Analysis of meristem shape and gene expression pattern has been conducted in many species over the past decades. Recent live imaging techniques have allowed for an unprecedented accumulation of data on the biology of meristematic cells, as well as a better understanding of the molecular and biophysical mechanisms behind shape changes in this tissue. Here we describe in detail how to prepare shoot apices of both Arabidopsis and tomato, in order to image them over time using a confocal microscope equipped with a long distance water-dipping lens.