Synchrotron "virtual archaeozoology" reveals how Ancient Egyptians prepared a decaying crocodile cadaver for mummification

Newly discovered crocodile mummies of variable quality from an undisturbed tomb at Qubbat al-Hawā (Aswan, Egypt)

A description is provided of the crocodile remains that were found during an excavation carried out in 2019 at Qubbat al-Hawā (Aswan, Egypt). The material consists of five more or less complete bodies and five heads that were in varying states of preservation and completeness. The absence of resin, which was apparently not used during the preparation of the mummies, and the almost complete loss of linen bandages, due to insect damage, allowed a detailed morphological and osteometric description of the remains. Attention was focused on the general state of preservation of the crocodiles, the completeness of their skeletons and skulls, the presence of cut or other marks that could indicate the cause of death, and the processing of the carcasses. Moreover, the possible provenance of the crocodiles, the methods of capture and killing of the animals and their possible chronological attribution are discussed. It is concluded that the manner in which these specimens were prepared, as well as the variation observed in the type of 'final product', are unlike any other crocodile material described so far. The preparation method suggests a pre-Ptolemaic date for the deposit. The morphological and metrical features indicate that both Crocodylus niloticus and the recently resurrected species Crocodylus suchus are present among these individuals that range from 1.8 to 3.5 m in length.

Automated segmentation of microtomography imaging of Egyptian mummies

Propagation Phase Contrast Synchrotron Microtomography (PPC-SRμCT) is the gold standard for non-invasive and non-destructive access to internal structures of archaeological remains. In this analysis, the virtual specimen needs to be segmented to separate different parts or materials, a process that normally requires considerable human effort. In the Automated SEgmentation of Microtomography Imaging (ASEMI) project, we developed a tool to automatically segment these volumetric images, using manually segmented samples to tune and train a machine learning model. For a set of four specimens of ancient Egyptian animal mummies we achieve an overall accuracy of 94-98% when compared with manually segmented slices, approaching the results of off-the-shelf commercial software using deep learning (97-99%) at much lower complexity. A qualitative analysis of the segmented output shows that our results are close in terms of usability to those from deep learning, justifying the use of these techniques.

Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)'s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).

Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography

Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facility's Extremely Brilliant Source: the world's first high-energy 4 th generation X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organ's structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organ's individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.