X-ray Computed Tomography Scanning Research Articles

Dolomite cement microstratigraphy: A record of brine evolution and ore precipitation mechanisms, upper Knox Group, Tennessee and Kentucky, USA

AbstractTrace element changes in fluids associated with ore-forming events in sedimentary basins may be recorded by contemporaneous cements, especially zoned carbonate minerals (microstratigraphy). Cement analysis using advanced mapping and analytical techniques including scanning electron microscopy cathodoluminescence (SEM-CL), charge contrast imaging, high-resolution X-ray computed tomography (XCT), and laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) documents geochemical changes associated with Mississippi Valley–type mineralization in solution-collapse breccias of the Cambrian–Ordovician Knox Group (Tennessee and Kentucky, USA). Dolomite cement zonation coincident with changes in Fe and Mn can be observed with optical microscope CL in bands as narrow as 5 µm, whereas panchromatic SEM-CL reveals microfractures and cement subzones coincident with changes in La and Ce concentrations in bands as narrow as 0.1 µm. XCT scans image a high-density (Fe-rich) dolomite zone at the onset of late sulfide precipitation. The transition from pre-ore to ore-stage cementation is marked by increased Fe, Mn, Zn, Cd, Ga, Pb, and Sr and decreased La and Ce concentrations. Fine-scale metal depletion cycles during this transition may record metal precipitation from brine in response to the availability of reduced sulfur. Except for Fe and Mn, post-ore dolomite zones generally have low metal concentrations. Thus, dolomite microstratigraphy tracks systematic changes in brine metal concentrations modified by episodes of localized sulfide mineral precipitation.

Convergent evolution of spherical shells in Miocene planktonic foraminifera documents the parallel emergence of a complex character in response to environmental forcing

AbstractThe spherical encompassing final chamber of the planktonic foraminifera Orbulina universa is a prime example of a complex character whose evolution has been documented by a sequence of intermediate forms. However, the mechanism that induced evolution of the spherical chamber remain unclear. Here we show that shortly after the emergence of Orbulina, documented throughout the oceans, a convergent evolutionary transition occurred in the semi-isolated Paratethys, leading to the emergence of the endemic Velapertina, which occupied a similar niche to Orbulina in the surface waters. Using X-ray computed tomography scanning, we show that the evolution of the encompassing final chamber involved the same sequence of steps in both lineages, combining a progressively spherical shell shape with changes in the position, number, and sizes of apertures. The similarity in the sequence of character acquisitions suggests structural determinism in the way foraminiferal shells are constructed and the presence of natural selection favoring a spherical morphology. Collectively, the emergence of spherical chambers in the two lineages at a similar time suggests that the evolution of this spectacular complex character occurred in response to a singular environmental driver.

The Effect of Macroscopic Particle Features on Mineral Dissolution

Mineral dissolution is a dynamic process in which kinetics depend on the reactive surface area, orientation, and geometry of the dissolving mineral grain. Dissolution rate is, thus, not represented by a single value, but rather, by a spectrum that is affected by the reactivity of different types of surface features. Such dissolution rate spectra are usually obtained by very detailed studies of perfectly cleaved surfaces by atomic force microscopy or in situ studies, such as flow-through experiments. This study visualizes dissolution progress by repeated X-ray computed tomography scans of a single particle. This allows studying the influence of larger particle features, such as corners and edges, at the interception of macroscopic faces of particles, as well as the influence of those macroscopic features on the dissolution rate spectra. As a suitable case study, the dissolution of a monomineralic galena (PbS) particle in ethaline is studied. The observed changes in particle geometry are evaluated using a newly developed empirical model in order to break down the rate spectra as a function of the particle geometry. Results illustrate that dissolution rates are exponentially correlated with the distance to crystal corners and edges. The reactivity map generated from these exponential relations shows a linear trendline with the dissolution rates over the entire surface of the studied galena particle. The empirical reactivity map developed here opens the possibility of predicting the dissolution rate of particulate materials based on computed tomography and the optimal geometrical properties of the particles that maximize the dissolution, e.g., size and shape.

WHAT IMAGING IS REQUIRED TO PLAN TKA? A COMPARISON BETWEEN EOS AND CT SCAN TO ASSESS CORONAL ALIGNMENT

The emergence of patient specific instrumentation has seen an expansion from simple radiographs to plan total knee arthroplasty (TKA) with modern systems using computed tomography (CT) or magnetic resonance imaging scans. Concerns have emerged regarding accuracy of these non-weight bearing modalities to assess true mechanical axis. The aim of our study was to compare coronal alignment on full length standing AP imaging generated by the EOS acquisition system with the CT coronal scout image.Eligible patients underwent unilateral or bilateral primary TKA for osteoarthritis under the care of investigating surgeon between 2017 and 2022, with both EOS X-Ray Imaging Acquisition System and CT scans performed preoperatively. Coronal mechanical alignment was measured on the supine coronal scout CT scan and the standing HKA EOS.Pre-operative lower limb coronal alignment was assessed on 96 knees prior to TKA on the supine coronal scout CT scan and the standing HKA EOS. There were 56 males (56%), and 44 right knees (44%). The mean age was 68 years (range 53-90). The mean coronal alignment was 4.7 degrees (SD 5.3) on CT scan and 4.6 degrees (SD 6.2) on EOS (p=0.70). There was a strong positive correlation of coronal alignment on CT scan and EOS (pearson0.927, p=0.001). The mean difference between EOS and CT scan was 0.9 degrees (SD 2.4). Less than 3 degrees variation between measures was observed in 87% of knees. On linear regression for every 1° varus increase in CT HKA alignment, the EOS HKA alignment increased by 0.93° in varus orientation. The model explained 86% of the variability.CT demonstrates excellent reliability for assessing coronal lower limb alignment compared to EOS in osteoarthritic knees. This supports the routine use of CT to plan TKA without further weight bearing imaging in routine cases.

Modeling knot features using branch scars from Mongolian oak (Quercus mongolica).

Wood quality is an important indicator for modern sawmills. Internal wood characteristics can be derived from their correlations with external appearances. In this study, we developed linear regression models to predict knot size from surface features of Mongolian oak (Quercus mongolica) using data collected from 53 trees. For this, manual measurements and X-ray computed tomography scanning technology was respectively used to obtain internal and external features of 1,297 knots. Our results showed that Mongolian oak knots were generally concentrated in the middle part of oak stems, with fewer knots observed at the top and base. The parameters of knot and scar showed significant correlations (P<0.01), where length and diameter of the corresponding external scar increase with increasing the length and diameter of a knot. The corresponding external scar can be used as an effective indicator to predict the internal value of oak logs. The accuracy of our constructed model is more than 95% when assessed against independent test samples. These models thus can be applied to improve the practical production of oak timber and reduce commercial loss caused by knots. These additional data can improve the estimation of the influence of knots on wood quality and provide a theoretical foundation for investigating the characteristics of hardwood knots.

IntelliScan: Improving the quality of x-ray computed tomography surface data through intelligent selection of projection angles.

X-ray computed tomography (XCT) enables the dimensional measurement and inspection of highly geometrically complex engineering components that are unmeasurable using optical and tactile instruments. Conventional XCT scans use a circular scan trajectory where X-ray projections are acquired with a uniform angular spacing; this approach treats all projections as being of equal importance, in practice, some projections contain more object information than others. In this work we capitalize on this concept by intelligently selecting projections with a view to improve the quality of surface models extracted from an XCT data-set. Our approach relies on using a priori object information to select X-ray projections in which the surfaces of the object are aligned with a ray-path, thus ensuring the surface of the object is fully sampled. Results are presented showing that the proposed method is able to reduce CAD comparison errors by 16%, reduce surface form error by 3%, and improve edge contrast by 14% for a machined aluminium component.

Simulation-based investigation of the metrological interface structural resolution capability of X-ray computed tomography scanners

Abstract. The miniaturisation of components leads to new demands on measurement systems. One of these is the resolution. As a volumetric analysis method and method of non-destructive testing, industrial X-ray computed tomography (XCT) has the ability to measure geometrical features and their corresponding dimensions without destroying them and can therefore be used for quality assurance. However, the concept of resolution is not trivial for XCT and has not yet been finally clarified. In particular, the interface structural resolution, the detectability of two surfaces facing each other after surface segmentation, faces a lack of a test specimen, a corresponding measurand and a reliable method. Simulation-based XCT investigations of a method to determine this type of resolution are presented in this article using the geometry of a test specimen that contains several radially arranged holes of the same size. The borehole diameters correspond to the distance between the holes to investigate the resolvability of surfaces and interfaces. The evaluation is based on mean and extreme values of grey value profiles between the individual boreholes of the reconstructed volume. It is shown that the geometrical detectability of the test specimen surface and interface can be extended by a reasonable choice of the threshold value for surface segmentation within a defined interval. With regard to the resolving capability, a distinction is made between assured detectability and possible detectability, as well as the threshold value used when using the ISO50 threshold for surface segmentation and measurement chain completion.

Seismically-induced down-sagging structures in tephra layers (tephra-seismites) preserved in lakes since 17.5 cal ka, Hamilton lowlands, New Zealand

We analysed numerous soft-sediment deformation structures (SSDSs) identified in seven unconsolidated, up to 8-cm thick, siliceous tephra layers that had been deposited in ~35 riverine-phytogenic lakes within the Hamilton lowlands, northern North Island, New Zealand, since 17.5 calendar (cal) ka BP. Based on sediment/tephra descriptions and X-ray computed tomography scanning of cores taken from ten lakes, we classified these SSDSs into elongated load structures (i.e., down-sagging structures) of different dimensions, ranging from millimetre- to decimetre-scale, and centimetre-long dykes. Down-sagging structures were commonly manifested as intrusions of internal tephra beds of very fine to medium sand into underlying organic lake sediments. The tephra layers commonly exhibited an upper silt bed, which was not directly affected by deformation. Dry bulk density and grain size distribution analyses of both the organic lake sediment and the internal tephra beds provided evidence for the deformation mechanism of down-sagging structures and their driving force: the organic lake sediment and the upper silt bed are less liquefiable, whereas the very fine to medium sand internal tephra beds are liquefiable. The tephra layers and encapsulating organic lake sediments formed three-layer (a–b–a) density systems, where ‘a’ denotes the sediment unit of lower density. We infer that downward-directed deformation was favoured by the a–b–a density system with the upper, less-liquefiable, silt bed within the tephra layer preventing upward intrusion during the liquefaction process. The spatial distribution and ages of SSDSs within the lakes provided some evidence that liquefaction of the older tephra layers, i.e., Rerewhakaaitu, Rotorua, and Waiohau tephras, deposited 17.5, 15.6, and 14 cal ka BP, respectively, was triggered by a seismic source to the northeast of the Hamilton lowlands (i.e., Kerepehi and/or Te Puninga faults). In contrast, the liquefaction of the younger tephra layers, i.e., Opepe, Mamaku, and Tuhua tephras, deposited 10.0, 8.0, and 7.6 cal ka BP, respectively, may have been triggered by movement on local faults within the Hamilton lowlands, namely the Hamilton Basin faults, or by distant faulting at the Hikurangi subduction margin east of North Island.

Thermomechanical response of thermoplastic polyurethane used in MEX additive manufacturing over repetitive mechanical recycling courses

Sustainability is critical nowadays, with a growing interest in polymers, due to their increasing usage in products. Mechanical recycling of polymers involves grinding/shredding and thermal extrusion of the material. This is a thermomechanical process, which negatively affects the bulk mechanical performance of the polymer and may potentially introduce contamination. This work investigates the response of Thermoplastic Polyurethane (TPU) in material extrusion (MEX) 3D printing, after multiple recycling courses. Each course comprises two thermal cycles, one in the extruder for filament fabrication and a second one in the 3D printer's nozzle, for the manufacturing of the parts, following corresponding standards. The response of the material after up to six repetitions of the process was studied in this work. In each repetition, the effect of the process on the mechanical (tensile, flexural, impact, microhardness, Dynamic Mechanical Analysis), thermal (Thermogravimetric Analysis), morphological (Scanning Electron Microscopy), and structural (Micro X-Ray Computed Tomography Scanning & Analysis) behavior of the material was studied. The results of the study show a reasonable potential for the sustainability of the TPU material, exploiting 3D printing advantages. The highest tensile strength is reported in the sixth repetition of the thermal reprocessing of the material, indicating that TPU mechanical recycling is a viable option.

Orientation-dependent fatigue assessment of Ti6Al4V manufactured by L-PBF: Size of surface features and shielding effect

The fatigue behaviour of as-built parts produced by means of Laser-Powder Bed Fusion process (L-PBF) is primarily influenced by the presence of stress raisers on the surface, whose morphology strongly depends on the relative orientation between the surface and the build direction. This study aims to shed light into the factors representing the surface morphology that correlate with the fatigue performance of L-PBF Ti6Al4V specimens manufactured in four different orientations. A Fracture Mechanics-based model based on measurable roughness parameters was employed for the prediction of the fatigue properties in both the finite life and endurance limit regions. The fatigue model considers an initial equivalent defect corresponding to the roughness parameter Rv,max. In addition, it includes a geometric factor F¯ accounting for the shielding present at the roots of the micro-notches which was calculated starting from profile roughness parameters determined by X-ray Computer Tomography (XCT) scans. The predicted stress–life curves show that the adoption of the maximum profile depth Rv,max and the shielding factor F¯ yields precise life predictions considering the effect of the surface orientation.

Ocular lens morphology is influenced by ecology and metamorphosis in frogs and toads.

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia: Anura) are ecologically diverse, with many species shifting from aquatic to terrestrial ecologies during metamorphosis. We quantified lens shape and relative size using 179 micro X-ray computed tomography scans of 126 biphasic anuran species and tested for correlations with life stage, environmental transitions, adult habits and adult activity patterns. Across broad phylogenetic diversity, tadpole lenses are more spherical than those of adults. Biphasic species with aquatic larvae and terrestrial adults typically undergo ontogenetic changes in lens shape, whereas species that remain aquatic as adults tend to retain more spherical lenses after metamorphosis. Further, adult lens shape is influenced by adult habit; notably, fossorial adults tend to retain spherical lenses following metamorphosis. Finally, lens size relative to eye size is smaller in aquatic and semiaquatic species than other adult ecologies. Our study demonstrates how ecology shapes visual systems, and the power of non-invasive imaging of museum specimens for studying sensory evolution.

Effect of chemical post-processing on surfaces and sub-surface defects in electron beam melted Ti-6Al-4V

Surfaces after chemical post-processing treatments of electron beam melting (EBM) produced Ti-6Al-4V have been studied. Targeted chemical treatment allowed the study of variation in surface quality with material removal depth. Characterization of surface and defect morphologies were made, comparing two chemical post-processing methods, Hirtisation® and chemical milling with different milling depths. Surface topography was characterized using white light interferometry and subsurface defect distribution was studied using X-ray computed tomography (XCT). The morphology of the surface at different milling depths was compared to the sub-surface information from XCT scans of the as-built material. Furthermore, Hot Isostatic Pressing (HIP) treated material was documented for comparison. Results show that post-processed surfaces contain a number of different defects of mixed morphology, position and origin. Post-processing deteriorates the surface quality with increased removal depth due to the presence of sub-surface defects. The position of sub-surface defects in relation to the material surface coincides with the depth at which contour-hatch interactions are likely to have occurred during the EBM building process. The distribution of this sub-surface defect population is anisotropic in the building (horizontal) plane and reasons for this are explored. Hirtisation® produces surfaces morphologically different from chemically milled surfaces. This difference was found to contribute to Hirtisation® producing surfaces with higher roughness (Sa) than chemically milled surfaces at comparable removal depth. HIP did remove all detectable sub-surface defects but microstructural artefacts indicating healed porosity were found.

Fatigue damage evolution in asphalt mixture based on X-ray CT images

The fatigue damage of asphalt pavement occurs and develops under repeated vehicle loads, and its macro manifestation is the deterioration of mechanical properties and serviceability. In order to explore the internal cause of fatigue damage of asphalt mixtures, this paper proposed a method to obtain the internal section images of asphalt mixtures in different fatigue damage stages based on the X-ray CT (Computed Tomography) scanning technique and indirect tensile fatigue test. The fatigue damage evolutions in two different gradation types of AC and OGFC asphalt mixture were studied. The results show that the difference in gradation type causes different initial air void shapes, size and distribution, which result in different formation modes of the main cracks and fatigue damage resistance of asphalt mixture. The evolution of air voids during fatigue loading can be divided into three stages: compression, steady growth and rapid expansion. The macro fatigue damage presents an excellent linear relation (R-values > 0.98) with the internal structural damage.

Effects of coarse aggregate morphology on concrete mechanical properties

The morphology of coarse aggregate can significantly affect the mechanical performance of concrete. In this study, the correlation between the compressive properties of concrete and the coarse aggregate morphology was systematically explored. Three kinds of aggregates with significant morphology differences were selected: Spherical Aggregates, Flaky Aggregates, and Elongated Aggregates. Three-dimensional morphological information was obtained by 3D Structured-Light Scanner, and quantitative statistical analyses were conducted to assess the distribution of morphological characteristics for these three-types aggregates. It is found that the three-type aggregates with the same mesh size can be properly discriminated through the axis length, flatness, elongation, the product of flatness and elongation, and sphericality. The simplex-centroid design was used to build the correlation between aggregate morphology and the compressive strengths of concrete with different water-cement ratios. The concrete with 100% spherical aggregates owns the highest compressive strength, which is higher than that of concrete mixed with other two aggregates by 9.4%–36.2% and 5.2%–28.8% at the curing of 3-day and 28-day, respectively. When the ratio of spherical aggregates reaches above 50%, the strength loss caused by the elongated aggregates and flaky aggregates content is not obvious. Further, the failure mechanism of concrete with 100% spherical aggregates, 100% flaky aggregates, and 100% elongated aggregates under cyclic loadings were investigated by X-ray computed tomography scanning. It is found that the cracks inside spherical aggregates concrete mainly initiate from the edges and the core section remains almost intact before the destruction by a major oblique crack. Meanwhile, the high residual strain after cyclic loadings can originate from the generated vertical cracks under compression. The research findings in this study can serve as a solid base for the designing of concrete structures.

Multiscale Progressive Failure Analysis of 3D Woven Composites.

Application of three-dimensional (3D) woven composites is growing as an alternative to the use of ply-based composite materials. However, the design, analysis, modeling, and optimization of these materials is more challenging due to their complex and inherently multiscale geometries. Herein, a multiscale modeling procedure, based on efficient, semi-analytical micromechanical theories rather than the traditional finite element approach, is presented and applied to a 3D woven carbon–epoxy composite. A crack-band progressive damage model was employed for the matrix constituent to capture the globally observed nonlinear response. Realistic microstructural dimensions and tow-fiber volume fractions were determined from detailed X-ray computed tomography (CT) and scanning electron microscopy data. Pre-existing binder-tow disbonds and weft-tow waviness, observed in X-ray CT scans of the composite, were also included in the model. The results were compared with experimental data for the in-plane tensile and shear behavior of the composite. The tensile predictions exhibited good correlations with the test data. While the model was able to capture the less brittle nature of the in-plane shear response, quantitative measures were underpredicted to some degree.

A Multiphysics Understanding of Internal Short Circuit Mechanisms in Lithium-Ion Batteries upon Mechanical Stress Abuse

Lithium-ion batteries (LIBs) have played an increasingly dominant role in the current mobile society. Due to the risky safety testing procedure, ultra-rigorous demands of the testing facility, and complicated multiphysics nature of the safety issues, lack of high-fidelity models to describe the safety behaviors of lithium-ion batteries upon abusive loading has significantly deferred the further application of LIBs. Herein, firstly, mechanical behaviors of the battery component materials are characterized by both in-situ and post-mortem experiments. Then, we reveal the formation process of various internal short circuit (ISC) modes inside batteries upon different abusive loadings with the aid of ex-situ observation using the X-ray Computed Tomography scanning technique and post-mortem characterization of the battery samples. To quantify the stress-driven ISC mode and failure behavior of the component material, numerical models for all component materials are established and applied in a cell model which can reveal the deformation-material failure-material contact-different ISC mode formation process. To further quantify the relationship between electrothermal response and mechanical response of battery, we develop a 2D detailed model with fully coupling of electrochemo-thermal-mechanics governing laws consisting of a 2D mechanical model, 2D ISC model, 2D heat model and Thermal Runaway model. The multiphysics model demonstrates a promising generalization in various SOC and loading situations. Results highlight the power of computational modeling to understand the underlying mechanism of safety issues in energy storage systems in a broader context.

Experimental and numerical study on the mechanical properties of compressively precracked sandstone repaired by grouting

• A set of laboratory grouting devices was developed to grout the precracked rock specimen. • The strength of grouted rock is observed to be determined by the interface between rock and cement. • A numerical simulation method of grouting was developed based on the Fish language of PFC 2D . Grouting is a common reinforcement method that is widely used in various geotechnical engineering applications. Studying the mechanical properties of grouted rock masses under different stress conditions is of great significance to geotechnical engineering, so a set of laboratory grouting devices was developed for this study. The mechanical properties of compressively precracked sandstone before and after grouting were studied by triaxial compression tests with different confining pressures, and the crack and cementation morphologies of precracked specimens were revealed by X-ray CT (Computed Tomography) scanning. According to the findings of the study, grouting significantly improves the integrity and mechanical properties of cracked specimens. The grouted specimens exhibit higher strengths and Mohr–Coulomb parameters ( c and φ), and these increments vary with confining pressures. The strength of grouted specimens depends mainly on the micromechanical properties of the contact surface between sandstone and cement grout. Affected by the mechanical properties of cement grout, the elastic modulus of the grouted specimens is lower than that of uncracked sandstone, and the deformation of the grouted specimen also exhibits an obvious ideal plasticity state under triaxial stress conditions. Thus, the grouted sandstone does not break suddenly. In addition, a numerical method of grouting was also developed in the PFC 2D program to investigate the micro mechanisms of fracturing and grouting sandstone. The numerical simulations represent the strength and progressive failure process of both intact and grouted specimens very well and reveal the micromechanical behaviors of the grouted rock mass.

Evidence for an evo-devo-derived hypothesis on three-dimensional flower shape modularity in a tropical orchid clade.

Covarying suites of phenotypic traits, or modules, are increasingly recognized to promote morphological evolution. However, information on how modularity influences flower diversity is rare and lacking for Orchidaceae. Here, we combine high-resolution X-ray computed tomography scanning with three-dimensional geometric morphometrics and phylogenetic comparative methods to test various hypotheses about three-dimensional patterns of flower evolutionary modularity in Malagasy Bulbophyllum orchids and examine rates and modes of module evolution. Based on the four evolutionary modules identified (i.e., sepals, lateral petals, labellum + column-foot, and column-part), our data support the hypothesis that both genetic-developmental and functional adaptive factors shaped evolutionary flower trait covariation in these tropical orchids. In line with "evo-devo" studies, we also find that the labellum evolved independently from the rest of the petal whorl. Finally, we show that modules evolved with different rates, and either in a neutral fashion (only column-part) or under selective constraints, as likely imposed by pollinators. Overall, this study supports current views that modular units can enhance the range and rate of morphological evolution.

Quantifying lung aeration in neonatal lambs at birth using lung ultrasound.

BackgroundLung ultrasound (LUS) is a safe and non-invasive tool that can potentially assess regional lung aeration in newborn infants and reduce the need for X-ray imaging. LUS produces images with characteristic artifacts caused by the presence of air in the lung, but it is unknown if LUS can accurately detect changes in lung air volumes after birth. This study compared LUS images with lung volume measurements from high-resolution computed tomography (CT) scans to determine if LUS can accurately provide relative measures of lung aeration.MethodsDeceased near-term newborn lambs (139 days gestation, term ∼148 days) were intubated and the chest imaged using LUS (bilaterally) and phase contrast x-ray CT scans at increasing static airway pressures (0–50 cmH2O). CT scans were analyzed to calculate regional air volumes and correlated with measures from LUS images. These measures included (i) LUS grade; (ii) brightness (mean and coefficient of variation); and (iii) area under the Fourier power spectra within defined frequency ranges.ResultsAll LUS image analysis techniques correlated strongly with air volumes measured by CT (p < 0.01). When imaging statistics were combined in a multivariate linear regression model, LUS predicted the proportion of air in the underlying lung with moderate accuracy (95% prediction interval ± 22.15%, r2 = 0.71).ConclusionLUS can provide relative measures of lung aeration after birth in neonatal lambs. Future studies are needed to determine if LUS can also provide a simple means to assess air volumes and individualize aeration strategies for critically ill newborns in real time.

4DRoot: Root phenotyping software for temporal 3D scans by X-ray computed tomography.

Currently, plant phenomics is considered the key to reducing the genotype-to-phenotype knowledge gap in plant breeding. In this context, breakthrough imaging technologies have demonstrated high accuracy and reliability. The X-ray computed tomography (CT) technology can noninvasively scan roots in 3D; however, it is urgently required to implement high-throughput phenotyping procedures and analyses to increase the amount of data to measure more complex root phenotypic traits. We have developed a spatial-temporal root architectural modeling software tool based on 4D data from temporal X-ray CT scans. Through a cylinder fitting, we automatically extract significant root architectural traits, distribution, and hierarchy. The open-source software tool is named 4DRoot and implemented in MATLAB. The source code is freely available at https://github.com/TIDOP-USAL/4DRoot. In this research, 3D root scans from the black walnut tree were analyzed, a punctual scan for the spatial study and a weekly time-slot series for the temporal one. 4DRoot provides breeders and root biologists an objective and useful tool to quantify carbon sequestration throw trait extraction. In addition, 4DRoot could help plant breeders to improve plants to meet the food, fuel, and fiber demands in the future, in order to increase crop yield while reducing farming inputs.