Adorym: A multi-platform generic x-ray image reconstruction framework based on automatic differentiation

We describe and demonstrate an optimization-based x-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to and fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement

Correlating Chemical Reaction and Mass Transport in Hydrogen-based Direct Reduction of Iron Oxide

Steelmaking contributes 8% to the total CO2 emissions globally, primarily due to coal-based iron ore reduction. Clean hydrogen-based ironmaking has variable performance because the dominant gas-solid reduction mechanism is set by the defects and pores inside the mm-nm sized oxide particles that change significantly as the reaction progresses. While these governing dynamics are essential to establish continuous flow of iron and its ores through reactors, the direct link between agglomeration and chemistry is still contested due to missing measurements. In this work, we directly measure the connection between chemistry and agglomeration in the smallest iron oxides relevant to magnetite ores. Using synthesized spherical 10-nm magnetite particles reacting in H2, we resolve the formation and consumption of w\"ustite (FeO) - the step most commonly attributed to agglomeration. Using X-ray scattering and microscopy, we resolve crystallographic anisotropy in the rate of the initial reaction, which becomes isotropic as the material sinters. Complementing with imaging, we demonstrate how the particles self-assemble, subsequently react and sinter into ~100x oblong grains. Our insights into how morphologically uniform iron oxide particles react and agglomerate H2 reduction enable future size-dependent models to effectively describe the multiscale iron ore reduction

Counting on the future: fast charge-integrating detectors for X-ray nanoimaging

A fast charge-integrating detector has been showcased for high-resolution X-ray ptychography. The advancement in developing detectors of this kind, with rapid framing capabilities, holds paramount significance in harnessing the full potential of emerging diffraction-limited synchrotron sources for X-ray nanoimaging

Productive Performance, Serum Antioxidant Status, Tissue Selenium Deposition, and Gut Health Analysis of Broiler Chickens Supplemented with Selenium and Probiotics—A Pilot Study

The effect and interaction of dietary selenium (Se) and probiotics on three yellow chicken growth performance, tissue Se content, antioxidant capacity, and gut health were studied from 0 to 70 days of age. A total of 400 one-day-old broilers were distributed into four groups (I-Se, O-Se, I-Se + pros, and O-Se + pros groups) consisting of a 2 × 2 factorial design. The main factors were the source of Se (I-Se = inorganic Se: 0.2 mg/kg sodium selenite; O-Se = organic Se: 0.2 mg/kg Selenium yeast) and the level of probiotics (0.5% EM or 0% EM, the component of EM mainly includes Lactobacillus and Yeast at the dose of 2 × 108 cfu/kg and 3 × 107 cfu/kg, respectively). Each treatment had 5 duplicates consisting of 20 broilers. The results showed that the I-Se group had a greater (p < 0.05) ratio of feed: weight gain (F/G) of broilers at Starter (0–35 d) than the other treatments. Compared to the I-Se group, the O-Se group increased (p < 0.05) Se concentrations in the liver, pancreas, breast muscles, thigh muscle, and the activity of total antioxidative capacity (T-AOC) in serum, as well as the relative abundance of Barnesiella and Lactobacillus in cecum. Meanwhile, probiotics enhanced (p < 0.05) Se concentrations in the pancreas, thigh muscle, serum, and the activity of T-AOC and glutathione peroxidase (GSH-Px), the duodenum’s ratio of villi height to crypt depth (V/C), the jejunum villus height and V/C, and the ileum’s villus height. Furthermore, the significant interactions (p < 0.05) between Se sources and the level of probiotics were observed in Se concentrations in the pancreas, thigh muscle, serum, crypt depth of duodenum, and villus height of jejunum of birds, and Barnesiella abundance in the cecal. In conclusion, our results demonstrate that the combination of O-Se + pros can improve broiler early growth performance, tissue Se content in the pancreas, thigh muscle, and serum, promote intestinal development, and regulate the composition of intestinal flora, suggesting a better combination. These findings provide an effective method of nutrient combination addition to improving the performance of three yellow chickens

Attentional Ptycho-Tomography (APT) for three-dimensional nanoscale X-ray imaging with minimal data acquisition and computation time

Abstract Noninvasive X-ray imaging of nanoscale three-dimensional objects, such as integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of the complex electromagnetic field through the IC; combined with a tomographic scan, which collects these complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach to drastically reduce the amount of angular scanning, and thus the total acquisition time. APT is machine learning-based, utilizing axial self-Attention for Ptycho-Tomographic reconstruction. APT is trained to obtain accurate reconstructions of the ICs, despite the incompleteness of the measurements. The training process includes regularizing priors in the form of typical patterns found in IC interiors, and the physics of X-ray propagation through the IC. We show that APT with ×12 reduced angles achieves fidelity comparable to the gold standard Simultaneous Algebraic Reconstruction Technique (SART) with the original set of angles. When using the same set of reduced angles, then APT also outperforms Filtered Back Projection (FBP), Simultaneous Iterative Reconstruction Technique (SIRT) and SART. The time needed to compute the reconstruction is also reduced, because the trained neural network is a forward operation, unlike the iterative nature of these alternatives. Our experiments show that, without loss in quality, for a 4.48 × 93.2 × 3.92 µm3 IC (≃6 × 108 voxels), APT reduces the total data acquisition and computation time from 67.96 h to 38 min. We expect our physics-assisted and attention-utilizing machine learning framework to be applicable to other branches of nanoscale imaging, including materials science and biological imaging

X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning.

X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. By working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change