Microscopy has revolutionised our understanding about the biology and genetics of prokaryotes and eukaryotes. For more than a century, it has provided a snapshot into the inner workings of whole organisms, tissues and cells. Modern day advances in microscopy tools, methods, and technologies, now enable a more detailed and precise quantitative and spatiotemporal insight into the cellular dynamics of living systems. This special issue, which is organised and introduced by Tetsuya Higashiyama, Alexis Maizel and Rüdiger Simon (see pp. 1217 – 1220), highlights some of the latest developments in plant functional imaging through a series of informative reviews and original research articles. Collectively, these papers should prove a useful resource for the plant research community.