The Mesoscale to Molecules Bioimaging Science Program (Bioimaging Program), within the Department of Energy?s (DOE) Office of Biological and Environmental Research (BER), sponsors research at national laboratories and universities that addresses grand challenges for biology. These projects are centered on developing a better understanding of the spatial and temporal distributions of key metabolites and biomarkers associated with microbial and plant systems related to bioenergy and environmental systems. The Bioimaging Program is developing new and improved instruments, which are being designed and constructed from the ground up, adapted from other scientific disciplines, or upgraded with new capabilities to create a comprehensive and versatile toolbox for imaging biological dynamics and chemistry. These approaches involve (1) hypothesis-based approaches focused on solving particular problems for plant biology, biofuels, and biogeochemistry and (2) broad-based systems and design-based technologies that can lead to new discoveries. Scientists developing both approaches keep in mind that versatility, transferability, and portability will help foster widespread adoption by the larger science community for future field and laboratory studies.