Transcriptional data must be placed within a spatial, cellular, and organismal context to understand how genes are regulated across tissues and organs. The rapid evolution of methods to visualize the spatial locations of proteins and transcripts has provided an exciting future for studying spatial biology in plants and animals. Additionally, obtaining 3D images of tissues and organs at nanoscale resolution will better elucidate how cells are spatially organized and help answer some key biological questions. I will focus my talk on some technologies our group is developing and applying to obtain multi-dimensional transcriptional data in organisms. I will then discuss projects involving spatial biology to answer biological questions in plant-pathogen interactions in Arabidopsis and duckweed biology.