A comprehensive understanding of the human body requires insight into the structural anatomy of tissues and organs and the functional physiological processes they govern together. Mapping these connections is a key goal in biomedical research that will have enormous implications for studying and treating different disease states. The field of spatial biology is rapidly growing, offering new glimpses into these detailed anatomical maps. Chapter 1 will provide an overview of the increasing number of in situ spatial technologies bridging these scales, from within the cell, to tissue organizations, and beyond. While these techniques have been fundamental, chapter 2 highlights some limitations with the currently available tools, briefly introducing Atlas-scale Transcriptome Localization using Aggregate Signatures (ATLAS), a scalable tissue mapping method. Chapter 2 goes over the initial challenges encountered when scaling up and the optimization requirements for ATLAS in greater detail. Finally, chapter 3 provides an indepth overview of ATLAS and demonstrates its scalability in generating organ-scale transcriptome maps, profiling over 40 million cells across three different conditions. iii Collectively, this thesis aims to highlight the wealth of data that will be generated as technological advancements continue to revolutionize the field of spatial biology, bringing us closer to uncovering fundamental connections between anatomy and physiology.