X-ray Micro Research Articles

Correlative X-ray micro-nanotomography with scanning electron microscopy at the Advanced Light Source.

Geological samples are inherently multi-scale. Understanding their bulk physical and chemical properties requires characterization down to the nano-scale. A powerful technique to study the three-dimensional microstructure is X-ray tomography, but it lacks information about the chemistry of samples. To develop a methodology for measuring the multi-scale 3D microstructure of geological samples, correlative X-ray micro- and nanotomography were performed on two rocks followed by scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS) analysis. The study was performed in five steps: (i) micro X-ray tomography was performed on rock sample cores, (ii) samples for nanotomography were prepared using laser milling, (iii) nanotomography was performed on the milled sub-samples, (iv) samples were mounted and polished for SEM analysis and (v) SEM imaging and compositional mapping was performed on micro and nanotomography samples for complimentary information. Correlative study performed on samples of serpentine and basalt revealed multiscale 3D structures involving both solid mineral phases and pore networks. Significant differences in the volume fraction of pores and mineral phases were also observed dependent on the imaging spatial resolution employed. This highlights the necessity for the application of such a multiscale approach for the characterization of complex aggregates such as rocks. Information acquired from the chemical mapping of different phases was also helpful in segmentation of phases that did not exhibit significant contrast in X-ray imaging. Adoption of the protocol used in this study can be broadly applied to 3D imaging studies being performed at the Advanced Light Source and other user facilities.

Characterisation of rouaite, an unusual copper-containing pigment in early modern English wall paintings, by synchrotron micro X-Ray diffraction and micro X-Ray absorption spectroscopy

Although the use of verditer, a synthetically produced copper carbonate pigment chemically analogous to azurite (Cu3(CO3)2(OH)2), in early modern wall paintings is regularly reported in grey literature, its detection in wall paintings is typically unavailable in a public forum. This article focusses on two particular samples (M9 and T1) initially suspected to contain copper blue pigments from decorative wall painting schemes in domestic houses across a range of status groups, in eastern and south-eastern England, dated to 1550-1650. Interest in verditer synthesis procedures is found in textual sources including both historic manuals and current scientific literature. The unreliability of the synthesis, particularly for blue verditer, however, is widely documented. Here, we report a multimodal study employing SEM-EDX, SR-μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mu$$\\end{document}PXRD mapping, and SR-μ\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\mu$$\\end{document}XANES spectroscopy to characterise the phases present in two wall painting samples, one c. 1600/early 1600s (M9) and the other c. 1600 (T1). In addition to assessment of the presence of verditer, this study presents the first identification of rouaite, a synthetic copper hydroxynitrate mineral (Cu2(NO3)(OH)3), in wall painting samples. Rouaite, shown in a previous publication to be a common byproduct of replications of the historical verditer synthetic recipes, appears in combination with verditer and alone. Its infrequent identification in paintings and murals is considered in light of analytical challenges. The presence of copper hydroxychlorides is also discussed in the context of rouaite stability and degradation. These results represent a significant development in our knowledge of the early modern palette in England and historical verditer synthesis and advances our understanding of how these painting schemes may be best preserved in the future.

Tracked evolution of single biochar particle’s morphology during pyrolysis in operando x-ray micro-computed tomography

The engineering of biochars with desired morphologies and pore structures is a far-reaching objective towards sustainable pore-dependent environmental technologies, such as water and soil remediation or catalysis. We hereby report a series of experiments that allow the direct following of the shape and porosity of single biochar particles during pyrolysis. Particles ~ 1–2 mm in diameter of unwashed and water-washed raw walnut shells were continuously 3D imaged during pyrolysis to 575 ℃ at a 10 K min−1 in Ar to obtain time- and temperature-resolved x-ray micro computed tomographies to a 0.82 μm resolution. Results showed visual evidence of a 30% and 70% v/v particle shrinkage for unwashed and washed samples, respectively. Particle swelling between 200 and 300 ℃ in the unwashed sample provided evidence of the softening of native biopolymers associated with lignin in untreated biomass. A purpose-defined parameter Λ shows the temperature-dependence of pore re-distribution towards the center of the particle to be linear for both samples. Λ was found to be 3.2×10-4K-1\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$3.2\ imes {10}^{-4}{K}^{-1}$$\\end{document} in the washed sample, approximately 3.5 times faster than in the unwashed one. Such linear dependence is significantly slower than an exponential Arrhenius-like trend thereby providing a qualitative measure of the heat and mass transport phenomena limiting the chemical reactions in the porous medium. This evidence is key to resolving the pathways to the thermochemical decomposition of biomass leading to preparation of precision-engineered biochars.Graphical

Influence of the painting medium on the alteration process of smalt in oil paintings studied using combined K and Co K-edge XANES

This study investigates the alteration processes affecting the smalt pigment in historical artworks through a combination of analytical techniques including X-ray Absorption Near Edge Structure (XANES) spectroscopy at the potassium (K) and cobalt (Co) K-edges, coupled with scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) and micro X-ray fluorescence elemental mapping (µ-XRF). Laboratory mock-up samples prepared with different oil binding media were artificially aged, revealing varying rates of smalt degradation. µ-XANES analyses at the K K-edge provided grain-scale insights into smalt alteration, highlighting the influence of binding media composition on degradation kinetics. Crossed clustering data analysis over K µ-XANES acquired on both model samples and historical cross-sections corroborated findings and identified distinct spectral signatures associated with different stages of smalt degradation. Furthermore, identification of potential transformation products such as potassium alum in historical samples emphasized the dynamic nature of pigment alteration processes.

Influence of the pressure of compacted glass powders on the final structure of sintered glass-ceramics

In reported investigation we studied sintered glass-ceramics from a model diopside glass with moderate crystallization ability by in-situ optical dilatometeric experiments. The initial glass was ground and sieved below 75 μm. Then thus prepared powders were pressed with different pressures between 50 and 250 MPa. In this way were obtained samples out of pressed powders with different initial porosities determined with gas pycnometry. Then the samples were heat treated in a contactless horizontal optical dilatometer and their porosities were measured one more time. Both pressed green samples and synthesized glass-ceramics were analyzed further with X-Ray micro tomography.We observed that the densification of all samples completes in the same moment which corresponds to the formation of a critical percentage crystal phase. Notwithstanding the continuation of the crystallization process, we obtain materials with different percentage of residual porosity. Then no volume variation of the system is observed. This approach is well demonstrated by the first derivative of the shrinkage curves with time.After the end of the shrinkage of the system, the crystallization leads to the formation of crystallization induced porosity (called by us CIPs) observed here.

X-ray Diffraction Analysis and Micro Hardness of Ternary Alloy (Ti – 6Al – 4Nb)

This research aims to prepare the ternary alloy (Ti-6Al-4Nb) Using powder technology and studying X-ray diffraction analysis and micro hardness of this alloy. Titanium, aluminum, and niobium, powders were mixed together to homogenize the elements, and then the pressing process was carried out under pressure (5Ton) and for a period of time(60sec) For the purpose of obtaining a cohesive alloy in the form of discs, then the heat Treatment process (annealing) was conducted at different temperatures. (650,750,850,950,1050)˚C for two hours, the structural properties were studied through X-ray diffraction examination (XRD)And studying the mechanical properties by measuring the micro hardness using the Vickers hardness method before and after annealing, the results of the tests showed (XRD)The phases of the basic materials that make up the alloy, as the crystalline structure of titanium appeared to be of the hexagonal stacked type(HCP)As for aluminum, it appeared in a cubic system with concentric faces(FCC) and niobium in a body-centered cubic system (BCC)A new phase also appeared after the annealing process, which is the phase(AlNbTi2)Has a right rhombic crystal structure(Orthorhombic)The results of the micro hardness test (Vickers) showed that the annealing process has a positive effect on improving the mechanical properties, as the hardness value increases when temperatures increase.

Effect of Zn amount on AlZn-based composite material produced by high speed mechanical alloying method

Purpose The purpose of this study is AlZn-based produced by high speed mechanical alloying method to investigate the effect of Zn amount on the composite material, Al-Zn-Mg-Cu-SiC composite material billets are obtained by sintering. Design/methodology/approach Mechanical alloying, X-ray diffraction analysis (XRD) graphics, sintering, polishing, scanning electron microscopy and energy dispersive X-ray analyzer (EDX) images and micro hardness tests were applied, respectively. Findings In the XRD analysis results, it was observed that the Al peak height decreased as the alloying time increased. When the samples sintered for 90 min are examined, it can be clearly seen that the hardness increases as the Zn ratio increases. EDX analysis results also support XRD results. Originality/value Increase in strength will require the use of thinner sheet metal and smaller rivets to achieve the same strength. This will reduce the weight of the aircraft. Weight reduction also means less fuel consumption and more economical flight. This increase in strength is a very important scientific achievement.

Advancing the hydrogen tolerance of ultrastrong aluminum alloys via nanoprecipitate modification

Ultrastrong metallic alloys, possessing unparalleled load-bearing abilities, are coveted in many sectors, thus attracting growing research efforts. However, these alloys encounter persistent usability challenges posed by hydrogen embrittlement, which causes unpredictable fracture through crack initiation. Due to complex hydrogen-microstructure interactions and their exacerbation under high stress, advances in hydrogen resistance in ultrastrong materials are sparse throughout their long history. Herein, we report a quantum-mechanics-informed strategy for hydrogen tolerance enhancement in ultrafine-grain-hardened Al-Zn-Mg-Cu alloys, approaching their current strength limit of approximately 1 GPa. This method involves the incorporation of hydrogen-absorbing T-phase precipitates into nanograins, to substantially reduce hydrogen coverage at potential crack initiation sites. We demonstrate, via synchrotron radiation X-ray micro-/nano-tomography, scanning transmission electron microscopy and atom probe tomography, that nanoprecipitates successfully withstand shear strains exceeding 1000 and are exploitable essentials for ultra strength-hydrogen synergy, contrasting their often-assumed secondary roles in nanocrystalline alloys due to possible strain-induced dissolution, which has intuitively excluded exploring them as central elements. Our approach potentially inspires new hydrogen-resisting alloys across a broad strength-composition space.

Experimental investigation of dynamic drying in single pharmaceutical granules containing acetaminophen or carbamazepine using synchrotron X-ray micro computed tomography

Drying time, velocity, and temperature are important aspects of the drying process for pharmaceutical granules observed during tablet manufacturing. However, the drying mechanism of single granules is often limited to modelling and simulation, with the internal and physical changes difficult to quantify at an experimental level. In this study, in-situ synchrotron-based X-ray imaging techniques were used for the first time to investigate the dynamic drying of single pharmaceutical granules, quantifying internal changes occurring over the drying time. Two commonly used excipients (lactose monohydrate (LMH) and microcrystalline cellulose (MCC)) were used as pure components and binary mixtures with one of either two active pharmaceutical ingredients of differing hydrophilicity/hydrophobicity (acetaminophen (APAP) and carbamazepine (CBZ)). Water was used as a liquid binder to generate single granules of 25 % to 30 % moisture content. Results showed that for most samples, the drying time and composition significantly influences the pore volume evolution and the moisture ratio, with the velocity and temperature of the drying air possessing mixed significance on increasing the rate of pore connectivity and moisture removal depending on the sample composition. Effects of active ingredient loading resulted in minimal influence on the drying of CBZ and generated binary mixtures, with APAP and its respective mixtures’ drying behaviour dominated by the material’s hydrophilic nature.

Impact of melt pool geometry variability on lack-of-fusion porosity and fatigue life in powder bed fusion-laser beam Ti–6Al–4V

Powder bed fusion-laser beam (PBF-LB) parts experience a significant decline in fatigue performance when process-induced defects are present. In this work, a decline in 4-point bend fatigue life was observed in PBF-LB Ti–6Al–4V coupons fabricated at constant power with increasing scanning velocity and which underwent subsequent stress relief and surface machining. Specifically, the presence of pores that resemble lack-of-fusion (LoF) and a decline in fatigue life were observed at scanning velocities lower than that expected from prior published work. It was hypothesized that this unexpected presence of LoF pores resulted from melt pool geometry variability that was not considered in prior work when the LoF criterion was implemented. Further, these pores can be small in size and infrequent in their occurrence when the melt pool geometry variability is not severe. Such sparse pores are challenging to characterize using conventional 2D characterization methods. This work leverages tall and narrow coupon geometry and high-resolution X-ray micro computed tomography (X-μCT) to capture LoF porosity. The results show that a modified melt pool overlap-based LoF criterion considering melt pool geometry variability captures the unexpected occurrence of LoF pores observed in X-μCT. In addition, the LoF percent metric displays a strongly negative correlation with fatigue performance. The insights from this work provide guidance on characterizing melt pool geometry variability across scan lines to systematically evaluate processing parameters that generate LoF pores, which, in turn, could lower fatigue performance.

The Influence of Post-Treatment on Micropore Evolution and Mechanical Performance in AlSi10Mg Alloy Manufactured by Laser Powder Bed Fusion.

Gas-induced porosity is almost inevitable in additively manufactured aluminum alloys due to the evaporation of low-melting point elements (e.g., Al, Mg, and Zn) and the encapsulation of gases (e.g., hydrogen) during the multiple-phase reaction in the melt pool. These micropores are highly unstable during post-heat treatment at elevated temperatures and greatly affect mechanical properties and service reliability. In this study, the AlSi10Mg samples prepared by LPBF were subjected to solution heat treatment at 560 °C for 0.5 and 2 h, followed by artificial aging at 160 °C, 180 °C and 200 °C, respectively. The defect tolerance of gas porosity and associated damage mechanisms in the as-built and heat treated AlSi10Mg alloy were elucidated using optical, scanning electron microscopic analysis, X-ray micro computed tomography (XCT) and room temperature tensile testing. The results showed the defect tolerance of AlSi10Mg alloy prepared by LPBF was significantly reduced by the artificial aging treatment due to the precipitation of Mg-Si phases. Fracture analysis showed that the cooperation of fine precipitates and coarsened micropores assists nucleation and propagation of microcracks sites due to stress concentration upon tensile deformation and reduces the tensile elongation at break.

Comprehensive characterization and simulation of the point spread function of lobster eye X-ray micro pore optics

Lobster eye micro pore optics has been extensively researched, developed, and experimented with over the past few decades since its proposal by Angel in 1979. The lobster eye X-ray telescope represents the next generation of X-ray time-domain astronomy. This study presents a novel semi-analytical numerical model for simulating and studying the optical performance of micro pore X-ray optics based on geometric physical models, channel errors, and Fresnel reflectance. The numerical method accurately and rapidly models the X-ray point-spread function through millions of square microchannels. Soft X-ray testing validates the semi-analytical numerical model, which simulates common channel errors in lobster eye optics manufacturing. The X-ray results demonstrated that tilt and shear channel errors significantly impacted the point spread function, which is consistent with simulation outcomes and has a significant guiding value for the subsequent process improvement.

A MATLAB approach for developing digital rock models of heterogeneous limestones for reactive transport modeling

Porosity is a key parameter controlling the physico-chemical behavior of porous rocks. Digital rock physics offers a unique technique for imaging the inherently heterogeneous rock microstructure at fine spatial resolutions and its computational reconstruction, through which a better understanding and prediction of the rock behavior can be achieved. In this study, we propose a simple but accurate method to build a 3D porosity map of centimeter-scale carbonate rock cores from X-ray Micro Computed Tomography (XMCT) imaging data. The method consists of 3 main steps: i) decomposition of 3D volumetric XMCT data into sub-volumes, ii) processing of equidistributed 2D cross-section images in each sub-volume and iii) 2D slice-by-slice calculation of porosity and its assembly to reconstruct a 3D continuum porosity map over the whole core domain using a MATLAB code. The proposed approach significantly conserves the required memory to manipulate large image datasets. The digitized porosity representations are used to build 3D permeability maps of the cores by applying an explicit permeability-porosity relationship. The permeability maps are used as input for numerical simulation of the rock response to the percolation of reactive fluids through which the general validity of the approach is verified. The developed digital rock model paves the way for an improved understanding of reactive transport in carbonate rocks.

Development of coffee bean porosity and thermophysical properties during roasting

The development of coffee bean porosity during roasting was captured for a Kenyan Arabica coffee roasted under different constant inlet air temperature conditions in a pilot-scale spouted bed roaster. Coffee bean porosity was characterised using X-ray Micro Computed Tomography (Micro-CT). These data demonstrated a significant increase in coffee bean porosity of up to 60% during roasting. The coffee's intrinsic physical properties were also analysed to identify the relationship between porosity, thermophysical properties (density, thermal conductivity, specific heat capacity) and common process indicators (colour, mass, moisture, volume). Implications for heat transfer during roasting are also discussed. As Micro-CT, pycnometry and thermal properties analysers are not readily available tools, correlation of costly analytical methods with rapid discriminative tests are presented, allowing developers to utilise more accessible characterisation techniques to inform modulation of their processes and products. The data-driven approach to map coffee's physicochemical development during roasting provides comprehensive data that could be used to calibrate mechanistic or kinetic models. These physics-driven models could then be used as routine equations nested in heat and mass transfer simulations for developers to predict coffee's thermal evolution and subsequent physical transformation during roasting.

A nondestructive method using X-ray micro computed tomography for variation analysis of bamboo nodes’ vascular bundle among species

Bamboo node is a specialized structure that has great effect on both bamboo growth, physical-mechanical properties, and its utilization. Compact structure and particularly high hardness make bamboo node very difficult for slice specimens preparation. In this study, in order to explore the differences in anatomical characteristics of bamboo nodes' vascular bundles among species, 3D structures of bamboo nodes in four bamboo species (Bambusa emeiensis, Phyllostachys edulis, Pleioblastus amarus, and Bambusa rigida) were reconstructed by the micro-CT technique. The characteristics of vascular bundles were comparatively analyzed based on the CT images. The results showed that the vascular bundle morphology of Pleioblastus amarus and Bambusa rigida changed significantly from node to internode. The areas of fiber cells in the middle part along the radial direction of bamboo culm wall has the largest area (0.204 mm2), followed by the inner part (0.151 mm2) and the outer part (0.072 mm2). The area of transport tissue in the inner part along the radial direction of bamboo culm wall has the largest area (0.046 mm2), followed by the middle part (0.028 mm2) and the outer part (0.002 mm2). The bending vascular bundles in bamboo node can be divided into thick and thin types. The average thickness of the thin bending vascular bundles among the four bamboo species was 125 μm, with the thinnest value of 109 μm. While, the average thickness of thick bending vascular bundles was 265 μm, with the thickest value of 335 μm. The number proportion of thick vascular bundles was 60.8%, 42.5%, 32.9%, and 10.7% for Bambusa rigida, Bambusa emeiensis, Pleioblastus amarus, and Bambusa rigida. This study set up a nondestructive and efficient method for 3D anatomical structure characterization of bamboo node and the variation analysis in bamboo nodes’ vascular bundles.

Retrieving images from tarnished daguerreotypes using X-ray fluorescence imaging with an X-ray micro beam with tunable energy

We report recent observations using a synchrotron X-ray micro-beam to retrieve images from tarnished 19th century daguerreotypes. We confirm that high quality image can always be retrieved from tarnished plates using Hg Lα XRF as long as the bulk of the image particles and their distribution remains intact. We also report results from using tunable tender X-rays (2 - 7 keV) to conduct imaging in high vacuum at energy above the Ag L-edge and the Hg M-edge, extracting images using Ag Lα and Hg Mα, respectively among others (e.g., S to track corrosion). Images obtained with the surface sensitive total electron yield (TEY) and the bulk sensitive fluorescence yield (FLY) as well as corresponding micro-XANES are reported. Flux tolerance to high intensity X-beam is also explored. These results and their implications for cultural heritage research are discussed.

Nondestructive geochemical characterization of fossil hominin taphonomy and burial history

To date, only three Homo habilis specimens have been discovered that have associated craniodental and postcranial elements, providing a limited fossil record of the ontogeny and morphology of early members of the genus Homo. Recently, a nearly complete dentition, likely attributable to H. habilis, was discovered and excavated from early Pleistocene-age fluvial-lacustrine sediments of the upper Burgi Member of the Koobi Fora Formation at site F25787 in Area 13, near Ileret, Kenya. On the surface less than 15 m away, at site F25966, postcranial elements were found, which, if from the same individual as the nearby dentition, would represent the fourth associated craniodental and postcranial assemblage of this species. We developed a geochemical taphonomic history of these ca. 2 Ma hominin fossils using nondestructive X-ray based microanalytical tools (synchrotron and benchtop X-ray fluorescence chemical imaging and micro- and nano-computed tomography volumetric reconstruction), bulk analyses of sediments and paleosols at the excavation sites, and sedimentologic and stratigraphic observations. We integrate the chemical and physical taphonomic histories to test whether teeth (excavated in situ) and postcranial bones (eroded onto the outcrop surface) derive from a single individual. Minor differences in taphonomic history are attributable to the different biomineral properties of the dental and osseous components and to differences in physical damage during early post-mortem scavenging, dispersal, and burial in adjacent depositional settings. Microscale geochemical mapping enabled the temporal ordination of chemical and physical events in the specimens’ chemical taphonomic histories. Specifically, authigenic Fe- and K-bearing clays and Y, U, and Sr uptake occurred in post-burial fractures in bones and were also incorporated pervasively throughout dentin in teeth. Barite mineralization occurred along the latest fractures in both materials, and as a coating on tooth roots. The stratigraphic, taphonomic, and geochemical evidence supports the interpretation that the hominin fossils represent a single individual. Successful application of these nondestructive sample characterization methods demonstrates capabilities for thorough interrogation of the taphonomic histories of other potential hominin fossil associations, enabling more robust and accurate palaeontologic constraints using those relationships.

Unravelling the role of iron and manganese oxides in colouring Late Antique glass by micro-XANES and micro-XRF spectroscopies

This research aims to understand colouring technologies in 5th–7th centuries glass imported to Atlantic Britain by correlating the iron (Fe) and manganese (Mn) ratios and oxidation states with colour. Despite having a similar matrix chemical composition and concentrations of Fe and Mn oxides, these vessels display different colours (from green to yellow/amber, sometimes with purple streaks). Colour changes can be induced by controlling the reduction-oxidation reactions that occur during glass production, which are influenced by the raw materials, furnace and melt atmosphere, and recycling. To evaluate these parameters, reference glasses were prepared, following the composition of Late Antique archaeological glass recovered from Tintagel (UK) and Whithorn (UK). A corpus of archaeological and experimental glass samples was analysed using bulk Fe and Mn K-edge x-ray absorption near edge structure (XANES) spectroscopy, micro-XANES and micro x-ray fluorescence (μ-XRF) at beamline ID21, at the European Synchrotron Radiation Facility. Fe and Mn XANES spectra of the archaeological glass indicate that Fe and Mn are in a similar oxidation state in all the yellow samples, predominantly Fe3+ and Mn2+. No detectable difference in Mn and Fe oxidation state occurs in the purple streaks compared to the yellow glass bulk but μ-XRF maps of the distribution of Fe and Mn show that Mn is more concentrated in the purple streaks. This indicates that the purple colour of the streaks is mainly due to a higher Mn/Fe ratio and persistence of more oxidised manganese in the purple areas, even though it is difficult to detect. Many archaeological fragments appear pale green in transmitted light but amber in reflected light. XANES studies detected the presence of surface layers where manganese is more oxidised. This layer is believed to scatter transmitted and reflected light differently and might be responsible for the optical features of the archaeological glass.

Semi-Automated MicroCT Analysis of Bone Anatomy and Mineralization in Mouse Models.

The skeletal system mirrors several processes in the vertebrate body that impact developmental malfunctions, hormonal disbalance, malfunction of calcium metabolism and turn over, and inflammation processes such as arthrosis. X-ray micro computed tomography is a useful tool for 3D in situ evaluation of the skeletal system in a time-related manner, but results depend highly on resolution. Here, we provide the methodological background for a graduated evaluation from whole-body analysis of skeletal morphology and mineralization to high-resolution analysis of femoral and vertebral microstructure. We combine an expert-based evaluation with a machine-learning-based computational approach, including pre-setup analytical task lists. © 2024 Wiley Periodicals LLC. Basic Protocol 1: In vivo microCT scanning and skeletal analysis in mice Basic Protocol 2: Ex vivo high-resolution microCT scanning and microstructural analysis of the femur and L4 vertebra.

Automatic 3D cell segmentation of fruit parenchyma tissue from X-ray micro CT images using deep learning

BackgroundHigh quality 3D information of the microscopic plant tissue morphology—the spatial organization of cells and intercellular spaces in tissues—helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual pore sizes and shapes of tissues. However, individual cell morphology is difficult to retrieve from micro-CT as cells cannot be segmented properly due to negligible density differences at cell-to-cell interfaces. To address this, deep learning-based models were trained and tested to segment individual cells using X-ray micro-CT images of parenchyma tissue samples from apple and pear fruit with different cell and porosity characteristics.ResultsThe best segmentation model achieved an Aggregated Jaccard Index (AJI) of 0.86 and 0.73 for apple and pear tissue, respectively, which is an improvement over the current benchmark method that achieved AJIs of 0.73 and 0.67. Furthermore, the neural network was able to detect other plant tissue structures such as vascular bundles and stone cell clusters (brachysclereids), of which the latter were shown to strongly influence the spatial organization of pear cells. Based on the AJIs, apple tissue was found to be easier to segment, as the porosity and specific surface area of the pore space are higher and lower, respectively, compared to pear tissue. Moreover, samples with lower pore network connectivity, proved very difficult to segment.ConclusionsThe proposed method can be used to automatically quantify 3D cell morphology of plant tissue from micro-CT instead of opting for laborious manual annotations or less accurate segmentation approaches. In case fruit tissue porosity or pore network connectivity is too low or the specific surface area of the pore space too high, native X-ray micro-CT is unable to provide proper marker points of cell outlines, and one should rely on more elaborate contrast-enhancing scan protocols.