+)-grown cells. Statistical analysis indicated that the expression of extracellular -SH for S. thermosulfidooxidans and A. manzaensis grown on S(0) was 2.37 times and 2.14 times, respectively, to that on Fe(2+). These results evidently demonstrate that the extracellular thiol groups are most probably involved in elemental sulfur activation and oxidation of the acidophilic sulfur-oxidizing microorganisms.

Dipolar energies in Nd-Fe-B nanocrystalline magnets with and without Nd-Cu infiltration

We analyze the dipolar energies of Nd-Cu-infiltrated Nd-Fe-B nanocrystalline magnets during magnetization reversals by visualizing the magnetic dipolar interactions. Non-magnetic phases from the grains were identified by analyzing the element-specific magnetization distribution images taken with scanning transmission X-ray microscopy. The magnetic dipolar interactions were calculated from the interactions between the magnetization at each point and those at other points in the scanning transmission X-ray microscopy images. We present the dipolar energy distributions in Nd-Cu infiltrated nanocrystalline Nd-Fe-B magnets and compare them with those in nanocrystalline Nd-Fe-B magnets without Nd-Cu infiltration. The interplay between the exchange and dipolar interactions in Nd-Fe-B magnets is found to be essential for obtaining high coercivities.

Unraveling the Redox Behavior of a CoMoS Hydrodesulfurization Catalyst: A Scanning Transmission X-ray Microscopy Study in the Tender X-ray Range

We visualize the elemental zoning in an alumina-supported cobalt molybdenum sulfide (CoMoS) catalyst with scanning transmission X-ray microscopy (STXM). We use the Canadian Light Source beamline 10-ID’s (SM) unique combination of soft X-ray and tender X-ray STXM to determine the spatial variation of Co, Al, Mo, and S species. The results clearly show the correlation between cobalt and molybdenum and the anticorrelation between cobalt and alumina, confirming that Co is closely associated with the MoS2 phase. The tender X-ray STXM images show that the fresh catalyst particle contains a 50 nm ring of molybdenum oxide encapsulating the supported MoS2 phase. After the reduction at 200 °C with H2, this oxide rim disappears and a uniform MoS2 distribution is found. Upon oxidation at 400 °C, the sulfur disappears from the catalyst sample and molybdenum is oxidized from a MoIV sulfide to a mainly tetrahedral MoVI oxide, while cobalt keeps its divalent nature and changes from a CoII sulfide to a CoII oxide.

X-ray and electron microscopy studies on the biodistribution and biomodification of iron oxide nanoparticles in Daphnia magna

Biodistribution and biomodification of iron oxide (Fe3O4 and α-Fe2O3) nanoparticles (NPs) in a well-known toxicity test organism, Daphnia magna (D. magna), were investigated using transmission electron microscopy (TEM) and scanning transmission X-ray microscopy (STXM). In addition to the morphological changes in the gut tissues of D. magna, biodistribution and biomodification of iron oxide NPs in the digestive tract of D. magna were also monitored in this study. Upon exposures to both iron oxide NPs, unique morphological changes (e.g., irregular shaped microvilli, epithelial cell protrusion, and dilatation of cytoplasmic inclusion) in the gut tissues of D. magna were observed along with bacterial colonization of the gut lumen. However, despite their heavy accumulations in the digesitive tract, TEM and STXM images confirmed us that both Fe3O4 and α-Fe2O3 NPs were not penetrating into the gut tissues of D. magna. Moreover, for the Fe3O4 NPs in direct contact with the gut microvilli of D. magna, slight but significant spectral changes were observed in their Fe L-edge X-ray absorption near edge structure (XANES) spectra, which indicated that there were biomodifications of Fe3O4 NPs, probably involving oxidative dissolution of Fe3O4 NPs followed by rapid precipitation of ferric oxide or hydroxide. However, no significant changes were observed in the Fe L-edge XANES spectra of the α-Fe2O3 NPs present in the gut lumen of D. magna. These X-ray and electron microscopic observations confirmed us that, despite similarities in core sizes and chemical compositions, NPs with different crystalline phase and dissolution rates can interact quite differently with their local environment, may result in different biodistribution and cause completely dissimilar toxicities.

Visualization of magnetic dipolar interaction based on scanning transmission X-ray microscopy

Using scanning transmission X-ray microscopy (STXM), in this report we visualized the magnetic dipolar interactions in nanocrystalline Nd-Fe-B magnets and imaged their magnetization distributions at various applied fields. We calculated the magnetic dipolar interaction by analyzing the interaction between the magnetization at each point and those at the other points on the STXM image.

Dipolar energy of Nd-Fe-B nanocrystalline magnets in magnetization reversal process

We analyzed the dipolar energy of Nd-Fe-B nanocrystalline magnets in magnetization reversal process through visualizing magnetic dipolar interaction. We obtained magnetization distribution images experimentally by using scanning transmission X-ray microscopy (STXM). The magnetic dipolar interaction was calculated by the interaction between the magnetization at each point and those at the other points on the STXM image. We showed the dipolar energy in the nanocrystalline Nd-Fe-B magnets and compared it with the exchange energy at various applied fields. Our results indicated the significance of the dipolar energy in magnetization reversal process.

X-ray spectromicroscopic study of interactions between NaCl and calcium silicate hydrates

X-ray diffraction (XRD), scanning transmission X-ray microscopy (STXM) and X-ray absorption near edge structure (XANES) spectra were used to investigate the interactions between sodium chloride (NaCl) and calcium silicate hydrate (C-S-H), the primary binding phase of hydrated Portland cement. XRD analysis indicates the interlayer expansion of C-S-H with a high Ca/Si ratio. Contrast maps of STXM images collected from C-S-Hs with different Ca/Si ratios reacted with NaCl solution reveal that sodium interacts with C-S-H with a low Ca/Si ratio, while chloride is intercalated into the interlayer of C-S-H with a high Ca/Si ratio. Silicon K-edge XANES spectra were analysed to understand the variation in the structure of silicate chains. This revealed that the interaction with the sodium cations depolymerises the silicate chains of C-S-H with a low Ca/Si ratio. The mechanism involved for the selection of adsorbed ions is probably due to the residual charge between the positive charge of interlayer calcium ions and the negative charge of the end group of silicate chains in C-S-H.

Synchrotron radiation based STXM analysis and micro-XRF mapping of differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on Fe2 + and S0

The differential expression of extracellular thiol groups by Acidithiobacillus ferrooxidans grown on substrates Fe2+ and S0 was investigated by using synchrotron radiation based scanning transmission X-ray microscopy (STXM) imaging and microbeam X-ray fluorescence (μ-XRF) mapping. The extracellular thiol groups (SH) were first alkylated by iodoacetic acid forming Protein-SCH2COOH and then the P-SCH2COOH was marked by calcium ions forming P-SCH2COOCa. The STXM imaging and μ-XRF mapping of SH were based on analysis of SCH2COO-bonded Ca2+. The results indicated that the thiol group content of A. ferrooxidans grown on S0 is 3.88 times to that on Fe2+. Combined with selective labeling of SH by Ca2+, the STXM imaging and μ-XRF mapping provided an in situ and rapid analysis of differential expression of extracellular thiol groups.

Correlation between the magnetic imaging of cobalt nanoconstrictions and their magnetoresistance response

Scanning transmission x-ray microscopy (STXM) and magnetoresistance (MR) measurements are used to investigate the magnetic behavior of a nanoconstriction joining two micrometric electrodes (a pad and a wire). The reversal of the magnetization under variable external static magnetic fields is imaged. By means of a detailed analysis of the STXM images at the nanocontact area, the MR is calculated, based on diffusive anisotropic-MR. This MR agrees well with that obtained from electrical transport measurements, allowing a direct correlation between the MR signal and the magnetic reversal of the system. The magnetization behavior depends on the sample thickness and constriction dimensions. In 40 nm-thick samples, with 20 × 175 nm2 contact areas, the magnetization at the two sides of the constriction forms a net angle of 90°, with a progressive evolution of the magnetization structure between the electrodes during switching. The MR in those cases has a more peaked shape than with 20 nm-thick electrodes and 10 × 80 nm2 contact areas, where the magnetization forms 180°between them, with a wide domain wall pinned at the constriction. As a consequence of this configuration, a plateau in the MR is observed for about 20 Oe.

STXM Study of the Ionomer Distribution in the PEM Fuel Cell Catalyst Layers

A method of imaging ionomer in the catalyst layer (CL) of the catalyst coated membrane (CCM) in the proton exchange membrane (PEM) fuel cell was developed using scanning transmission X-ray microscopy (STXM). Component maps for ionomer in CL relative to the catalyst/carbon-support were obtained from STXM images at a few specifically pre-defined energies in the C 1s (on/off a peak characteristic for carbon support in the catalyst layer) and F 1s edges (on/off a peak characteristic for the fluorine in the ionomer). Comparing the different approaches, an optimized strategy to study the spatial distributions of chemical components in the catalyst layer was determined. C 1s multi-energy imaging was most informative for mapping all components of the carbon catalyst support. The F 1s maps offer a rapid and powerful way for visualization of ionomer in the catalyst layer.

A median-Gaussian filtering framework for Moiré pattern noise removal from X-ray microscopy image

Moiré pattern noise in Scanning Transmission X-ray Microscopy (STXM) imaging introduces significant errors in qualitative and quantitative image analysis. Due to the complex origin of the noise, it is difficult to avoid Moiré pattern noise during the image data acquisition stage. In this paper, we introduce a post-processing method for filtering Moiré pattern noise from STXM images. This method includes a semi-automatic detection of the spectral peaks in the Fourier amplitude spectrum by using a local median filter, and elimination of the spectral noise peaks using a Gaussian notch filter. The proposed median-Gaussian filtering framework shows good results for STXM images with the size of power of two, if such parameters as threshold, sizes of the median and Gaussian filters, and size of the low frequency window, have been properly selected.

Imaging local electronic corrugations and doped regions in graphene

Electronic structure heterogeneities are ubiquitous in two-dimensional graphene and profoundly impact the transport properties of this material. Here we show the mapping of discrete electronic domains within a single graphene sheet using scanning transmission X-ray microscopy in conjunction with ab initio density functional theory calculations. Scanning transmission X-ray microscopy imaging provides a wealth of detail regarding the extent to which the unoccupied levels of graphene are modified by corrugation, doping and adventitious impurities, as a result of synthesis and processing. Local electronic corrugations, visualized as distortions of the π*cloud, have been imaged alongside inhomogeneously doped regions characterized by distinctive spectral signatures of altered unoccupied density of states. The combination of density functional theory calculations, scanning transmission X-ray microscopy imaging, and in situ near-edge X-ray absorption fine structure spectroscopy experiments also provide resolution of a longstanding debate in the literature regarding the spectral assignments of pre-edge and interlayer states.

Structural variation and water adsorption of a SnO2 coated carbon nanotube: a nanoscale chemical imaging study

The local chemistry and electronic structure variations of an individual carbon nanotube coated with tin oxide nanoparticles have been studied by nanoscale chemical imaging using Scanning Transmission X-ray Microscopy (STXM). Specifically, STXM images at the O and C K-edges with a spatial resolution of 30 nm have been obtained and in turn used to extract X-ray absorption near edge structures (XANES) at both edges from regions of different morphology, i.e. core/shell and side by side. A comparison of the spectra at these regions reveals their structural and bonding variation. In situSTXM with humidity control was then used to image water adsorption on the nanocomposite and its effect on the electronic structure of the nanocomposite, which is crucial for its applications.

Direct observation of water uptake and release in individual submicrometer sized ammonium sulfate and ammonium sulfate/adipic acid particles using X-ray microspectroscopy

Scanning transmission X-ray microscopy (STXM), a microscopy method which allows imaging with a spatial resolution of 40 nm, and X-ray absorption spectroscopy were used to follow in situ the water uptake and release in submicrometer sized particles on a substrate enclosed in a microreactor. Oxygen K-edge near edge X-ray absorption fine structure (NEXAFS) spectra from supported ammonium sulfate particles in their dry salt, saturated solution and supersaturated solution states were obtained for the first time. The variations at the oxygen edge were related to the water content as a function of relative humidity (RH), consistent with mass growth measurements done on larger samples or suspended particle ensembles. Investigations on morphological changes upon water uptake were performed in mixed ammonium sulfate-adipic acid particles using STXM images and NEXAFS spectra taken at the oxygen and the carbon absorption edges, confirming the two phase structure suspected from previous hygroscopicity studies, where adipic acid forms a separate phase of complex morphology partially enclosed by the ammonium sulfate solution at high RH. This example emphasizes the combination of chemical resolution provided via NEXAFS, spatial resolution via STXM and the in situ capability provided by the novel microreactor to obtain information about the microstructure of mixed organic/inorganic particles under close to ambient conditions.

Imaging Nitrogen in Individual Carbon Nanotubes

Semiquantitative chemical imaging of the spatial distribution of nitrogen in a carbon matrix, adsorbed/intercalated N2, and highly concentrated N2 in nitrogen-doped carbon nanotubes (N-CNTs) with a spatial resolution of 30 nm has been obtained by scanning transmission X-ray microscopy (STXM). The local electronic structures of individual N-CNTs at C and N K-edges have been extracted from STXM image stacks (sensitive to bulk) and compared with that of N-CNT using X-ray absorption near-edge structure spectroscopy in total electron yield mode (sensitive to surface). The polarization-dependent STXM measurement has revealed the preferred orientation of N2, parallel to the N-CNT long axis.

Quantitative Analysis of Scanning Transmission X-ray Microscopy Images of Gas-Filled PVA-Based Microballoons

We report on the quantitative analysis of scanning transmission X-ray microscopy (STXM) images of gas-filled, poly(vinyl alcohol) (PVA)-based microballoons (MB) in a water environment. A model for the transmitted intensity is proposed on the basis of a perfect spherical shell stabilizing the microballoon. An extension of this model to take into account the deformation of the MBs is also presented. Taking into consideration a density gradient of the shell and the STXM resolution, we were able to explain very precisely two types of experimental STXM profiles observed on gas-filled MBs. This enables the detailed characterization of MB properties such as radius and wall thickness and the determination of their wall density with unprecedented high resolution.

Mapping the Speciation of Iron in Pseudomonas aeruginosa Biofilms Using Scanning Transmission X-ray Microscopy

An important feature of microbial communities is the spatial heterogeneity of extracellular chemistry. Scanning transmission X-ray microscopy (STXM) was used to map the spatial distribution of iron speciesthroughout Pseudomonas aeruginosa biofilms to assess the influence of chemical heterogeneity on biomineralization. P. aeruginosa biofilms were treated with Fe(III)-amended media. Speciation and quantitative mapping using STXM image sequences in the Fe 2p(3/2) (L3) absorption edge region revealed both Fe(II) and Fe(III) in localized microenvironments. Fe(III) was mainly associated with cell surfaces, while small amounts of Fe(II) was found in the extracellular space. Biofilms were also characterized using C 1s edge STXM image sequences. Anaerobic growth assays and confocal microscopy revealed the inability of P. aeruginosa to directly reduce Fe(III), implicating indirect iron reduction mechanisms in the formation of fine-grained, multivalent minerals. These studies suggest that geochemical microenvironments found throughout microbial communities are even more complex than previously believed.