Imaging and optical manipulation enable an ever-expanding array of insights into biological and soft-matter systems, allowing not only observation of structures, but more subtle biophysical characterizations of forces and interactions. I’ll describe two projects from my lab that rely on microscopy. The first involves the mechanics of lipid membranes. Cellular membranes are remarkable materials – self-assembled, flexible, two-dimensional fluids. Understanding how proteins manipulate membranes is crucial to understanding the transport of cargo in cells, yet the mechanical activities of trafficking proteins remain poorly understood. Using an optical-trap based assay involving dynamic deformation of biomimetic membranes, we have examined the behavior of Sar1, a key component of the COPII family of transport proteins. We find that Sar1 from yeast (S. cerevisiae) has the ability to lower membrane rigidity by up to 100% as a function of its concentration, thereby lowering the energetic cost of membrane deformation, but that human Sar1 proteins show different behaviors. The second topic involves gut microbes. The digestive tracts of vertebrates are home to vast numbers of microbes that play significant roles in host health, but the structure and dynamics of microbial communities remain mysterious. Using light-sheet microscopy to perform three-dimensional imaging of well-defined bacterial components inside live larval zebrafish, we are beginning to visualize and characterize the assembly of microbial communities, highlighting the roles that the timing of colonization and the response of the host play.