MetaVision3D: Automated Framework for the Generation of Spatial Metabolome Atlas in 3D

High-resolution spatial imaging is transforming our understanding of foundational biology. Spatial metabolomics is an emerging field that enables the dissection of the complex metabolic landscape and heterogeneity from a thin tissue section. Currently, spatial metabolism highlights the remarkable complexity in two-dimensional space and is poised to be extended into the three-dimensional world of biology. Here, we introduce MetaVision3D, a novel pipeline driven by computer vision techniques for the transformation of serial 2D MALDI mass spectrometry imaging sections into a high-resolution 3D spatial metabolome. Our framework employs advanced algorithms for image registration, normalization, and interpolation to enable the integration of serial 2D tissue sections, thereby generating a comprehensive 3D model of unique diverse metabolites across host tissues at mesoscale. As a proof of principle, MetaVision3D was utilized to generate the mouse brain 3D metabolome atlas (available at ) as an interactive online database and web server to further advance brain metabolism and related research. ### Competing Interest Statement R.C.S. has research support and received consultancy fees from Maze Therapeutics. R.C.S., M.S.G., and R.C.B. are co-founders of Attrogen LLC. R.C.S. is a member of the Medical Advisory Board for Little Warrior Foundation. M.S.G. has research support and research compounds from Maze Therapeutics, Valerion Therapeutics, Ionis Pharmaceuticals. M.S.G. also received consultancy fee from Maze Therapeutics, PTC Therapeutics, and the Glut1-Deficiency Syndrome Foundation. The remaining authors declare no competing interests.