Spatial multiplexing and omics

Much like solving a game of Clue, understanding physiological mysteries involves answering who, what, when and where. Multiomics approaches delve into cellular and molecular identities (the who and what), whereas longitudinal data collection addresses the when. Spatial dimensions address the where. This Primer discusses current technologies enabling quantification across biological scales, emphasizing the importance of retaining the spatial dimension of that data. We outline experimental design considerations, including targeted versus untargeted approaches, sample types, biological scale and four main classes of molecule detection. Spatial analytics are explored, covering questioning approaches, analytical platforms, image segmentation and sampling. Example applications, reproducibility considerations, limitations and our outlook for the future are provided. Our goal is to unite spatial platforms and biological scales that not commonly brought together to encourage collaboration and innovation between diverse biological fields, offering a conceptional framework and an apples-to-apples comparison for understanding major technologies to foster cross-disciplinary dialogue. Spatial multiomics is an interdisciplinary field combining all molecular omics using advanced imaging techniques to explore interactions within tissues and cells. In this Primer, Carstens et al. examine current technologies for quantification across biological scales and discuss considerations for establishing cross-disciplinary projects.