Understanding the formation of the coral skeleton has been a common subject uniting various marine and materials study fields. Two main regions dominate coral skeleton growth: Rapid Accretion Deposits (RADs) and Thickening Deposits (TDs). These have been extensively characterized at the 2D level, but their 3D characteristics are still poorly described. Here, we present an innovative approach to combine synchrotron phase contrast-enhanced microCT (PCE-CT) with artificial intelligence (AI) to explore the 3D architecture of RADs and TDs within the coral skeleton. As a reference study system, we used recruits of the stony coral Stylophora pistillata from the Red Sea, grown under both natural and simulated ocean acidification conditions. We thus studied the recruit’s skeleton under both regular and morphologically-altered acidic conditions. By imaging the corals with PCE-CT, we revealed the interwoven morphologies of RADs and TDs. Deep-learning neural networks were invoked to explore AI segmentation of these regions, to overcome limitations of common segmentation techniques. This analysis yielded highly-detailed 3D information about the RAD’s and TD’s architecture. Our results demonstrate how AI can be used as a powerful tool to obtain 3D data essential for studying coral biomineralization and for exploring the effects of environmental change on coral growth.

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Bones are nanocomposites of protein, mineral and water that form mineralized collagen fibrils arranged in a variety of layered lamellae. Bone material has a long evolutionary record and specific bones attain shapes and microstructures that have well stood the test of time such that they can be considered optimized to match their function. Further, most bones typically contain entombed living cells, osteocytes responsible for adaptation, healing and biochemical signaling. The bones of pike fish (Esox lucius) are different because, as with other advanced teleost species, they evolved to eliminate osteocytes from the microstructure. This suggests that these cells are not needed because these bones are more damage resistant than mammalian bones. Here we explore details of this biologically-grown structure, using a combination of light and X-ray based characterization methods. We report the three-dimensional arrangement and composition of the heavily cyclically-loaded pivot of the cleithrum bone in the pectoral girdle of pike. By combining absorption and phase contrast-enhanced micro-computed tomography, electron microscopy, polarized light microscopy and second harmonic generation multi-photon confocal laser scanning microscopy we reveal the principle layout of the bone of this predator which we determine at the millimeter, micrometer and nanometer lengthscales.

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X-rays are invaluable for imaging and sterilization of bones, yet the resulting ionization and primary radiation damage mechanisms are poorly understood. Here we monitor in-situ collagen backbone degradation in dry bones using second-harmonic-generation and X-ray diffraction. Collagen breaks down by cascades of photon-electron excitations, enhanced by the presence of mineral nanoparticles. We observe protein disintegration with increasing exposure, detected as residual strain relaxation in pre-stressed apatite nanocrystals. Damage rapidly grows from the onset of irradiation, suggesting that there is no minimal ‘safe’ dose that bone collagen can sustain. Ionization of calcium and phosphorous in the nanocrystals yields fluorescence and high energy electrons giving rise to structural damage that spreads beyond regions directly illuminated by the incident radiation. Our findings highlight photoelectrons as major agents of damage to bone collagen with implications to all situations where bones are irradiated by hard X-rays and in particular for small-beam mineralized collagen fiber investigations.