Synchrotron Microtomography Research Articles

Virtual dissection of Thoropa miliaris tadpole using phase-contrast synchrotron microtomography

In this work, in-line phase-contrast synchrotron microtomography was used in order to study the external and internal morphology of Thoropa miliaris tadpoles. Whole-specimens of T. miliaris in larval stages of development 28, 37 and 42, collected in the municipality of Mangaratiba (Rio de Janeiro, Brazil) were used for the study. The samples were scanned in microtomography beamline (IMX) at the Brazilian Synchrotron Light Laboratory (LNLS). The phase-contrast technique allowed us to obtain high quality images which made possible the structures segmentation on the rendered volume by the Avizo graphic image editing software. The combination of high quality images and segmentation process provides adequate visualization of different organs and soft (liver, notochord, brain, crystalline, cartilages) and hard (elements of the bone skeleton) tissues.

Wing bone geometry reveals active flight in Archaeopteryx

Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomotory context. Here, we compare new data from three Archaeopteryx specimens obtained through phase-contrast synchrotron microtomography to a representative sample of archosaurs employing a diverse array of locomotory strategies. Our analyses reveal that the architecture of Archaeopteryx’s wing bones consistently exhibits a combination of cross-sectional geometric properties uniquely shared with volant birds, particularly those occasionally utilising short-distance flapping. We therefore interpret that Archaeopteryx actively employed wing flapping to take to the air through a more anterodorsally posteroventrally oriented flight stroke than used by modern birds. This unexpected outcome implies that avian powered flight must have originated before the latest Jurassic.

Critical Evolution of Damage Toward System‐Size Failure in Crystalline Rock

AbstractRock failure under shear loading conditions controls earthquake and faulting phenomena. We study the dynamics of microscale damage precursory to shear faulting in a quartz‐monzonite rock representative of crystalline rocks of the continental crust. Using a triaxial rig that is transparent to X‐rays, we image the mechanical evolution of centimeter‐size core samples by in situ synchrotron microtomography with a resolution of 6.5 μm. Time‐lapse three‐dimensional images of the samples inside the rig provide a unique data set of microstructural evolution toward faulting. Above a yield point there is a gradual weakening during which microfractures nucleate and grow until this damage span the whole sample. This leads to shear faults oriented about 30° to the main compressive stress in agreement with Anderson's theory and macroscopic failure. The microfractures can be extracted from the three‐dimensional images, and their dynamics and morphology (i.e., number, volume, orientation, shape, and largest cluster) are quantified as a function of increasing stress toward failure. The experimental data show for the first time that the total volume of microfractures, the rate of damage growth, and the size of the largest microfracture all increase and diverge when approaching faulting. The average flatness of the microfractures (i.e., the ratio between the second and third eigenvalues of their covariance matrix) shows a significant decrease near failure. The precursors to faulting developing in the future faulting zone are controlled by the evolving microfracture population. Their divergent dynamics toward failure is reminiscent of a dynamical critical transition.

Advanced characterization unravels the structure and reactivity of wood-based chars

This study aims at understanding the structural changes occurring in the carbonaceous matrix of wood-based chars during their thermal conversion. Although chars are routinely characterized by porosity measurements or scanning electron microscopy, the composition and structure of the carbonaceous matrix is often not investigated. Here, advanced characterization using X-ray synchrotron microtomography, transmission electron microscopy, Raman spectroscopy and X-ray diffraction provided a precise description of the char properties, allowing for an accurate discussion of their catalytic properties. Two chars were produced by slow pyrolysis of wood waste (400 and 700 °C) and a third one was fabricated by activation under steam at 850 °C of the char obtained at 700 °C. The results show that the pyrolysis temperature and the activation performed did not affect the macrostructure of the chars and that the pores were interconnected at the macroscopic scale. However, at 700 °C, the micro- and nanostructures were modified: short-range organized graphene fringes were observed. The activated char showed a homogeneous microstructure similar to that of its precursor. Besides, the ratio of graphene-like structures, the local organization of graphene sheets, and the imperfections in graphene-like sheets were clearly improved by the post-treatment. To our knowledge, this is the first time that such an approach, combining various tools, is applied for the study of pyrolysis chars.

Synchrotron microtomography of a Nothosaurus marchicus skull informs on nothosaurian physiology and neurosensory adaptations in early Sauropterygia.

Nothosaurs form a subclade of the secondarily marine Sauropterygia that was well represented in late Early to early Late Triassic marine ecosystems. Here we present and discuss the internal skull anatomy of the small piscivorous nothosaur Nothosaurus marchicus from coastal to shallow marine Lower Muschelkalk deposits (Anisian) of Winterswijk, The Netherlands, which represents the oldest sauropterygian endocast visualized to date. The cranial endocast is only partially encapsulated by ossified braincase elements. Cranial flattening and lateral constriction by hypertrophied temporal musculature grant the brain a straight, tubular geometry that lacks particularly well-developed cerebral lobes but does potentially involve distinguishable optic lobes, suggesting vision may have represented an important sense during life. Despite large orbit size, the circuitous muscular pathway linking the basisphenoidal and orbital regions indicates poor oculomotor performance. This suggests a rather fixed ocular orientation, although eye placement and neck manoeuvrability could have enabled binocular if not stereoscopic vision. The proportionally large dorsal projection of the braincase endocast towards the well-developed pineal foramen advocates substantial dependence on the corresponding pineal system in vivo. Structures corroborating keen olfactory or acoustic senses were not identified. The likely atrophied vomeronasal organ argues against the presence of a forked tongue in Nothosaurus, and the relative positioning of external and internal nares contrasts respiratory configurations proposed for pistosauroid sauropterygians. The antorbital domain furthermore accommodates a putative rostral sensory plexus and pronounced lateral nasal glands that were likely exapted as salt glands. Previously proposed nothosaurian ‘foramina eustachii’ arose from architectural constraints on braincase development rather than representing functional foramina. Several modifications to brain shape and accessory organs were achieved through heterochronic development of the cranium, particularly the braincase. In summary, the cranium of Nothosaurus marchicus reflects important physiological and neurosensory adaptations that enabled the group’s explosive invasion of shallow marine habitats in the late Early Triassic.

In vitro effect of amorphous calcium phosphate paste applied for extended periods of time on enamel remineralization.

Dental applications based on the unique characteristics of amorphous calcium phosphate stabilized by casein phosphopeptides (CPP-ACP) have been proposed, as well as the improvement of its properties.Objectives:The objective of this study was to determine the ability of topically applied CPP-ACP from a commercial product to remineralize subsurface lesions when applied for extended periods of time (3 h and 8 h).Material and Methods:Artificially induced carious lesions were produced in 50 bovine enamel blocks previously selected by surface hardness. After treatments with gel without F and CPP-ACP applied for 1 minute (Placebo); 2% NaF neutral gel applied for 1 minute (Fluoride 1 min); CPP-ACP applied for 3 min (ACP 3 min); and CPP-ACP applied for 3 h (ACP 3 h) and for 8 h (ACP 8 h), the enamel blocks were submitted to the remineralization pH-cycling. Surface hardness and synchrotron micro-tomography were used to determine the percentage of surface hardness recovery (%SHR) and to calculate mineral concentration (gHAp.cm−3), respectively. The data were submitted to ANOVA followed by the Student-Newman-Keuls test (p<0.05).Results:Fluoride gel presented higher %SHR followed by ACP 3 min (p<0.001). No difference (p = 0.148) was found for Placebo, ACP 3 h and ACP 8 h groups for %SHR. Fluoride gel showed greater mineral concentration (p<0.001) when compared with the other groups. ACP 3 min demonstrated a significant difference (p<0.001) from ACP 3 h and ACP 8 h. The ACP 3 h and 8 h presented a subsurface lesion with development of laminations in all blocks.Conclusion:In this in vitro study the use of CPP-ACP for extended periods of time did not produce an additive effect in the remineralization process.

Synchrotron scanning reveals amphibious ecomorphology in a new clade of bird-like dinosaurs.

Maniraptora includes birds and their closest relatives among theropod dinosaurs. During the Cretaceous period, several maniraptoran lineages diverged from the ancestral coelurosaurian bauplan and evolved novel ecomorphologies, including active flight, gigantism, cursoriality and herbivory. Propagation X-ray phase-contrast synchrotron microtomography of a well-preserved maniraptoran from Mongolia, still partially embedded in the rock matrix, revealed a mosaic of features, most of them absent among non-avian maniraptorans but shared by reptilian and avian groups with aquatic or semiaquatic ecologies. This new theropod, Halszkaraptor escuilliei gen. et sp. nov., is related to other enigmatic Late Cretaceous maniraptorans from Mongolia in a novel clade at the root of Dromaeosauridae. This lineage adds an amphibious ecomorphology to those evolved by maniraptorans: it acquired a predatory mode that relied mainly on neck hyperelongation for food procurement, it coupled the obligatory bipedalism of theropods with forelimb proportions that may support a swimming function, and it developed postural adaptations convergent with short-tailed birds.

Quantification of synthesized hydration products using synchrotron microtomography and spectral analysis

The use of x-ray computed tomography (CT) as a standalone method has primarily been used to characterize pore structure, cracking and mechanical damage in cementitious systems due to low contrast in the hydrated phases. These limitations have resulted in the inability to extract quantifiable information on such phases. The goal of this research was to address the limitations caused by low contrast and improving the ability to distinguish the four primary hydrated phases in portland cement; C-S-H, calcium hydroxide, monosulfate, and ettringite. X-ray CT on individual layers, binary mixtures of phases, and quaternary mixtures of phases to represent a hydrated portland cement paste were imaged with synchrotron radiation. Known masses of each phase were converted to a volume and compared to the segmented image volumes. It was observed that adequate contrast in binary mixing of phases allowed for segmentation, and subsequent image analysis indicated quantifiable volumes could be extracted from the tomographic volume. However, low contrast was observed when C-S-H and monosulfate were paired together leading to difficulties segmenting in an unbiased manner. Quantification of phases in quaternary mixtures included larger errors than binary mixes due to histogram overlaps of monosulfate, C-S-H, and calcium hydroxide.

Characterization of microstructural and physical properties changes in biocemented sand using 3D X-ray microtomography

An experimental study has been performed to investigate the effect of the biocalcification process on the microstructural and the physical properties of biocemented Fontainebleau sand samples. The microstructural properties (porosity, volume fraction of calcite, total specific surface area, specific surface area of calcite, etc.) and the physical properties (permeability, effective diffusion) of the biocemented samples were computed for the first time from 3D images with a high-resolution images obtained by X-ray synchrotron microtomography. The evolution of all these properties with respect to the volume fraction of calcite is analysed and compared with success to experimental data, when it is possible. In general, our results point out that all the properties are strongly affected by the biocalcification process. Finally, all these numerical results from 3D images and experimental data were compared to numerical values or analytical estimates computed on idealized microstructures constituted of periodic overlapping and random non-overlapping arrangements of coated spheres. These comparisons show that these simple microstructures are sufficient to capture and to predict the main evolution of both microstructural and physical properties of biocemented sands for the whole range of volume fraction of calcite investigated.

Evolutionary origins of teeth in jawed vertebrates: conflicting data from acanthothoracid dental plates (‘Placodermi’)

AbstractPlacoderms (Devonian fossil fishes) are resolved phylogenetically to the base of jawed vertebrates and provide important evidence for evolutionary origins of teeth, particularly with respect to the Arthrodira. The arthrodires represent a derived group of placoderms; the dentition of other more primitive placoderms such as the acanthothoracids is less well known. Articulated acanthothoracid dental plates are rare; x‐ray computed tomography of a single, unique specimen, along with 3D segmentation of bone, oral denticles and vascular spaces, provides intrinsic developmental and topological information relevant to tooth origins. Recently, a disarticulated element was identified as a dental plate of the acanthothoracid Romundina stellina, with synchrotron microtomography providing characters to comment on ongoing debates regarding the evolution of teeth. We used segmental quantitative methods to re‐analyse this data, for comparison to the articulated and unquestionable acanthothoracid dental plates above. We demonstrate substantial differences between these, disputing the identity of the isolated plate of R. stellina as a dental plate, and thus its relevance to questions of tooth evolution.

Cracking in a hot deformed SiCP/A6061 composite investigated using synchrotron microtomography

We present the first investigation of cracking by hot compression of any metal matrix composite in zones deforming under tri-axial state of stress using synchrotron microtomography (SRμCT). The task required to reduce the unfavourable manifestations of phase contrast in the reconstructed slices is simplified by developing a Fourier domain based filter for processing of reconstructed slices. As a result for the first time an accurate characterisation of the state of 3-D damage developed by compression at 500°C and 1s−1 to strains of ~1 is achieved in the bulge region of a hot worked SiCP/A6061 composite. The composition of the damage is found to predominately consist of acicular shaped large to very large pores and “coalesced” micro-cracks. The quantification of the Fourier domain filtered dataset and the analysis of the spatial proximity of the different types of damage provided the mechanism of cracking in metal matrix composites near regions of tri-axial stress at high compressive strains. The propensity for cracking in bulge region of SiCP/A6061 composite is attributed to the development and growth of acicularly shaped pores facilitated by repeated particle fragmentation. It results in a damage architecture that promotes the coalescence of the closely spaced pores and micro-cracks. This mechanism rationalises the high efficiency of power dissipation observed in hot working of SiCP/A6061composite in the absence of microstructural restoration processes.

Differential synchrotron X-ray imaging markers based on the renal microvasculature for tubulointerstitial lesions and glomerulopathy

High resolution synchrotron microtomography capable of revealing microvessels in three dimensional (3D) establishes distinct imaging markers of mouse kidney disease strongly associated to renal tubulointerstitial (TI) lesions and glomerulopathy. Two complementary mouse models of chronic kidney disease (CKD), unilateral ureteral obstruction (UUO) and focal segmental glomerulosclerosis (FSGS), were used and five candidates of unique 3D imaging markers were identified. Our characterization to differentially reflect the altered microvasculature of renal TI lesions and/or glomerulopathy demonstrated these image features can be used to differentiate the disease status and the possible cause therefore qualified as image markers. These 3D imaging markers were further correlated with the histopathology and renal microvessel-based molecular study using antibodies against vascular endothelial cells (CD31), the connective tissue growth factor or the vascular endothelial growth factor. We also found that these 3D imaging markers individually characterize the development of renal TI lesions or glomerulopathy, quantitative and integrated use of all of them provide more information for differentiating the two renal conditions. Our findings thus establish a practical strategy to characterize the CKD-associated renal injuries by the microangiography-based 3D imaging and highlight the impact of dysfunctional microvasculature as a whole on the pathogenesis of the renal lesions.

Synchrotron phase-contrast microtomography of coprolites generates novel palaeobiological data

Coprolites (fossil faeces) reveal clues to ancient trophic relations, and contain inclusions representing organisms that are rarely preserved elsewhere. However, much information is lost by classical techniques of investigation, which cannot find and image the inclusions in an adequate manner. We demonstrate that propagation phase-contrast synchrotron microtomography (PPC-SRμCT) permits high-quality virtual 3D-reconstruction of coprolite inclusions, exemplified by two coprolites from the Upper Triassic locality Krasiejów, Poland; one of the coprolites contains delicate beetle remains, and the other one a partly articulated fish and fragments of bivalves.

Synchrotron Microtomography Investigation of the Filament Microstructure in Differently Processed Bi-2212 Wires

The Bi-2212 microstructure and porosity distribution in entire state-of-the-art multifilament wires was characterized by high-energy synchrotron X-ray absorption microtomography after meltprocessing at ambient pressure, at 100 bar overpressure, and at ambient pressure after prior cold isostatic pressing of initially identical as-drawn wires. Beyond the visualization of the Bi-2212 microstructure, the porosity distribution in the different filament bundles has been quantified. Spherical granulometry and finite percolation probability calculations have been performed in order to provide a measure for the porosity distribution and to compare filament connectivity in the axial wire direction. Possible artifacts of the microtomography (μ-CT) experiment and the possibility to estimate the effect of the Bi-2212 microstructure as seen in the μ-CT images on critical current density are discussed.

Dental development and age at death of the holotype of Anapithecus hernyaki (RUD 9) using synchrotron virtual histology

The chronology of dental development and life history of primitive catarrhines provides a crucial comparative framework for understanding the evolution of hominoids and Old World monkeys. Among the extinct groups of catarrhines are the pliopithecoids, with no known descendants. Anapithecus hernyaki is a medium-size stem catarrhine known from Austria, Hungary and Germany around 10 Ma, and represents a terminal lineage of a clade predating the divergence of hominoids and cercopithecoids, probably more than 30 Ma. In a previous study, Anapithecus was characterized as having fast dental development. Here, we used non-destructive propagation phase contrast synchrotron micro-tomography to image several dental microstructural features in the mixed mandibular dentition of RUD 9, the holotype of A. hernyaki. We estimate its age at death to be 1.9 years and describe the pattern, sequence and timing of tooth mineralization. Our results do not support any simplistic correlation between body mass and striae periodicity, since RUD 9 has a 3-day periodicity, which was previously thought unlikely based on body mass estimates in Anapithecus. We demonstrate that the teeth in RUD 9 grew even faster and initiated even earlier in development than suggested previously. Permanent first molars and the canine initiated 49 and 38 days prenatally, respectively. These results contribute to a better understanding of dental development in Anapithecus and may provide a window into the dental development of the last common ancestor of hominoids and cercopithecoids.

Development of structural colour in leaf beetles

Structural colours in living organisms have been observed and analysed in a large number of species, however the study of how the micro- and nano-scopic natural structures responsible of such colourations develop has been largely ignored. Understanding the interplay between chemical composition, structural morphology on multiple length scales, and mechanical constraints requires a range of investigation tools able to capture the different aspects of natural hierarchical architectures. Here, we report a developmental study of the most widespread strategy for structural colouration in nature: the cuticular multilayer. In particular, we focus on the exoskeletal growth of the dock leaf beetle Gastrophysa viridula, capturing all aspects of its formation: the macroscopic growth is tracked via synchrotron microtomography, while the submicron features are revealed by electron microscopy and light spectroscopy combined with numerical modelling. In particular, we observe that the two main factors driving the formation of the colour-producing multilayers are the polymerization of melanin during the ecdysis and the change in the layer spacing during the sclerotisation of the cuticle. Our understanding of the exoskeleton formation provides a unique insight into the different processes involved during metamorphosis.

Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus.

The numerous cushion-shaped tooth-bearing plates attributed to the stem group osteichthyan Lophosteus superbus, which are argued here to represent an early form of the osteichthyan inner dental arcade, display a previously unknown and presumably primitive mode of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional reconstruction from propagation phase-contrast synchrotron microtomography (PPC-SRµCT) reveals remnants of the first-generation teeth embedded in the basal plate, a feature never previously observed in any taxon. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth at the growing edge of the plate. The first generation of teeth is thus diachronous. Successor teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus, the replacement tooth buds cannot have been generated by a single permanent dental lamina at the lingual edge of the tooth cushion, but must have arisen either from successional dental laminae associated with the individual predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement.

Stochastic characterisation methodology for 3-D textiles based on micro-tomography

A recently developed framework to quantify variability of common textile reinforcements of unit cell size is extended to allow for a stochastic description of complex three-dimensional (3-D) textile architectures spanning multiple unit cells. The reinforcement geometry is characterised from synchrotron micro-tomography images in terms of centroid coordinates and tow cross-section. The statistical information includes an average trend, standard deviation and correlation information. A general representation of correlation information is proposed to account for the different tow correlations depending on the location inside the 3-D architecture.The methodology is applied to the characterisation of a 3-D carbon fabric considered for NASA’s Adaptive Deployable Entry Placement Technology (ADEPT) system. Determining geometrical variability in the weave is of importance during the process of setting design margins and risk analysis. Statistical analysis demonstrates strong dependency on the crossover positions for the average trends and correlation data, with a substantially higher variation for the Z-interconnecting tows.

Synchrotron microtomography to evaluate effects of different polychemotherapy drugs on cortical bone structure

Purpose: To determine the effects of different polychemotherapy drugs on cortical bone structure, the femur diaphysis of rats were treated with two different chemotherapy drugs, AC (doxorubicin + cyclophosphamide) and TC (docetaxel + cyclophosphamide), and evaluated by 3D morphological analysis using synchrotron radiation microtomography.Materials and methods: Wistar rats were classified into three groups. One group received doses of docetaxel and cyclophosphamide (G1) – TC regimen; a second group received doses of doxorubicin and cyclophosphamide (G2) – AC regimen; while a control group (G0) received no further treatment. 3D tomographic images of the rats’ femurs were obtained at the SYRMEP (Synchrotron Radiation for Medical Physics) beamline at the ELETTRA Synchrotron Laboratory in Trieste, Italy, using monochromatic X-rays with resolution of 9 μm.Results: It could be shown that the treatment caused significant differences in morphological parameters measured from the 3D images of femur diaphysis of rats, among the studied groups, complementing a previous study using stereological methods, biochemistry and electron microscopy.Conclusions: Our results indicate that the same process of osteoporosis caused by advancing age might occur in young women treated with docetaxel + cyclophosphamide (TC) and doxorubicin + cyclophosphamide (AC). 3D microtomography was shown to be an outstanding technique for bone analysis.

Phase-contrast synchrotron microtomography reveals the internal morphology of a new fossil species of the Corticaria-sylvicola-group (Coleoptera: Latridiidae).

Corticaria amberica sp. nov. (Coleoptera: Latridiidae) from Baltic amber is described and illustrated using the features of the male genitalia. To study these features, phase-contrast synchrotron microtomography was used for the first time with a member of this family. A literature-based checklist of fossil and subfossil Latridiidae is provided. The following new synonymy is established: Latridius alexeevi Bukejs, Kirejtshuk & Rücker, 2011 = Latridius usovae Sergi & Perkovsky, 2014 syn. nov. New fossil records for the species Latridius alexeevi Bukejs, Kirejtshuk & Rücker, Latridius jantaricus Borowiec, Revelieria groehni Sergi, Perkovsky & Reike, and Corticarina palaeominuta Reike are also presented.