scholarly journals Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm

2017 ◽  
Vol 23 (5) ◽  
pp. 951-966 ◽  
Author(s):  
Juan Wu ◽  
Mirna Lerotic ◽  
Sean Collins ◽  
Rowan Leary ◽  
Zineb Saghi ◽  
...  
Keyword(s):  
Compressed Sensing ◽  
Iterative Reconstruction ◽  
Three Dimensional ◽  
Chemical Imaging ◽  
Reconstruction Technique ◽  
Back Projection ◽  
X Ray ◽  
Reconstruction Methods ◽  
Scanning Transmission ◽  
X Ray Absorption

AbstractSoft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.

scholarly journals Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria

2020 ◽  
Vol 27 (3) ◽  
pp. 753-761
Author(s):  
Meng-Wen Peng ◽  
Yong Guan ◽  
Jian-Hong Liu ◽  
Liang Chen ◽  
Han Wang ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Morphological Structure ◽  
Anammox Bacteria ◽  
Reconstruction Technique ◽  
X Ray ◽  
Shape Adaptation ◽  
Nondestructive Imaging ◽  
Quantitative Analyses ◽  
X Ray Absorption

Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored.

Origin of luminescence from ZnO/CdS core/shell nanowire arrays

Nanoscale ◽  
2014 ◽  
Vol 6 (16) ◽  
pp. 9783-9790 ◽  
Author(s):  
Zhiqiang Wang ◽  
Jian Wang ◽  
Tsun-Kong Sham ◽  
Shaoguang Yang
Keyword(s):  
Optical Properties ◽  
Chemical Imaging ◽  
Nanowire Arrays ◽  
Nano Composites ◽  
Core Shell ◽  
Edge Structure ◽  
X Ray ◽  
Optical Luminescence ◽  
Scanning Transmission ◽  
X Ray Absorption

Chemical imaging, electronic structure and optical properties of ZnO/CdS nano-composites have been investigated using scanning transmission X-ray microscopy (STXM), X-ray absorption near-edge structure (XANES) and X-ray excited optical luminescence (XEOL) spectroscopy.

Chemical and orientational imaging of polymeric samples

1994 ◽  
Vol 52 ◽  
pp. 68-69
Author(s):  
H. Ade ◽  
B. Hsiao ◽  
G. Mitchell ◽  
E. Rightor ◽  
A. P. Smith ◽  
...  
Keyword(s):  
Ethylene Terephthalate ◽  
National Laboratory ◽  
Brookhaven National Laboratory ◽  
Carbonyl Groups ◽  
Aromatic Rings ◽  
Edge Structure ◽  
X Ray ◽  
Scanning Transmission ◽  
Polymeric Samples ◽  
X Ray Absorption

We have used the Scanning Transmission X-ray Microscope at beamline X1A (X1-STXM) at Brookhaven National Laboratory (BNL) to acquire high resolution, chemical and orientation sensitive images of polymeric samples as well as point spectra from 0.1 μm areas. This sensitivity is achieved by exploiting the X-ray Absorption Near Edge Structure (XANES) of the carbon K edge. One of the most illustrative example of the chemical sensitivity achievable is provided by images of a polycarbonate/pol(ethylene terephthalate) (70/30 PC/PET) blend. Contrast reversal at high overall contrast is observed between images acquired at 285.36 and 285.69 eV (Fig. 1). Contrast in these images is achieved by exploring subtle differences between resonances associated with the π bonds (sp hybridization) of the aromatic groups of each polymer. PET has a split peak associated with these aromatic groups, due to the proximity of its carbonyl groups to its aromatic rings, whereas PC has only a single peak.

3D Observation of Elemental Distribution of Si-Device using a Dedicated FIB/STEM System

2005 ◽  
Author(s):  
T. Yaguchi ◽  
M. Konno ◽  
T. Kamino ◽  
M. Ogasawara ◽  
K. Kaji ◽  
...  
Keyword(s):  
Focused Ion Beam ◽  
Ion Beam ◽  
Three Dimensional ◽  
Elemental Distribution ◽  
Multivariate Statistical ◽  
X Ray ◽  
Sample Rotation ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Elemental Maps

Abstract A technique for preparation of a pillar shaped sample and its multi-directional observation of the sample using a focused ion beam (FIB) / scanning transmission electron microscopy (STEM) system has been developed. The system employs an FIB/STEM compatible sample rotation holder with a specially designed rotation mechanism, which allows the sample to be rotated 360 degrees [1-3]. This technique was used for the three dimensional (3D) elemental mapping of a contact plug of a Si device in 90 nm technology. A specimen containing a contact plug was shaped to a pillar sample with a cross section of 200 nm x 200 nm and a 5 um length. Elemental analysis was performed with a 200 kV HD-2300 STEM equipped with the EDAX genesis Energy dispersive X-ray spectroscopy (EDX) system. Spectrum imaging combined with multivariate statistical analysis (MSA) [4, 5] was used to enhance the weak X-ray signals of the doped area, which contain a low concentration of As-K. The distributions of elements, especially the dopant As, were successfully enhanced by MSA. The elemental maps were .. reconstructed from the maps.

scholarly journals Three-dimensional focal stack imaging in scanning transmission X-ray microscopy with an improved reconstruction algorithm

2019 ◽  
Vol 27 (5) ◽  
pp. 7787 ◽  
Author(s):  
Limei Ma ◽  
Xiangzhi Zhang ◽  
Zijian Xu ◽  
Andreas Späth ◽  
Zhenjiang Xing ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Reconstruction Algorithm ◽  
X Ray ◽  
Scanning Transmission ◽  
Focal Stack

scholarly journals Temperature dependence of amorphous magnesium carbonate structure studied by PDF and XAFS analyses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gen-ichiro Yamamoto ◽  
Atsushi Kyono ◽  
Satoru Okada
Keyword(s):  
Temperature Dependence ◽  
Three Dimensional ◽  
Magnesium Carbonate ◽  
Range Order ◽  
Edge Structure ◽  
Medium Range Order ◽  
X Ray ◽  
Medium Range ◽  
Mineral Trapping ◽  
X Ray Absorption

AbstractMineral trapping through the precipitation of carbonate minerals is a potential approach to reduce CO2 accumulation in the atmosphere. The temperature dependence of amorphous magnesium carbonate (AMC), a precursor of crystalline magnesium carbonate hydrates, was investigated using synchrotron X-ray scattering experiments with atomic pair distribution function (PDF) and X-ray absorption fine structure analysis. PDF analysis revealed that there were no substantial structural differences among the AMC samples synthesized at 20, 60, and 80 °C. In addition, the medium-range order of all three AMC samples was very similar to that of hydromagnesite. Stirring in aqueous solution at room temperature caused the AMC sample to hydrate immediately and form a three-dimensional hydrogen-bonding network. Consequently, it crystallized with the long-range structural order of nesquehonite. The Mg K-edge X-ray absorption near-edge structure spectrum of AMC prepared at 20 °C was very similar to that of nesquehonite, implying that the electronic structure and coordination geometry of Mg atoms in AMC synthesized at 20 °C are highly similar to those in nesquehonite. Therefore, the short-range order (coordination environment) around the Mg atoms was slightly modified with temperature, but the medium-range order of AMC remained unchanged between 20 and 80 °C.

scholarly journals Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm

2005 ◽  
Vol 71 (3) ◽  
pp. 1300-1310 ◽  
Author(s):  
Brandy Toner ◽  
Sirine Fakra ◽  
Mario Villalobos ◽  
Tony Warwick ◽  
Garrison Sposito
Keyword(s):  
Careful Consideration ◽  
Bacterial Biofilm ◽  
Bacterial Cells ◽  
X Ray ◽  
Spatially Resolved ◽  
Nexafs Spectroscopy ◽  
Promising Tool ◽  
Scanning Transmission ◽  
X Ray Absorption

ABSTRACT Pseudomonas putida strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn+2 [Mn+2 (aq)] by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L2,3 absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn+2 (aq) was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

scholarly journals Diverse Chemical Mixing States of Aerosol Particles in the Southeastern United States

2018 ◽  
Author(s):  
Amy L. Bondy ◽  
Daniel Bonanno ◽  
Ryan C. Moffet ◽  
Bingbing Wang ◽  
Alexander Laskin ◽  
...  
Keyword(s):  
Chemical Species ◽  
Accumulation Mode ◽  
X Ray ◽  
Internal Mixing ◽  
Scanning Transmission ◽  
Sea Spray Aerosol ◽  
Cloud Activation ◽  
Mixing States ◽  
X Ray Absorption ◽  
Individual Particles

Abstract. Aerosols in the atmosphere are chemically complex with thousands or more chemical species distributed in different proportions across individual particles in an aerosol population. An internal mixing assumption, with species present in the same proportions across all aerosols, is used in many models and calculations of secondary organic aerosol (SOA) formation, cloud activation, and aerosol optical properties. However, many of these effects depend on the distribution of species within individual particles, and important information can be lost when internal mixtures are assumed. Herein, we show that during the Southern Oxidant and Aerosol Study (SOAS) in Centreville, Alabama, at a rural, forested location, that aerosols frequently are not purely internally mixed, even in the accumulation mode (0.2–1.0 µm). A range of aerosol sources and mixing states were obtained using computer controlled scanning electron microscopy with energy dispersive X-ray spectroscopy (CCSEM-EDX) and scanning transmission X-ray microscopy-near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS). Particles that were dominated by SOA and inorganic salts were the majority of particles by number fraction from 0.2–5 microns with an average of 78 % SOA in the accumulation mode. However, during certain periods contributions by sea spray aerosol (SSA) and mineral dust were significant to accumulation (22 % SSA and 26 % dust) and coarse mode number concentrations (38 % SSA and 63 % dust). The fraction of particles containing key elements (Na, Mg, K, Ca, and Fe) were determined as a function of size for specific classes of particles. Within internally mixed SOA/sulfate particles

Solving the 3D structure of metal nanoparticles

2007 ◽  
Vol 222 (11/2007) ◽  
Author(s):  
Anatoly Frenkel
Keyword(s):  
Metal Nanoparticles ◽  
Short Range ◽  
Short Range Order ◽  
3D Structure ◽  
Three Dimensional ◽  
X Ray ◽  
Particle Distributions ◽  
Structure Of Metal ◽  
X Ray Absorption

We discuss methods of Extended X-ray Absorption Fine-Structure (EXAFS) analysis that provide three-dimensional structural characterization of metal nanoparticles, both mono- and bi-metallic. For the bimetallic alloys, we use short range order measurements to discriminate between random and non-random inter-particle distributions of atoms. We also discuss the application of EXAFS to heterogeneous nanoparticle systems.

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