microtomography
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The outcomes from the feasibility study on utilization of synchrotron radiation X-ray microtomography (SR-μCT) to investigate the texture and the quantitative mineralogical composition of selected calcium oxalate-based urinary calculi fragments are presented. The comparison of the results obtained by SR-μCT analysis with those derived from current standard analytical approaches is provided. SR-μCT is proved as a potential effective technique for determination of texture, 3D microstructure, and composition of kidney stones.
- MeSH
- krystalizace MeSH
- lidé středního věku MeSH
- lidé MeSH
- močové kameny chemie MeSH
- rentgenová mikrotomografie MeSH
- studie proveditelnosti MeSH
- synchrotrony MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Reptiles exhibit a large heterogeneity in teeth morphology. The main variability comprises the different tooth shape, the type of tooth attachment to the underlying bone, or the ability to replace the teeth. FINDINGS: Here, we provide full datasets of microtomography scans and 3D models of reptilian dentitions and skulls. We selected representative species for each of 9 reptilian families on the basis of their characteristic dental features. Because there are ≥4 different types of tooth-bone attachments, ranging from the mammalian-like thecodont attachment found in crocodilians to the simple acrodont implantation observed in some lizards, we aimed to evaluate species with different types of tooth-bone attachments. Moreover, another interesting feature varying in reptilian species is the complexity of tooth shape or the number of tooth generations, which can be associated with the type of tooth attachment to the jawbone. Therefore, selected model species also include animals with distinct tooth morphology along the jaw or different number of tooth generations. The development of tooth attachment and relationship of the tooth to the jaw can be further analysed in detail on a large collection of pre-hatching stages of chameleon. Next, we introduce different possibilities for how these datasets can be further used to study tooth-bone relationships or tooth morphology in 3D space. Moreover, these datasets can be valuable for additional morphological and morphometric analyses of reptilian skulls or their individually segmented skeletal elements. CONCLUSIONS: Our collection of microcomputed tomography scans can bring new insight into dental or skeletal research. The broad selection of reptilian species, together with their unique dental features and high quality of these scans including complete series of developmental stages of our model species and provide large opportunities for their reuse. Scans can be further used for virtual reality, 3D printing, or in education.
- MeSH
- dentice MeSH
- ještěři * anatomie a histologie MeSH
- lebka anatomie a histologie diagnostické zobrazování MeSH
- lidé MeSH
- rentgenová mikrotomografie MeSH
- savci MeSH
- zuby * anatomie a histologie diagnostické zobrazování MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
One of the greatest enigmas of modern biology is how the geometry of muscular and skeletal structures are created and how their development is controlled during growth and regeneration. Scaling and shaping of vertebrate muscles and skeletal elements has always been enigmatic and required an advanced technical level in order to analyse the cell distribution in 3D. In this work, synchrotron X-ray computed microtomography (µCT) and chemical contrasting has been exploited for a quantitative analysis of the 3D-cell distribution in tissues of a developing salamander (Pleurodeles waltl) limb - a key model organism for vertebrate regeneration studies. We mapped the limb muscles, their size and shape as well as the number and density of cells within the extracellular matrix of the developing cartilage. By using tomographic approach, we explored the polarity of the cells in 3D, in relation to the structure of developing joints. We found that the polarity of chondrocytes correlates with the planes in joint surfaces and also changes along the length of the cartilaginous elements. Our approach generates data for the precise computer simulations of muscle-skeletal regeneration using cell dynamics models, which is necessary for the understanding how anisotropic growth results in the precise shapes of skeletal structures.
PURPOSE: Quantitative description of hepatic microvascular bed could contribute to understanding perfusion CT imaging. Micro-CT is a useful method for the visualization and quantification of capillary-passable vascular corrosion casts. Our aim was to develop and validate open-source software for the statistical description of the vascular networks in micro-CT scans. METHODS: Porcine hepatic microvessels were injected with Biodur E20 resin, and the resulting corrosion casts were scanned with 1.9-4.7 [Formula: see text] resolution. The microvascular network was quantified using newly developed QuantAn software both in randomly selected volume probes (n = 10) and in arbitrarily outlined hepatic lobules (n = 4). The volumes, surfaces, lengths, and numbers of microvessel segments were estimated and validated in the same data sets with manual stereological counting. Calculations of tortuosity, radius histograms, length histograms, exports of the skeletonized vascular network into open formats, and an assessment of the degree of their anisotropy were performed. RESULTS: Within hepatic lobules, the microvessels had a volume fraction of 0.13 [Formula: see text] 0.05, surface density of 21.0 [Formula: see text] 2.0 [Formula: see text], length density of 169.0 [Formula: see text] 40.2 [Formula: see text], and numerical density of 588.5 [Formula: see text] 283.1 [Formula: see text]. Sensitivity analysis of the automatic analysis to binary opening, closing, threshold offset, and aggregation radius of branching nodes was performed. CONCLUSION: The software QuantAn and its source code are openly available to researchers working in the field of stochastic geometry of microvessels in micro-CT scans or other three-dimensional imaging methods. The implemented methods comply with reproducible stereological techniques, and they were highly consistent with manual counting. Preliminary morphometrics of the classical hepatic lobules in pig were provided.
- MeSH
- interpretace obrazu počítačem metody MeSH
- játra krevní zásobení diagnostické zobrazování MeSH
- koroze MeSH
- mikrocévy diagnostické zobrazování MeSH
- prasata MeSH
- rentgenová mikrotomografie metody MeSH
- software MeSH
- zobrazování trojrozměrné metody MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Quantification of the structure and composition of biomaterials using micro-CT requires image segmentation due to the low contrast and overlapping radioopacity of biological materials. The amount of bias introduced by segmentation procedures is generally unknown. We aim to develop software that generates three-dimensional models of fibrous and porous structures with known volumes, surfaces, lengths, and object counts in fibrous materials and to provide a software tool that calibrates quantitative micro-CT assessments. Virtual image stacks were generated using the newly developed software TeIGen, enabling the simulation of micro-CT scans of unconnected tubes, connected tubes, and porosities. A realistic noise generator was incorporated. Forty image stacks were evaluated using micro-CT, and the error between the true known and estimated data was quantified. Starting with geometric primitives, the error of the numerical estimation of surfaces and volumes was eliminated, thereby enabling the quantification of volumes and surfaces of colliding objects. Analysis of the sensitivity of the thresholding upon parameters of generated testing image sets revealed the effects of decreasing resolution and increasing noise on the accuracy of the micro-CT quantification. The size of the error increased with decreasing resolution when the voxel size exceeded 1/10 of the typical object size, which simulated the effect of the smallest details that could still be reliably quantified. Open-source software for calibrating quantitative micro-CT assessments by producing and saving virtually generated image data sets with known morphometric data was made freely available to researchers involved in morphometry of three-dimensional fibrillar and porous structures in micro-CT scans.
The complex shape of embryonic cartilage represents a true challenge for phenotyping and basic understanding of skeletal development. X-ray computed microtomography (μCT) enables inspecting relevant tissues in all three dimensions; however, most 3D models are still created by manual segmentation, which is a time-consuming and tedious task. In this work, we utilised a convolutional neural network (CNN) to automatically segment the most complex cartilaginous system represented by the developing nasal capsule. The main challenges of this task stem from the large size of the image data (over a thousand pixels in each dimension) and a relatively small training database, including genetically modified mouse embryos, where the phenotype of the analysed structures differs from the norm. We propose a CNN-based segmentation model optimised for the large image size that we trained using a unique manually annotated database. The segmentation model was able to segment the cartilaginous nasal capsule with a median accuracy of 84.44% (Dice coefficient). The time necessary for segmentation of new samples shortened from approximately 8 h needed for manual segmentation to mere 130 s per sample. This will greatly accelerate the throughput of μCT analysis of cartilaginous skeletal elements in animal models of developmental diseases.
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.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
- Publikační typ
- tisková chyba MeSH
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.
- MeSH
- biologická evoluce * MeSH
- dinosauři anatomie a histologie MeSH
- kosti a kostní tkáň anatomie a histologie diagnostické zobrazování MeSH
- křídla zvířecí anatomie a histologie MeSH
- let zvířat * MeSH
- ptáci * MeSH
- rentgenová mikrotomografie MeSH
- zkameněliny anatomie a histologie diagnostické zobrazování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
