Quantifying Cell Shape and Gene Expression in the Shoot Apical Meristem Using MorphoGraphX

Confocal microscopy is a technique widely used to live-image plant tissue. Cells can be visualized by using fluorescent probes that mark the cell wall or plasma membrane. This enables the confocal microscope to be used as a 3D scanner with submicron precision. Here we present a protocol using the 3D image processing software MorphoGraphX (http://www.MorphoGraphX.org ) to extract the surface geometry and cell shapes in the shoot apex. By segmenting cells over consecutive time points, precise growth maps of the shoot apex can be produced. It is also possible to tag a protein of interest with a fluorescent marker and quantify protein expression at the cellular level.