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Acantharia ( Acantharea ) are wide-spread marine protozoa, presenting one of the rare examples of stron- tium sulfate mineralization in the biosphere. Their endoskeletons consist of 20 spicules arranged accord- ing to a unique geometric pattern named Müller’s principle. Given the diverse mineral architecture of the Acantharia class, we set out to examine the complex three-dimensional skeletal morphology at the nanometer scale using synchrotron X-ray nanotomography, followed by image segmentation based on deep learning methods. The present study focuses on how the spicules emanate from the robust central junction in the orders Symphyacanthida and Arthracanthida , the geometry of lateral spicule wings as well as pockets of interspicular space, which may be involved in cell compartmentalization. Through these morphometric studies, we observed subtle deviations from the previously described spatial arrangement of the spicules. According to our data, spicule shapes are adjusted in opposite spicules as to accommodate the overall spicule arrangement. In all types examined, previously unknown interspicular interstices were found in areas where radial spicules meet, which could have implications for the crystal growth mecha- nism and overall endoskeletal integrity. A deeper understanding of the spiculogenesis in Acantharia can provide biomimetic routes towards complex inorganic shapes.