A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application

Biological macromolecules assemble into sophisticated spatial architectures to orchestrate fundamental cellular processes. Understanding this architecture is therefore essential for deciphering the mechanisms of life. Driven by advances in high-throughput sequencing and single-molecule imaging, spatial omics technologies have emerged as powerful tools that are revolutionizing biomedical research. This review systematically evaluates current spatial omics methodologies by comparing their key performance parameters. We critically assess their optimal applications and discuss strategies to overcome prevailing challenges in spatial resolution, capture efficiency, robustness, data analysis, and clinical translation. Furthermore, we highlight how these technologies provide unique insights into tissue heterogeneity, cell-cell interactions, developmental dynamics, microenvironmental composition, and neuroanatomy. Our analysis offers guidance for selecting appropriate spatial omics approaches and outlines promising directions for future technological innovation and expanded biomedical applications.