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Jupyter notebooks to reconstruct and visualize microCT data from ALS beamline 8.3.2. Relies on standard tomography and image processing tools (astra, tomopy, itk, scikit-image) and ipywidgets (sliders, drop down menus, etc) to make parameter selection and data visualization easy for users.
Abstract Background Heterotopic ossification (HO) is a frequent and debilitating complication of traumatic musculoskeletal injuries and orthopedic procedures. Prophylactic dosing of botulinum toxin type A (BTxA) holds potential as a novel treatment option if accurately distributed throughout soft-tissue volumes where protection is clinically desired. We developed a high-resolution, microcomputed tomography (microCT)-based imaging strategy to assess drug distribution and validated this platform by quantifying distribution achieved via a prototype delivery system versus a single-bolus injection. Methods We injected an iodine-containing contrast agent (iodixanol 320 mg I/mL) into dissected rabbit musculature followed by microCT imaging and analysis. To contrast the performance of distributed versus bolus injections, a three-dimensional (3D) 64-cm 3 -printed soft-tissue holder was developed. A centered 2-cm 3 volume of interest (VOI) was targeted with a single-bolus injection or an equal volume distributed injection delivered via a 3D-printed prototype. VOI drug coverage was quantified as a percentage of the VOI volume that was < 1.0 mm from the injected fluid. Results The microCT-based approach enabled high-resolution quantification of injection distribution within soft tissue. The distributed dosing prototype provided significantly greater tissue coverage of the targeted VOI (72 ± 3%, mean ± standard deviation) when compared to an equal volume bolus dose (43 ± 5%, p = 0.031) while also enhancing the precision of injection targeting. Conclusions A microCT-based imaging technique precisely quantifies drug distribution within a soft-tissue VOI, providing a path to overcome a barrier for clinical translation of prophylactic inhibition of HO by BTxA. Relevance statement This platform will facilitate rapid optimization of injection parameters for clinical devices used to effectively and safely inhibit the formation of heterotopic ossification. Key points • MicroCT provides high-resolution quantification of soft-tissue drug distribution. • Distributed dosing is required to maximize soft-tissue drug coverage. • Imaging platform will enable rapid screening of 3D-printed drug distribution prototypes. Graphical Abstract
The enamel of mammalian teeth is a highly mineralized tissue that must endure a lifetime of cyclic contact and is inspiring the development of next-generation engineering materials. Attempts to implement enamel-inspired structures in synthetic materials have had limited success, largely due to the absence of a detailed understanding of its microstructure. Here, the present work used synchrotron phase-contrast microCT imaging to evaluate the three-dimensional microstructure of enamel from four mammals including Lion, Gray Wolf, Snow Leopard, and Black Bear. Quantitative results of image analysis revealed that the decussation pattern of enamel consists of discrete diazone (D) and parazone (P) bands of rods organized with stacking arrangement of D+/P/D-/P in all mammals evaluated; the D+ and D- refer to distinct diazone bands with juxtaposed rod orientations from the reference plane. Furthermore, the rod orientations in the bands can be described in terms of two principal angles, defined here as the pitch and yaw. While the pitch angle increases from the outer enamel to a maximum (up to ≈ 40°) near the dentin enamel junction, minimal spatial variations are observed in yaw across the enamel thickness. There are clear differences in the decussation parameters of enamel across species that are interpreted here with respect to the structural demands placed on their teeth. The rod pitch and band width of enamel are identified as important design parameters and appear to be correlated with the bite force quotient of the four mammals evaluated.
Includes three different types of stacks, in two folders: "REC_RAW_STACKS.zip" contains: (1) Raw gray-scale reconstructed microCT x-ray scans, in the form of individual stacks per sample. "ML_STACKS.zip" contains: (2) Stacks that have been labeled using a machine-learning mask-RCNN pipeline identifying epidermis, mesophyll, airspace, vascular bundle, and background. (3) Stacks that have stomata locations labeled using a small point. The three types of stacks were used to calculate a variety of anatomical and physiological traits, using ImageJ Macros provided on Github: https://github.com/leakey-lab/microCT-Macros-Fischer. Young leaves from WT and transgenic Sorghum plants. CSV "microCT_REC2_META.csv" contains metadata, including sample/sub-sample labels.
We have measured the spatial resolution of the 450 kV test-bed microCT scanner. We have also modeled the resolution analytically. The model and measurement show correspondence within 5%. Our measurement method was to use a thin tungsten wire to act as an impulse function. Therefore, the image is the impulse response, also called the point spread function (PSF) of the system. The Fourier transform (FT) of the impulse response is the modulation transfer function (MTF) of the system. We report the MTF here. By moving the wire at different positions in the scan field of view (FOV), we can measure MTF at different positions in the FOV. Since our imaging system is radially symmetric, we report MTF in two directions, radial and tangential as shown in Figure 1. The radial direction is along the line from isocenter to the wire, and the tangential is perpendicular to it.
This document is a short summary of the steps required for MicroCT evaluation of a specimen. This includes data acquisition through image analysis, for the Explosives Threat Assessment (ETA) program. Expected outputs for each stage are outlined. Information and data shall be shipped to LLNL as described herein.
Background: {sup 18}F-NaF positron emission tomography (PET) targets microcalcifications. We compared in vitro microPET assessed {sup 18}F-NaF uptake between culprit and non-culprit human carotid plaques. Furthermore, we compared {sup 18}F-NaF uptake with calcification visualized on microcomputed tomography (microCT). Methods: Carotid plaques from stroke patients undergoing surgery were incubated in {sup 18}F-NaF and scanned using a microPET and a microCT scan. The average PET assessed {sup 18}F-NaF uptake was expressed as percentage of the incubation dose per gram (%Inc/g). {sup 18}F-NaF PET volume of interest (VOI) was compared with CT calcification VOI. Results: 23 carotid plaques (17 culprit, 6 non-culprit) were included. The average {sup 18}F-NaF uptake in culprit carotid plaques was comparable with the uptake in non-culprit carotid plaques (median 2.32 %Inc/g [IQR 1.98 to 2.81] vs. median 2.35 %Inc/g [IQR 1.77 to 3.00], P = 0.916). Only a median of 10% (IQR 4 to 25) of CT calcification VOI showed increased {sup 18}F-NaF uptake, while merely a median of 35% (IQR 6 to 42) of {sup 18}F-NaF PET VOI showed calcification on CT. Conclusions: {sup 18}F-NaF PET represents a different stage in the calcification process than CT. We observed a similar PET assessed {sup 18}F-NaF uptake and pattern in culprit and non-culprit plaques of high-risk patients, indicating that this method may be of more value in early atherosclerotic stenosis development. [French] French Abstract: Contexte: La tomographie par émission de positons (TEP) au {sup 18}F-NaF marque les micro-calcifications. Nous avons comparé in vitro les plaques carotidiennes humaines responsable d’accident vasculaire cérébrales marquées au {sup 18}F-NaF avec une microTEP et leur calcification au moyen d’un microCT Méthodes: Les plaques carotidiennes de patients victimes d’un accident vasculaire cérébral qui ont bénéficié d’ une intervention chirurgicale ont été incubées dans du {sup 18}F-NaF et imagées avec une microTEP et un microCT. Le pourcentage d’absorption moyen de {sup 18}F-NaF par gr de tissu (% Inc/g) ont été comparées au volume d’intérêt (VOI) des calcifications mesurées par CT. Résultats: 23 plaques carotidiennes (17 responsables d’un AVC et 6 non responsables) ont été incluses. Le % moyen d’absorption de {sup 18}F-NaF dans les plaques carotidiennes responsables furent comparable à l’absorption dans les plaques non responsables (2,32% Inc/g vs 2,35% Inc/g , p = 0,916). Dix pourcent seulement des calcifications visualisées par CT démontrèrent une augmentation d’absorption de {sup 18}F-NaF et 35% des plaques montrant une absorption de {sup 18}F-NaF PET VOI démontrèrent des calcifications au CT. Conclusions: L’imagerie de l’absorption de {sup 18}F-NaF par tomographie à positrons représente un processus physiopathologique différent de l’imagerie des calcifications par CT. L’absorption du {sup 18}F-NaF par les plaques responsables et non responsables d’accidents vasculaire cérébraux pourrait s’avérer utile dans le diagnostic précoce des sténoses athéromateuses. [Spanish] Spanish Abstract: Antecedentes: La tomografía por emisión de positrones (PET) con {sup 18}F-floruro de sodio ({sup 18}F-NaF) demuestra microcalcificaciones. En este estudio, comparamos la captación de {sup 18}F-NaF entre placas carotideas culpables y no culpables valorada con microPET in vitro. Además, comparamos la captación de {sup 18}F-NAF con las calcificaciones detectadas por microtomografía computada (microCT). Métodos: Placas carotídeas de pacientes postoperados que sufrieron de un evento vascular cerebral fueron incubadas en 18-NaF y escaneadas usando microPET y microCT. El promedio de la captación fue expresado como porcentaje de la dosis de incubación por gramo (%Inc/gr). El volumen de interés (VOI) del PET {sup 18}F-NaF se comparó con el VOI de calcificación por CT. Resultados: Se incluyeron 23 placas carotídeas (17 culpables y 6 no culpables). El promedio de la captación de {sup 18}F-NaF en placas carotídeas culpable fue comparable al de las placas no culpables. (mediana 2.32%Inc/gr [IQR1.98-2.81] vs. mediana 2.35%Inc/gr [IQR1.77-3], p=.916). Solo una mediana de 10% (IQR 4-25) del VOI en CT mostró un aumento en la captación de {sup 18}F-NaF, mientras una mediana de 35% (IQR 6-42) del VOI de PET {sup 18}F-NaF mostró calcificación en CT. Conclusiones: La tomografía por emisión de positrones con {sup 18}F-NaF evalúa una etapa distinta en el proceso de calcificación que la CT. El patrón de captación de {sup 18}F-NaF que observamos en este estudio fue similar entre placas culpables y no culpables de pacientes de alto riesgo, lo cual indica que este método puede ser de mayor valor en el desarrollo temprano de la estenosis ateroesclerótica. [Chinese] Chinese Abstract: 背景: F18 氟化钠正电子发射断层扫描 (PET) 可用于检测微钙化。我们使用微型 PET 来评估病人体外 F18 氟化钠在颈动脉罪犯和非罪犯斑块之间的的摄取区别。此外, 我们还将 F18 氟化钠的摄取与 microCT 扫描检测的钙化进行对比。 方法: 将接受手术的中风患者的颈动脉斑块在 F18 氟化钠中培养并用 microPE 和 microCT 进行扫描。PET 对 F18 氟化钠的平均摄取率表示为每克培养剂量的百分比。F18 氟化钠 PET 中的感兴趣区域和 CT 钙化图像中的感兴趣区域 (VOI) 进行比较。 结果: 一共有 23个颈动脉斑块, 其中 17个罪犯斑块和 6个非罪犯斑块。罪犯和非罪犯颈动脉斑块的 F18 氟化钠的平均摄取率无明显差异 (中值 2.32 % Inc/g [IQR 1.98-2.81] vs. 中值2.35 % Inc/g [IQR 1.77-3.00], p = 0.916)。仅中值为10% [IQR 4-25] 的 CT 钙化 VOI 显示有F18氟化钠的摄取增加, 中值为 35%[IQR 6-42] 的 F18 氟化钠 PET VOI 显示有CT 上的钙化。 结论: 相较于 CT, F18 氟化钠 PET 展现了钙化过程中的一个不同阶段。在高危病人中, 我们观察到罪犯和非罪犯斑块具有类似的 PET F18 氟化钠摄取和模式, 表明该方法可能在早期动脉粥样硬化狭窄发展中具有更高的价值。.
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Bone consists mainly of carbonated apatite (cAp) nanoplatelets embedded in a matrix of collagen fibrils. Earlier, high-energy small angle X-ray scattering (SAXS) studies of archaeological adult human second metacarpal bones (mc2) found collagen D-period peaks with high-intensity I D in specimens in which microcomputed tomography (microCT) showed little diagenesis and I D ~ 0 for specimens where microCT revealed severe diagenesis (Park et al. 2022 Int. J. Osteoarchaeol. 32, 170–181 (doi:10.1002/oa.3053); Stock et al. 2022 Int. J. Osteoarchaeol. 32, 120–131 (doi:10.1002/oa.3049)). Here, the present paper uses SAXS at beamline 1-ID, Advanced Photon Source, Argonne National Laboratory and other techniques to study a set of 10 mc2 from an early Medieval cemetery at Greding, Germany. We hypothesized that non-invasive measurement of I D would provide an accurate and rapid (approx. 6 min/specimen) assessment of diagenesis in archaeological mc2. Results of Raman spectroscopy, laboratory microCT and backscattered electron, reflected light and polarized transmitted light microscopies confirmed the SAXS determinations, but lattice parameter values from X-ray diffraction were uncorrelated with I D value. Age-at-death estimates placed the 10 mc2 in three age categories (young adult, middle adult, old adult): lattice parameters from X-ray diffraction were uncorrelated with age at death. Cross-sectional bone area fraction from microCT dropped noticeably for the older age cohort.
Dissecting the heads of small insects belonging to the order Hemiptera for detailed anatomical investigation with light or scanning electron microscopy is difficult, time-consuming, and destructive, often resulting in sample preparation artifacts. Nevertheless, the structural details of these insects often hold critical information regarding their interactions with bacterial pathogens. For example, the glassy-winged sharpshooter (GWSS) is an efficient vector of the bacterium Xylella fastidiosa, the causal agent of Pierce’s disease in grape vines, but the foregut of this species is exceptionally difficult to dissect. Here, we describe a simple, non-destructive method to investigate the structure of the anterior gut of GWSS using high-resolution micro-computed X-ray tomography (microCT). The use of microCT eliminates the need for destructive dissection and reveals the morphology of small insects in three dimensions, allowing the user to virtually dissect the sample. The use of microCT imaging is a promising and powerful tool in the entomological sciences for studying the structures of vector insects, especially for difficult-to-dissect regions such as the foregut.
Soil ecosystem services, like the ability to store water, have been depleted after a century of conventional, annual cropping, and perennial crops offer a solution to this and other agricultural environmental issues. We assessed the impact of Miscanthus × giganteus (miscanthus), a perennial biomass crop, on soil water holding capacity and structure compared to continuous maize (Zea mays L.) at two sites in Iowa. After three growing seasons, we measured the following: (1) maximum water holding capacity (MWHC) with and without soil structure, and (2) total porosity and pore size distribution (PSD) via micro-computed tomography (microCT). Miscanthus increased MWHC by 14.7% across both sites relative to maize (p = 0.002), and we attributed this to structural changes due to the lack of a crop effect when measured on structureless soils. No significant changes were detected in soil organic matter, texture, total porosity, or PSD that could explain the increase in MWHC under miscanthus. Our findings suggest that the increases in MWHC are primarily due to structural changes rather than increases in soil organic matter or porosity (at least porosity detectable by microCT). This study highlights miscanthus' potential to enhance soil water storage and underscores the need for further investigation to clarify the mechanisms through which this biomass crop influences soil structural properties.
Injection of supercritical carbon dioxide (CO 2 ) into geological formations is a strategy for both atmospheric greenhouse gas reduction (climate change mitigation) and enhanced oil recovery. To understand CO 2 trapping efficiency, the capillary trapping behaviors that immobilize subsurface fluids were analyzed at the pore-scale using pairs of proxy fluids representing the range of in situ nonwetting and wetting fluid properties encountered in geologic storage reservoirs. The pairs of fluids were cycled through imbibition and drainage processes using a flow cell apparatus containing a sintered glass bead column. Computed x-ray microtomography (microCT) was used to identify immobilized nonwetting fluid after imbibition and drainage events. From microCT images, the trapped residual (post-secondary imbibition) nonwetting phase was spatially correlated to both the original (post-primary imbibition) and the initial (post-primary drainage) nonwetting phase; this relationship is referred to here as the original saturation dependence (SO-dependence) and initial saturation dependence (SI-dependence), respectively. Significant trends of decreasing SO- and SI-dependence with increasing wetting and nonwetting fluid phase viscosities were observed. This finding implies that the amount of CO 2 injected and ultimately trapped is dependent on the nonwetting phase (e.g. oil or gas) already present in the formation, as well as on the manner in which supercritical CO 2 is initially injected, which are factors not considered in current trapping models. To explore the potential effect that varying viscosity and interfacial tension (IFT) might have on this process, we report on a variety of fluid pairs with different viscosities and IFT.
Nineteen short sections of core were taken from the BCH-03 borehole at Brady’s Hot Springs, Churchill County, Nevada, between 2,945 ft and the total depth of 4,885 ft. This well is in a geothermal field. Data collected includes thin section photomicrographs, Medical CT tiff stacks, microCT tiff stacks, XRD, porosity (from thin sections, He porosimeter, microCT segmentation) and P/S wave velocities.
Understanding mechanical failure, crack propagation, and compressive behavior at the micrometer scale is essential for tailoring material properties for structural performance in cellular materials. Typically, modeling of traditional polymer foam materials is clouded by the lack of control in material morphology and its inherent stochastic structure. Additive manufacturing with sub-micrometer resolution provides a direct path for experimenters to specifically tailor structures needed by modelers to explicitly probe mechanical performance. Using laboratory-based 3D X-ray computed tomographic imaging (CT), the examination of deformation and damage provides a critical path to understand how these soft materials behave. Additionally, synchrotron CT yields realistic information at higher strain rates to directly validate the robustness of our finite element modeling. For this study, nanolithographic printing was employed to generate a series of engineered lattices with increasing levels of defects through the random removal of ligaments. These structures were mechanically tested and imaged with laboratory-based microCT. Additionally, synchrotron experiments were conducted in which the structures were imaged in 3D at 14 Hz during compression at a 0.4 s –1 strain rate. These 3D images show the changes in the structure as the ligaments bend, buckle and fracture in real time. This technique provides a robust framework for developing our methodologies and future exploration of engineered structures.
Here, in this work we infer the underlying distribution on pore radius in human cortical bone samples using ultrasonic attenuation data. We first discuss how to formulate polydisperse attenuation models using a probabilistic approach and the Waterman Truell model for scattering attenuation. We then compare the Independent Scattering Approximation and the higher-order Waterman Truell models’ forward predictions for total attenuation in polydisperse samples. Following this, we formulate an inverse problem under the Prohorov Metric Framework coupled with variational regularization to stabilize this inverse problem. We then use experimental attenuation data taken from human cadaver samples and solve inverse problems resulting in nonparametric estimates of the probability density function on pore radius. We compare these estimates to the “true” microstructure of the bone samples determined via microCT imaging. We find that our methodology allows us to reliably estimate the underlying microstructure of the bone from attenuation data.
Thermal conductivity of cement paste is significantly influenced by the presence of macro-pores within it. These pores (pores with size greater than 6 μm, measured using microCT) which may be filled with air and/or water significantly alters the thermal conductivity of the resulting material. A combination of experiments, molecular dynamic investigations of major constituents of the cement paste, multiscale homogenization techniques, and inclusion of thermal conductivity of the pores containing either air or water has been utilized in this study to reveal the influence of pores in the calculation of thermal conductivity of the composite material.
A new image analysis procedure for quantifying microcracks from three-dimensional (3D) X-ray microCT images of concrete is presented. The method separates microcracks from air voids and aggregates by combining filtering and morphological operations. It was applied to study the effects of supplementary cementitious materials (SCMs) and curing age on autogenous shrinkage-induced microcracks in low w/b ratio concretes, and to determine the representative elementary volume (REV) for various properties of microcracks and air voids. Results showed that slag and silica fume significantly increased autogenous shrinkage and related microcracking. These SCMs increased volume fraction, width, length, dendritic density, anisotropy, and connectivity of microcracks, but decreased specific surface and tortuosity. Similar trends were observed with age. Comparison between 3D and 2D measurements was made. REV analysis showed that a sampling volume of ~20 × 20 × 25 mm{sup 3} is sufficient for characterising most parameters of autogenous shrinkage microcracks and air voids in concrete.
Abstract Ice loss in the Southern Hemisphere has been greatest over the past 30 years in West Antarctica. The high sensitivity of this region to climate change has motivated geologists to examine marine sedimentary records for evidence of past episodes of West Antarctic Ice Sheet (WAIS) instability. Sediments accumulating in the Scotia Sea are useful to examine for this purpose because they receive iceberg‐rafted debris (IBRD) sourced from the Pacific‐ and Atlantic‐facing sectors of West Antarctica. Here we report on the sedimentology and provenance of the oldest of three cm‐scale coarse‐grained layers recovered from this sea at International Ocean Discovery Program Site U1538. These layers are preserved in opal‐rich sediments deposited ∼1.2 Ma during a relatively warm regional climate. Our microCT‐based analysis of the layer's in‐situ fabric confirms its ice‐rafted origin. We further infer that it is the product of an intense but short‐lived episode of IBRD deposition. Based on the petrography of its sand fraction and the Phanerozoic 40 Ar/ 39 Ar ages of hornblende and mica it contains, we conclude that the IBRD it contains was likely sourced from the Weddell Sea and/or Amundsen Sea embayment(s) of West Antarctica. We attribute the high concentrations of IBRD in these layers to “dirty” icebergs calved from the WAIS following its retreat inland from its modern grounding line. These layers also sit at the top of a ∼366‐m thick Pliocene and early Pleistocene sequence that is much more dropstone‐rich than its overlying sediments. We speculate this fact may reflect that WAIS mass‐balance was highly dynamic during the ∼41‐kyr (inter)glacial world.