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

Abstract

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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