Semantic segmentation of vertebrate microfossils from computed tomography data using a deep learning approach

Abstract. Vertebrate microfossils have broad applications in evolutionary biology and stratigraphy research areas such as the evolution of hard tissues and stratigraphic correlation. Classification is one of the basic tasks of vertebrate microfossil studies. With the development of techniques for virtual paleontology, vertebrate microfossils can be classified efficiently based on 3D volumes. The semantic segmentation of different fossils and their classes from CT data is a crucial step in the reconstruction of their 3D volumes. Traditional segmentation methods adopt thresholding combined with manual labeling, which is a time-consuming process. Our study proposes a deep-learning-based (DL-based) semantic segmentation method for vertebrate microfossils from CT data. To assess the performance of the method, we conducted extensive experiments on nearly 500 fish microfossils. The results show that the intersection over union (IoU) performance metric arrived at least 94.39 %, meeting the semantic segmentation requirements of paleontologists. We expect that the DL-based method could also be applied to other fossils from CT data with good performance.