Micro-CT is an X-ray imaging technique that enables the visualization of both internal and external structures of a sample in three dimensions. The technique is based on generating a series of projection images by rotating a specimen positioned between an X-ray source and a detector. Owing to its non-destructive nature, micro-CT has become an essential tool in taxonomic research, as it reveals taxonomically important internal structures in their original spatial context. Beyond taxonomy, micro-CT datasets allow for advanced 3D morphological analyses, including measurements of density, porosity, and structural thickness. Such quantitative traits can be proposed as novel numerical trait data for marine invertebrates, helping to address the gaps in the existing morphological data repositories and relevant literature. Moreover, these traits may also serve as “response traits,” as they can reflect organismal response to environmental shifts induced by anthropogenic stressors such as climate change and ocean acidification. For instance, density and structural thickness of calcified structures can provide valuable insights into calcification processes and reef-building functions, while 3D porosity analysis can inform estimates of the filtration capacity in marine invertebrates such as sponges.