BEATS: BEAmline for synchrotron X-ray microTomography at SESAME.

The ID10 beamline of the SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) synchrotron light source in Jordan was inaugurated in June 2023 and is now open to scientific users. The beamline, which was designed and installed within the European Horizon 2020 project BEAmline for Tomography at SESAME (BEATS), provides full-field X-ray radiography and microtomography imaging with monochromatic or polychromatic X-rays up to photon energies of 100 keV. The photon source generated by a 2.9 T wavelength shifter with variable gap, and a double-multilayer monochromator system allow versatile application for experiments requiring either an X-ray beam with high intensity and flux, and/or a partially spatial coherent beam for phase-contrast applications. Sample manipulation and X-ray detection systems are designed to allow scanning samples with different size, weight and material, providing image voxel sizes from 13 µm down to 0.33 µm. A state-of-the-art computing infrastructure for data collection, three-dimensional (3D) image reconstruction and data analysis allows the visualization and exploration of results online within a few seconds from the completion of a scan. Insights from 3D X-ray imaging are key to the investigation of specimens from archaeology and cultural heritage, biology and health sciences, materials science and engineering, earth, environmental sciences and more. Microtomography scans and preliminary results obtained at the beamline demonstrate that the new beamline ID10-BEATS expands significantly the range of scientific applications that can be targeted at SESAME.

Alrecon: computed tomography reconstruction web application based on Solara.

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user.

Non-destructive 3D exploration of silicate glass corrosion: a combined multiscale approach from the macro to the nanoscale.

In this research, a comprehensive multi-technique analysis, including synchrotron-based X-ray micro-computed tomography, is used to visualize the microstructure of alteration in a very particular Roman glass fragment, in which millennia of corrosion history have not significantly impacted the integrity of the fragment itself. This exceptionally rare occurrence has allowed for the maximization of meaningful data acquisition, by examining the alteration structures from the macro to the nanoscale. This study elucidates the intricate mechanisms underlying glass corrosion when in contact with soil, providing quantitative data and phase correlations in the alteration structures. These findings validate and refine existing predictive corrosion models.

Estimation of Cortical Bone Microstructure From Ultrasound Backscatter.

Multichannel pulse-echo ultrasound using linear arrays and single-channel data acquisition systems opens new perspectives for the evaluation of cortical bone. In combination with spectral backscatter analysis, it can provide quantitative information about cortical microstructural properties. We present a numerical study, based on the finite-difference time-domain method, to estimate the backscatter cross section of randomly distributed circular pores in a bone matrix. A model that predicts the backscatter coefficient using arbitrary pore diameter distributions was derived. In an ex vivo study on 19 human tibia bones (six males, 13 females, 83.7 ± 8.4 years), multidirectional ultrasound backscatter measurements were performed using an ultrasound scanner equipped with a 6-MHz 128-element linear array with sweep motor control. A normalized depth-dependent spectral analysis was performed to derive backscatter and attenuation coefficients. Site-matched reference values of tissue acoustic impedance Z , cortical thickness (Ct.Th), pore density (Ct.Po.Dn), porosity (Ct.Po), and characteristic parameters of the pore diameter (Ct.Po.Dm) distribution were obtained from 100-MHz scanning-acoustic microscopy images. Proximal femur areal bone mineral density (aBMD), stiffness S , and ultimate force Fu from the same donors were available from a previous study. All pore structure and material properties could be predicted using linear combinations of backscatter parameters with a median to high accuracy (0.28 ≤ adjusted R2 ≤ 0.59). The combination of cortical thickness and backscatter parameter provided similar or better prediction accuracies than aBMD. For the first time, a method for the noninvasive assessment of the pore diameter distribution in cortical bone by ultrasound is proposed. The combined assessment of cortical thickness, sound velocity, and pore size distribution in a mobile, nonionizing measurement system could have a major impact on preventing osteoporotic fractures.

Cortical thinning and accumulation of large cortical pores in the tibia reflect local structural deterioration of the femoral neck.

INTRODUCTION: Cortical bone thinning and a rarefaction of the trabecular architecture represent possible causes of increased femoral neck (FN) fracture risk. Due to X-ray exposure limits, the bone microstructure is rarely measurable in the FN of subjects but can be assessed at the tibia. Here, we studied whether changes of the tibial cortical microstructure, which were previously reported to be associated with femur strength, are also associated with structural deteriorations of the femoral neck. METHODS: The cortical and trabecular architectures in the FN of 19 humans were analyzed ex vivo on 3D microcomputed tomography images with 30.3 µm voxel size. Cortical thickness (Ct.Thtibia), porosity (Ct.Potibia) and pore size distribution in the tibiae of the same subjects were measured using scanning acoustic microscopy (12 µm pixel size). Femur strength during sideways falls was simulated with homogenized voxel finite element models. RESULTS: Femur strength was associated with the total (vBMDtot; R2 = 0.23, p < 0.01) and trabecular (vBMDtrab; R2 = 0.26, p < 0.01) volumetric bone mineral density (vBMD), with the cortical thickness (Ct.ThFN; R2 = 0.29, p < 0.001) and with the trabecular bone volume fraction (Tb.BV/TVFN; R2 = 0.34, p < 0.001), separation (Tb.SpFN; R2 = 0.25, p < 0.01) and number (Tb.NFN; R2 = 0.32, p < 0.001) of the femoral neck. Moreover, smaller Ct.Thtibia was associated with smaller Ct.ThFN (R2 = 0.31, p < 0.05), lower Tb.BV/TVFN (R2 = 0.29, p < 0.05), higher Tb.SpFN (R2 = 0.33, p < 0.05) and lower Tb.NFN (R2 = 0.42, p < 0.01). A higher prevalence of pores with diameter > 100 µm in tibial cortical bone (relCt.Po100µm-tibia) indicated higher Tb.SpFN (R2 = 0.36, p < 0.01) and lower Tb.NFN (R2 = 0.45, p < 0.01). CONCLUSION: Bone resorption and structural decline of the femoral neck may be identified in vivo by measuring cortical bone thickness and large pores in the tibia.

Femur strength predictions by nonlinear homogenized voxel finite element models reflect the microarchitecture of the femoral neck.

In the human femoral neck, the contribution of the cortical and trabecular architecture to mechanical strength is known to depend on the load direction. In this work, we investigate if QCT-derived homogenized voxel finite element (hvFE) simulations of varying hip loading conditions can be used to study the architecture of the femoral neck. The strength of 19 pairs of human femora was measured ex vivo using nonlinear hvFE models derived from high-resolution peripheral QCT scans (voxel size: 30.3 µm). Standing and side-backwards falling loads were modeled. Quasi-static mechanical tests were performed on 20 bones for comparison. Associations of femur strength with volumetric bone mineral density (vBMD) or microstructural parameters of the femoral neck obtained from high-resolution QCT were compared between mechanical tests and simulations and between standing and falling loads. Proximal femur strength predictions by hvFE models were positively associated with the vBMD of the femoral neck (R² > 0.61, p < 0.001), as well as with its cortical thickness (R² > 0.27, p < 0.001), trabecular bone volume fraction (R² = 0.42, p < 0.001) and with the first two principal components of the femoral neck architecture (R² > 0.38, p < 0.001). Associations between femur strength and femoral neck microarchitecture were stronger for one-legged standing than for side-backwards falling. For both loading directions, associations between structural parameters and femur strength from hvFE models were in good agreement with those from mechanical tests. This suggests that hvFE models can reflect the load-direction-specific contribution of the femoral neck microarchitecture to femur strength.

Acoustic diffusion constant of cortical bone: Numerical simulation study of the effect of pore size and pore density on multiple scattering.

While osteoporosis assessment has long focused on the characterization of trabecular bone, the cortical bone micro-structure also provides relevant information on bone strength. This numerical study takes advantage of ultrasound multiple scattering in cortical bone to investigate the effect of pore size and pore density on the acoustic diffusion constant. Finite-difference time-domain simulations were conducted in cortical microstructures that were derived from acoustic microscopy images of human proximal femur cross sections and modified by controlling the density (Ct.Po.Dn) ∈[5-25] pore/mm2 and size (Ct.Po.Dm) ∈[30-100] µm of the pores. Gaussian pulses were transmitted through the medium and the backscattered signals were recorded to obtain the backscattered intensity. The incoherent contribution of the backscattered intensity was extracted to give access to the diffusion constant D. At 8 MHz, significant differences in the diffusion constant were observed in media with different porous micro-architectures. The diffusion constant was monotonously influenced by either pore diameter or pore density. An increase in pore size and pore density resulted in a decrease in the diffusion constant (D =285.9Ct.Po.Dm-1.49, R2=0.989 , p=4.96×10-5,RMSE=0.06; D=6.91Ct.Po.Dn-1.01, R2=0.94, p=2.8×10-3 , RMSE=0.09), suggesting the potential of the proposed technique for the characterization of the cortical microarchitecture.

Correction: Large cortical bone pores in the tibia are associated with proximal femur strength.

[This corrects the article DOI: 10.1371/journal.pone.0215405.].

Large cortical bone pores in the tibia are associated with proximal femur strength.

Alterations of structure and density of cortical bone are associated with fragility fractures and can be assessed in vivo in humans at the tibia. Bone remodeling deficits in aging women have been recently linked to an increase in size of cortical pores. In this ex vivo study, we characterized the cortical microarchitecture of 19 tibiae from human donors (aged 69 to 94 years) to address, whether this can reflect impairments of the mechanical competence of the proximal femur, i.e., a major fracture site in osteoporosis. Scanning acoustic microscopy (12 µm pixel size) provided reference microstructural measurements at the left tibia, while the bone vBMD at this site was obtained using microcomputed tomography (microCT). The areal bone mineral density of both left and right femoral necks (aBMDneck) was measured by dual-energy X-ray absorptiometry (DXA), while homogenized nonlinear finite element models based on high-resolution peripheral quantitative computed tomography provided hip stiffness and strength for one-legged standing and sideways falling loads. Hip strength was associated with aBMDneck (r = 0.74 to 0.78), with tibial cortical thickness (r = 0.81) and with measurements of the tibial cross-sectional geometry (r = 0.48 to 0.73) of the same leg. Tibial vBMD was associated with hip strength only for standing loads (r = 0.59 to 0.65). Cortical porosity (Ct.Po) of the tibia was not associated with any of the femoral parameters. However, the proportion of Ct.Po attributable to large pores (diameter > 100 µm) was associated with hip strength in both standing (r = -0.61) and falling (r = 0.48) conditions. When added to aBMDneck, the prevalence of large pores could explain up to 17% of the femur ultimate force. In conclusion, microstructural characteristics of the tibia reflect hip strength as well as femoral DXA, but it remains to be tested whether such properties can be measured in vivo.

Ex vivo cortical porosity and thickness predictions at the tibia using full-spectrum ultrasonic guided-wave analysis.

The estimation of cortical thickness (Ct.Th) and porosity (Ct.Po) at the tibia using axial transmission ultrasound was successfully validated ex vivo against site-matched micro-computed tomography. The assessment of cortical parameters based on full-spectrum guided-wave analysis might improve the prediction of bone fractures in a cost-effective and radiation-free manner. PURPOSE: Cortical thickness (Ct.Th) and porosity (Ct.Po) are key parameters for the identification of patients with fragile bones. The main objective of this ex vivo study was to validate the measurement of Ct.Po and Ct.Th at the tibia using a non-ionizing, low-cost, and portable 500-kHz ultrasound axial transmission system. Additional ultrasonic velocities and site-matched reference parameters were included in the study to broaden the analysis. METHODS: Guided waves were successfully measured ex vivo in 17 human tibiae using a novel 500-kHz bi-directional axial transmission probe. Theoretical dispersion curves of a transverse isotropic free plate model with invariant matrix stiffness were fitted to the experimental dispersion curves in order to estimate Ct.Th and Ct.Po. In addition, the velocities of the first arriving signal (υFAS) and A0 mode (υA0) were measured. Reference Ct.Po, Ct.Th, and vBMD were obtained from site-matched micro-computed tomography. Scanning acoustic microscopy (SAM) provided the acoustic impedance of the axial cortical bone matrix. RESULTS: The best predictions of Ct.Po (R2 = 0.83, RMSE = 2.2%) and Ct.Th (R2 = 0.92, RMSE = 0.2 mm, one outlier excluded) were obtained from the plate model. The second best predictors of Ct.Po and Ct.Th were vBMD (R2 = 0.77, RMSE = 2.6%) and υA0 (R2 = 0.28, RMSE = 0.67 mm), respectively. CONCLUSIONS: Ct.Th and Ct.Po were accurately predicted at the human tibia ex vivo using a transverse isotropic free plate model with invariant matrix stiffness. The model-based predictions were not further enhanced when we accounted for variations in axial tissue stiffness as reflected by the acoustic impedance from SAM.

BMD-based assessment of local porosity in human femoral cortical bone.

Cortical pores are determinants of the elastic properties and of the ultimate strength of bone tissue. An increase of the overall cortical porosity (Ct.Po) as well as the local coalescence of large pores cause an impairment of the mechanical competence of bone. Therefore, Ct.Po represents a relevant target for identifying patients with high fracture risk. However, given their small size, the in vivo imaging of cortical pores remains challenging. The advent of modern high-resolution peripheral quantitative computed tomography (HR-pQCT) triggered new methods for the clinical assessment of Ct.Po at the peripheral skeleton, either by pore segmentation or by exploiting local bone mineral density (BMD). In this work, we compared BMD-based Ct.Po estimates with high-resolution reference values measured by scanning acoustic microscopy. A calibration rule to estimate local Ct.Po from BMD as assessed by HR-pQCT was derived experimentally. Within areas of interest smaller than 0.5 mm2, our model was able to estimate the local Ct.Po with an error of 3.4%. The incorporation of the BMD inhomogeneity and of one parameter from the BMD distribution of the entire scan volume led to a relative reduction of the estimate error of 30%, if compared to an estimate based on the average BMD. When applied to the assessment of Ct.Po within entire cortical bone cross-sections, the proposed BMD-based method had better accuracy than measurements performed with a conventional threshold-based approach.

Computational Study of the Effect of Cortical Porosity on Ultrasound Wave Propagation in Healthy and Osteoporotic Long Bones.

Computational studies on the evaluation of bone status in cases of pathologies have gained significant interest in recent years. This work presents a parametric and systematic numerical study on ultrasound propagation in cortical bone models to investigate the effect of changes in cortical porosity and the occurrence of large basic multicellular units, simply called non-refilled resorption lacunae (RL), on the velocity of the first arriving signal (FAS). Two-dimensional geometries of cortical bone are established for various microstructural models mimicking normal and pathological tissue states. Emphasis is given on the detection of RL formation which may provoke the thinning of the cortical cortex and the increase of porosity at a later stage of the disease. The central excitation frequencies 0.5 and 1 MHz are examined. The proposed configuration consists of one point source and multiple successive receivers in order to calculate the FAS velocity in small propagation paths (local velocity) and derive a variation profile along the cortical surface. It was shown that: (a) the local FAS velocity can capture porosity changes including the occurrence of RL with different number, size and depth of formation; and (b) the excitation frequency 0.5 MHz is more sensitive for the assessment of cortical microstructure.