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

High-resolution X-ray computed tomography, or microCT (μCT), enables the collection of three-dimensional phenotypic data from whole objects. The power of μCT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house huge numbers of small specimens that document the spatio-temporal patterns of life. Despite its potential for systematic analyses, most comparative studies employ only few μCT models, due to the challenges associated with scanning multiple specimens within a project scope. Here we describe a new method for high-throughput μCT scanning of dozens of small (< 2 cm) fossils in a single container, while maintaining nanometre-scale resolution and low consumable costs. Simple objects like pharmaceutical capsules and paper drinking straws are used to safely secure specimens inside a plastic tube on the instrument stage, allowing accurate tracking and digital labelling of individuals in the 3D volume. We also explore the effects of various packing materials and multiple specimens per capsule to minimize reconstruction artefacts caused by sample movement that can degrade image quality and hence μCT investment. We illustrate this method using vertebrate fossils from Queensland Museum, Australia, as part of an ongoing effort to track community responses to climate change over evolutionary time. To stabilise specimens during image acquisition, each fossil was wrapped in archival tissue and placed inside a clear two-piece capsule with its label, making it suitable for long-term storage. Following this system, we optimize the quantity of samples per tube to over 70 fossils, generating high quality 3D models for over 1,000 mammal, frog, and lizard specimens. We provide step-by-step instructions on specimen packing, labelling and μCT scanning, with suggestions on how they can be modified to suit user needs. The proposed method offers a simple and cost-effective technique for collecting consistent, high quality μCT data from hundreds of small specimens with minimal time, handling, and error. This system can be easily amended for other types of wet and dry material such as geological, botanical, and zoological samples, providing greater access to large-scale phenotypic data and contributing new information on the biodiversity of our planet.