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A challenge in the numerical modeling of irregular stone masonry is the generation of realistic 3D microstructures. To address this problem, we have developed a database of microstructures for a wide range of masonry typologies. The database comprises 36 distinct microstructures of which 12 are generated through digital twinning of real stone masonry walls and 24 through virtual microstructure generators for 3D stone masonry walls. All the microstructures in the database are categorized according to the Italian code. In addition, we have calculated the geometric masonry quality index for all walls and classified them according to their masonry quality. The database is publicly available and provides access to ready-to-use 3D realistic microstructures for numerical simulations.