X-ray microtomography in herpetological research: a review

Broeckhoven, Chris; Plessis, Anton du

doi:10.1163/15685381-20181102

Cited by 26 publications

(17 citation statements)

References 111 publications

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“…Although some digital morphology studies have included hundreds of 18 , 19 or over a thousand 20 – 23 3D models, their images are often aggregated using different sources (museums, repositories, laboratories), methods (surface scanning, μCT), and parameters (X-ray energy, voxel size, number of projections), making it difficult to integrate and compare findings. For smaller specimens in particular, variation in spatial resolution can result in significant measurement errors, for example in estimated volumes or relationships between traits 24 , 25 . Limitations on time and money for μCT scanning also mean that specimen data are often collected haphazardly, constraining systematic analyses to one or few individuals per species 6 .…”

Section: Introductionmentioning

confidence: 99%

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

Hipsley

Aguilar

Black

et al. 2020

Sci Rep

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High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections. High-resolution X-ray microcomputed tomography, also known as HRXMT or microCT (μCT), is an increasingly powerful tool for the non-destructive investigation of whole objects. Functioning like a microscope with X-ray vision, μCT generates high fidelity 3D models of solid material from which the outer layers can be virtually dissected or removed, revealing the inner structures. Starting with radiographs of an object taken over multiple angles, a computer algorithm is used to digitally reconstruct a stack of 2D X-ray projections, or tomograms, into a 3D volume. Whereas in human medicine the X-ray source rotates around the patient (e.g., computerized axial tomography, or CAT scan), in μCT the object is typically fixed on a rotating stage while the X-ray tube remains stationary. The differential properties of the object's matter, including thickness and atomic number, interact with the X-ray's energy beam to determine the number of photons that pass through it to reach the detector on the other side. This decrease in electromagnetic radiation, termed X-ray attenuation, results in detector pixels with grayscale values proportional to the radiopacity of the material, meaning that dense regions such as bone or rock appear white or light gray (radiopaque), while muscle or skin appears dark (radiolucent). The improved resolution of μCT over standard imaging techniques can achieve a detail detectability down to 200 nm (0.2 µm)-less than the diameter of a single red blood cell. Since publication of the first X-ray microtomographic figures nearly four decades ago 1-3 , μCT has had profound impacts across scientific disciplines. Studies in biomedicine, zoology, geology and paleontology now regularly incorp...

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Section: Introductionmentioning

confidence: 99%

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

Hipsley

Aguilar

Black

et al. 2020

Sci Rep

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“…As a result, the distribution of inclusions, fractures, internal defects, and impurities, as well as surface features of gems can be easily distinguished (Figure 1). Despite the high cost of µCT hardware, it is a technology used in a wide variety of applications such as geosciences [23][24][25], materials science [26], civil engineering materials [27], biological applications [28], herpetology [29], biomimicry [30] and additive manufacturing [31]. This broad application ability has resulted in increased availability in the form of service laboratories all over the world.…”

Section: X-ray Micro Computed Tomography (µCt)mentioning

confidence: 99%

Characterization of Coloured Gemstones by X-ray Micro Computed Tomography

et al. 2021

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The monetary value of gemstones is based on five variables: rarity, cut, weight, color and clarity. The latter refers to internal impurities and defects. Fashion may also dictate demand and price. To enhance some of these features and value, gemstones are treated. Disclosure or nondisclosure thereof has been controversial and affected consumer confidence. Most of these treatments are difficult to detect with the naked eye and accurately quantify with traditional optical and analytical methods. X-ray micro computed tomography (micro-CT or μCT) is proposed as a relatively low cost, physically non-destructive and complementary method to detect and quantify clarity enhancement and also to provide a unique 3D fingerprint of each gemstone. A collection of 14 cut colored gemstones was selected. Micro-CT scans allowed fracture detection, their distribution and calculation of filler volume as well as 3D mapping of inclusions, surface and internal imperfections and artificially induced modifications. As a result the method allows the construction of a digital twin. X-ray exposure could however induce unwanted color changes. This effect was minimized or eliminated by optimizing dosage and exposure time.

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“…Recent studies have focused on adult morphology and on descriptive aspects of biology of several species of living fishes 5 – 7 , salamanders 8 – 10 , caecilians 11 – 14 , frogs and toads 15 – 19 , lizards 20 – 22 , snakes 23 – 25 , amphisbaenians 26 – 28 , turtles 29 – 31 , crocodiles 32 – 34 , birds 35 – 37 , and mammals 38 – 40 , besides fossils of several vertebrate groups 41 , 42 . On herpetological research, studies that encompass developmental series, together with other purely anatomical studies, represents the most of works reported this way, mainly for anurans and squamates species 43 . However, in developmental studies, is still hard to obtaining complete (or almost) developmental series and/or to discriminate soft tissues (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, if changes of a particular element were to be followed, and one wants, for instance, to follow the amount of bone deposition and ossification, and elaborate area reconstructions have been devised to account for that 52 . One of the advantages of microtomography reconstruction, and software developed for it (as for example, the software used herein; see below), is that volume and other sort of measurements can be performed 43 to selected tissues and organs.…”

Section: Introductionmentioning

confidence: 99%

Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles

Fidalgo

Paiva

Mendes

et al. 2020

Sci Rep

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Amphibians are models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change due to their sensitivity and vulnerability to changes in the environment. Developmental series of amphibians are informative about their biology, and X-ray based 3D reconstruction holds promise for quantifying morphological changes during growth—some with a direct impact on the possibility of an experimental investigation on several of the ecological topics listed above. However, 3D resolution and discrimination of their soft tissues have been difficult with traditional X-ray computed tomography, without time-consuming contrast staining. Tomographic data were initially performed (pre-processing and reconstruction) using the open-source software tool SYRMEP Tomo Project. Data processing and analysis of the reconstructed tomography volumes were conducted using the segmentation semi-automatic settings of the software Avizo Fire 8, which provide information about each investigated tissues, organs or bone elements. Hence, volumetric analyses were carried out to quantify the development of structures in different tadpole developmental stages. Our work shows that synchrotron X-ray microtomography using phase-contrast mode resolves the edges of the internal tissues (as well as overall tadpole morphology), facilitating the segmentation of the investigated tissues. Reconstruction algorithms and segmentation software played an important role in the qualitative and quantitative analysis of each target structure of the Thoropa miliaris tadpole at different stages of development, providing information on volume, shape and length. The use of the synchrotron X-ray microtomography setup of the SYRMEP beamline of Elettra Synchrotron, in phase-contrast mode, allows access to volumetric data for bone formation, eye development, nervous system and notochordal changes during the development (ontogeny) of tadpoles of a cycloramphid frog Thoropa miliaris. As key elements in the normal development of these and any other frog tadpole, the application of such a comparative ontogenetic study, may hold interest to researchers in experimental and environmental disciplines.

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X-ray microtomography in herpetological research: a review

Cited by 26 publications

References 111 publications

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

Characterization of Coloured Gemstones by X-ray Micro Computed Tomography

Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles

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