Laminography as a tool for imaging large-size samples with high resolution.

Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.

Structural aging of human neurons is opposite of the changes in schizophrenia.

Human mentality develops with age and is altered in psychiatric disorders, though their underlying mechanism is unknown. In this study, we analyzed nanometer-scale three-dimensional structures of brain tissues of the anterior cingulate cortex from eight schizophrenia and eight control cases. The distribution profiles of neurite curvature of the control cases showed a trend depending on their age, resulting in an age-correlated decrease in the standard deviation of neurite curvature (Pearson's r = -0.80, p = 0.018). In contrast to the control cases, the schizophrenia cases deviate upward from this correlation, exhibiting a 60% higher neurite curvature compared with the controls (p = 7.8 × 10-4). The neurite curvature also showed a correlation with a hallucination score (Pearson's r = 0.80, p = 1.8 × 10-4), indicating that neurite structure is relevant to brain function. This report is based on our 3D analysis of human brain tissues over a decade and is unprecedented in terms of the number of cases. We suggest that neurite curvature plays a pivotal role in brain aging and can be used as a hallmark to exploit a novel treatment of schizophrenia.

Transperineal Laser Ablation for Benign Prostatic Enlargement: A Systematic Review and Pooled Analysis of Pilot Studies.

Transperineal laser ablation (TPLA) of the prostate is a new minimally invasive treatment option in men with lower urinary tract symptoms (LUTS) due to benign prostatic enlargement (BPE). The aim of this systematic review was to investigate the efficacy and safety of TPLA in the management of BPE. The primary outcomes were the improvement in urodynamic parameters (maximum urinary flow (Qmax) and postvoiding residue (PVR)) and LUTS relief, assessed using the IPSS questionnaire. The secondary outcomes were the preservation of sexual and ejaculatory functions, assessed with the IEEF-5 and MSHQ-EjD questionnaires, respectively, and rates of postoperative complications. We reviewed the literature for prospective or retrospective studies evaluating the use of TPLA in the treatment of BPE. A comprehensive search in PubMed, Scopus, Web of Science, and ClinicalTrials.gov was performed for English language articles published between January 2000 and June 2022. Pooled analysis of the included studies with available follow-up data for the outcomes of interest was additionally performed. After screening 49 records, six full-text manuscripts were identified, including two retrospective and four prospective non-comparative studies. Overall, 297 patients were included. All the studies independently reported a statistically significant improvement, from baseline, in Qmax, PVR, and IPSS score at each timepoint. Three studies additionally demonstrated that TPLA did not affect sexual function, reporting no change in the IEEF-5 score, and a statistically significant improvement in MSHQ-EjD score at each timepoint. Low rates of complications were recorded in all the included studies. Pooled analysis showed a clinically meaningful improvement in both micturition and sexual outcomes mean values at 1, 3, 6, and 12 months of follow-up, compared with baseline. Transperineal laser ablation of the prostate for the treatment of BPE showed interesting results in pilot studies. However, higher level and comparative studies are needed to confirm its efficacy in relieving obstructive symptoms and preserving sexual function.

MRI-Derived Apparent Diffusion Coefficient of Peri-Prostatic Adipose Tissue Is a Potential Determinant of Prostate Cancer Aggressiveness in Preoperative Setting: A Preliminary Report.

Background: The aim of this study was to test the association between periprostatic adipose tissue (PPAT)­apparent diffusion coefficient (ADC) value recorded at multiparametric magnetic resonance imaging (mpMRI) and determinants of prostate cancer (PCa) aggressiveness in the preoperative setting. Methods: Data from 219 consecutive patients undergoing prostate biopsy (PBx) for suspicion of PCa, between January 2020 and June 2022, at our institution were retrospectively evaluated. Only patients who had mpMRI performed before PBx were included. The distribution of demographics and clinical features among PPAT-ADC values up to vs. above the median was studied using both parametric and non-parametric tests, according to variables. Linear and logistic regression models tested the association between PPAT-ADC values and determinants of PCa aggressiveness and the presence of intermediate-high risk PCa, respectively. Results: Of 132 included patients, 76 (58%) had PCa. Median PPAT-ADC was 876 (interquartile range: 654 − 1112) × 10−6 mm2/s. Patients with PPAT-ADC up to the median had a higher rate of PIRADS (Prostate Imaging­Reporting and Data System) 5 lesions (41% vs. 23%, p = 0.032), a higher percentage of PBx positive cores (25% vs. 6%, p = 0.049) and more frequently harbored ISUP (International Society of Urological Pathology) > 1 PCa (50% vs. 28%, p = 0.048). At univariable linear regression analyses, prostate-specific antigen (PSA), PSA density, PIRADS 5, and percentage of PBx positive cores were associated with lower PPAT-ADC values. PPAT-ADC up to the median was an independent predictor for intermediate-high risk PCa (odds ratio: 3.24, 95%CI: 1.17−9.46, p = 0.026) after adjustment for age and body mass index. Conclusions: Lower PPAT-ADC values may be associated with higher biopsy ISUP grade group PCa and a higher percentage of PBx-positive cores. Higher-level studies are needed to confirm these preliminary results.

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest.

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ, a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

Deep learning-based segmentation of lithium-ion battery microstructures enhanced by artificially generated electrodes.

Accurate 3D representations of lithium-ion battery electrodes, in which the active particles, binder and pore phases are distinguished and labeled, can assist in understanding and ultimately improving battery performance. Here, we demonstrate a methodology for using deep-learning tools to achieve reliable segmentations of volumetric images of electrodes on which standard segmentation approaches fail due to insufficient contrast. We implement the 3D U-Net architecture for segmentation, and, to overcome the limitations of training data obtained experimentally through imaging, we show how synthetic learning data, consisting of realistic artificial electrode structures and their tomographic reconstructions, can be generated and used to enhance network performance. We apply our method to segment x-ray tomographic microscopy images of graphite-silicon composite electrodes and show it is accurate across standard metrics. We then apply it to obtain a statistically meaningful analysis of the microstructural evolution of the carbon-black and binder domain during battery operation.

Improving reproducibility in synchrotron tomography using implementation-adapted filters.

For reconstructing large tomographic datasets fast, filtered backprojection-type or Fourier-based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black-box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation-adapted filters for several open-source implementations and applying them to simulated phantoms and real-world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline.

Fast X-ray Nanotomography with Sub-10 nm Resolution as a Powerful Imaging Tool for Nanotechnology and Energy Storage Applications.

In the last decade, transmission X-ray microscopes (TXMs) have come into operation in most of the synchrotrons worldwide. They have proven to be outstanding tools for non-invasive ex and in situ 3D characterization of materials at the nanoscale across varying range of scientific applications. However, their spatial resolution has not improved in many years, while newly developed functional materials and microdevices with enhanced performances exhibit nanostructures always finer. Here, optomechanical breakthroughs leading to fast 3D tomographic acquisitions (85 min) with sub-10 nm spatial resolution, narrowing the gap between X-ray and electron microscopy, are reported. These new achievements are first validated with 3D characterizations of nanolithography objects corresponding to ultrahigh-aspect-ratio hard X-ray zone plates. Then, this powerful technique is used to investigate the morphology and conformality of nanometer-thick film electrodes synthesized by atomic layer deposition and magnetron sputtering deposition methods on 3D silicon scaffolds for electrochemical energy storage applications.

Structural diverseness of neurons between brain areas and between cases.

The cerebral cortex is composed of multiple cortical areas that exert a wide variety of brain functions. Although human brain neurons are genetically and areally mosaic, the three-dimensional structural differences between neurons in different brain areas or between the neurons of different individuals have not been delineated. Here we report a nanometer-scale geometric analysis of brain tissues of the superior temporal gyrus of schizophrenia and control cases. The results of the analysis and a comparison with results for the anterior cingulate cortex indicated that (1) neuron structures are significantly dissimilar between brain areas and that (2) the dissimilarity varies from case to case. The structural diverseness was mainly observed in terms of the neurite curvature that inversely correlates with the diameters of the neurites and spines. The analysis also revealed the geometric differences between the neurons of the schizophrenia and control cases. The schizophrenia cases showed a thin and tortuous neuronal network compared with the controls, suggesting that the neuron structure is associated with the disorder. The area dependency of the neuron structure and its diverseness between individuals should represent the individuality of brain functions.

Linking void and interphase evolution to electrochemistry in solid-state batteries using operando X-ray tomography.

Despite progress in solid-state battery engineering, our understanding of the chemo-mechanical phenomena that govern electrochemical behaviour and stability at solid-solid interfaces remains limited compared to at solid-liquid interfaces. Here, we use operando synchrotron X-ray computed microtomography to investigate the evolution of lithium/solid-state electrolyte interfaces during battery cycling, revealing how the complex interplay among void formation, interphase growth and volumetric changes determines cell behaviour. Void formation during lithium stripping is directly visualized in symmetric cells, and the loss of contact that drives current constriction at the interface between lithium and the solid-state electrolyte (Li10SnP2S12) is quantified and found to be the primary cause of cell failure. The interphase is found to be redox-active upon charge, and global volume changes occur owing to partial molar volume mismatches at either electrode. These results provide insight into how chemo-mechanical phenomena can affect cell performance, thus facilitating the development of solid-state batteries.

In-Situ Characterization of Dynamic Morphological and Phase Changes of Selenium-doped Germanium Using a Single Particle Cell and Synchrotron Transmission X-ray Microscopy.

The dynamic information of lithium-ion battery active materials obtained from coin cell-based in-situ characterizations might not represent the properties of the active material itself because many other factors in the cell could have impacts on the cell performance. To address this problem, a single particle cell was developed to perform the in-situ characterization without the interference of inactive materials in the battery electrode as well as the X-ray-induced damage. In this study, the dynamic morphological and phase changes of selenium-doped germanium (Ge0.9 Se0.1 ) at the single particle level were investigated via synchrotron-based in-situ transmission X-ray microscopy. The results demonstrate the good reversibility of Ge0.9 Se0.1 at high cycling rate that helps understand its good cycling performance and rate capability. This in-situ and operando technique based on a single particle battery cell provides an approach to understanding the dynamic electrochemical processes of battery materials during charging and discharging at the particle level.

Strategies for simultaneous strengthening and toughening via nanoscopic intracrystalline defects in a biogenic ceramic.

While many organisms synthesize robust skeletal composites consisting of spatially discrete organic and mineral (ceramic) phases, the intrinsic mechanical properties of the mineral phases are poorly understood. Using the shell of the marine bivalve Atrina rigida as a model system, and through a combination of multiscale structural and mechanical characterization in conjunction with theoretical and computational modeling, we uncover the underlying mechanical roles of a ubiquitous structural motif in biogenic calcite, their nanoscopic intracrystalline defects. These nanoscopic defects not only suppress the soft yielding of pure calcite through the classical precipitation strengthening mechanism, but also enhance energy dissipation through controlled nano- and micro-fracture, where the defects' size, geometry, orientation, and distribution facilitate and guide crack initialization and propagation. These nano- and micro-scale cracks are further confined by larger scale intercrystalline organic interfaces, enabling further improved damage tolerance.

TomoGAN: low-dose synchrotron x-ray tomography with generative adversarial networks: discussion.

Synchrotron-based x-ray tomography is a noninvasive imaging technique that allows for reconstructing the internal structure of materials at high spatial resolutions from tens of micrometers to a few nanometers. In order to resolve sample features at smaller length scales, however, a higher radiation dose is required. Therefore, the limitation on the achievable resolution is set primarily by noise at these length scales. We present TomoGAN, a denoising technique based on generative adversarial networks, for improving the quality of reconstructed images for low-dose imaging conditions. We evaluate our approach in two photon-budget-limited experimental conditions: (1) sufficient number of low-dose projections (based on Nyquist sampling), and (2) insufficient or limited number of high-dose projections. In both cases, the angular sampling is assumed to be isotropic, and the photon budget throughout the experiment is fixed based on the maximum allowable radiation dose on the sample. Evaluation with both simulated and experimental datasets shows that our approach can significantly reduce noise in reconstructed images, improving the structural similarity score of simulation and experimental data from 0.18 to 0.9 and from 0.18 to 0.41, respectively. Furthermore, the quality of the reconstructed images with filtered back projection followed by our denoising approach exceeds that of reconstructions with the simultaneous iterative reconstruction technique, showing the computational superiority of our approach.

Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography.

Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.

Three-dimensional alteration of neurites in schizophrenia.

Psychiatric symptoms of schizophrenia suggest alteration of cerebral neurons. However, the physical basis of the schizophrenia symptoms has not been delineated at the cellular level. Here, we report nanometer-scale three-dimensional analysis of brain tissues of schizophrenia and control cases. Structures of cerebral tissues of the anterior cingulate cortex were visualized with synchrotron radiation nanotomography. Tissue constituents visualized in the three-dimensional images were traced to build Cartesian coordinate models of tissue constituents, such as neurons and blood vessels. The obtained Cartesian coordinates were used for calculating curvature and torsion of neurites in order to analyze their geometry. Results of the geometric analyses indicated that the curvature of neurites is significantly different between schizophrenia and control cases. The mean curvature of distal neurites of the schizophrenia cases was ~1.5 times higher than that of the controls. The schizophrenia case with the highest neurite curvature carried a frame shift mutation in the GLO1 gene, suggesting that oxidative stress due to the GLO1 mutation caused the structural alteration of the neurites. The differences in the neurite curvature result in differences in the spatial trajectory and hence alter neuronal circuits. It has been shown that the anterior cingulate cortex analyzed in this study has emotional and cognitive functions. We suggest that the structural alteration of neurons in the schizophrenia cases should reflect psychiatric symptoms of schizophrenia.

Nanoporous gold: a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems.

Full-field transmission X-ray microscopy (TXM) is a well established technique, available at various synchrotron beamlines around the world as well as by laboratory benchtop devices. One of the major TXM challenges, due to its nanometre-scale resolution, is the overall instrument stability during the acquisition of the series of tomographic projections. The ability to correct for vertical and horizontal distortions of each projection image during acquisition is necessary in order to achieve the effective 3D spatial resolution. The effectiveness of such an image alignment is also heavily influenced by the absorption properties and strong contrast of specific features in the scanned sample. Here it is shown that nanoporous gold (NPG) can be used as an ideal 3D test pattern for evaluating and optimizing the performance of a TXM instrument for hard X-rays at a synchrotron beamline. Unique features of NPG, such as hierarchical structures at multiple length scales and high absorbing capabilities, makes it an ideal choice for characterization, which involves a combination of a rapid-alignment algorithm applied on the acquired projections followed by the extraction of a set of both 2D- and 3D-descriptive image parameters. This protocol can be used for comparing the efficiency of TXM instruments at different synchrotron beamlines in the world or benchtop devices, based on a reference library of scanned NPG samples, containing information about the estimated horizontal and vertical alignment values, 2D qualitative parameters and quantitative 3D parameters. The possibility to tailor the ligament sizes of NPG to match the achievable resolution in combination with the high electron density of gold makes NPG an ideal 3D test pattern for evaluating the status and performance of a given synchrotron-based or benchtop-based TXM setup.

Xi-cam: a versatile interface for data visualization and analysis.

Xi-cam is an extensible platform for data management, analysis and visualization. Xi-cam aims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core of Xi-cam is an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. With Xi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data. Xi-cam's plugin-based architecture targets cross-facility and cross-technique collaborative development, in support of multi-modal analysis. Xi-cam is open-source and cross-platform, and available for download on GitHub.

Quantification and modeling of mechanical degradation in lithium-ion batteries based on nanoscale imaging.

Capacity fade in lithium-ion battery electrodes can result from a degradation mechanism in which the carbon black-binder network detaches from the active material. Here we present two approaches to visualize and quantify this detachment and use the experimental results to develop and validate a model that considers how the active particle size, the viscoelastic parameters of the composite electrode, the adhesion between the active particle and the carbon black-binder domain, and the solid electrolyte interphase growth rate impact detachment and capacity fade. Using carbon-silicon composite electrodes as a model system, we demonstrate X-ray nano-tomography and backscatter scanning electron microscopy with sufficient resolution and contrast to segment the pore space, active particles, and carbon black-binder domain and quantify delamination as a function of cycle number. The validated model is further used to discuss how detachment and capacity fade in high-capacity materials can be minimized through materials engineering.

Three-Dimensional Reconstruction and Analysis of All-Solid Li-Ion Battery Electrode Using Synchrotron Transmission X-ray Microscopy Tomography.

A synchrotron transmission X-ray microscopy tomography system with a spatial resolution of 58.2 nm at the Advanced Photon Source was employed to obtain three-dimensional morphological data of all-solid Li-ion battery electrodes. The three-phase electrode was fabricated from a 47:47:6 (wt %) mixture of Li(Ni1/3Mn1/3Co1/3)O2 as active material, Li1.3Ti1.7Al0.3(PO4)3 as Li-ion conductor, and Super-P carbon as electron conductor. The geometric analysis show that particle-based all-solid Li-ion battery has serious contact interface problem which significantly impact the Li-ion transport and intercalation reaction in the electrode, leading to low capacity, poor rate capability and cycle life.

Low-dose x-ray tomography through a deep convolutional neural network.

Synchrotron-based X-ray tomography offers the potential for rapid large-scale reconstructions of the interiors of materials and biological tissue at fine resolution. However, for radiation sensitive samples, there remain fundamental trade-offs between damaging samples during longer acquisition times and reducing signals with shorter acquisition times. We present a deep convolutional neural network (CNN) method that increases the acquired X-ray tomographic signal by at least a factor of 10 during low-dose fast acquisition by improving the quality of recorded projections. Short-exposure-time projections enhanced with CNNs show signal-to-noise ratios similar to long-exposure-time projections. They also show lower noise and more structural information than low-dose short-exposure acquisitions post-processed by other techniques. We evaluated this approach using simulated samples and further validated it with experimental data from radiation sensitive mouse brains acquired in a tomographic setting with transmission X-ray microscopy. We demonstrate that automated algorithms can reliably trace brain structures in low-dose datasets enhanced with CNN. This method can be applied to other tomographic or scanning based X-ray imaging techniques and has great potential for studying faster dynamics in specimens.