Plants are able to perceive and respond to harsh changes in the environment. To understand the complex networks underlying such mechanisms, novel analytical methods are often required. In this special focus issue, Nagatani and Mimura (pp.1249–1251) introduce new technologies that have been recently developed for: high spatial resolution transcriptome and metabolome analyses; structural analysis of macromolecules and organelles by advanced optical methods; and mechanical manipulation of cells and whole plants with femtosecond pulsed lasers. These technologies will undoubtedly prove valuable for studying plant environmental sensing and other areas of plant research.