The shoot apical meristem is the plant tissue that produces the plant aerial organs such as flowers and leaves. To better understand how does the shoot apical meristem develop and adapt to the environment, imaging developing shoot meristems expressing fluorescence reporters through laser confocal microscopy is becoming increasingly important. Yet, there are not many computational pipelines enabling a systematic and high-throughput characterisation of the produced microscopy images. This chapter provides a simple method to analyse 3D images obtained through laser scanning microscopy and quantitatively characterise radially or axially symmetric 3D fluorescence domains expressed in a tissue or organ by a reporter. Then, it presents different computational pipelines aiming at performing high-throughput quantitative image analysis of gene expression in plant inflorescence and floral meristems. This methodology has notably enabled to characterise quantitatively how stem cells responded to environmental perturbations in the Arabidopsis inflorescence meristem and will open new avenues in the use of quantitative analysis of gene expression in shoot apical meristems. Overall, the presented methodology provides a simple framework to analyse quantitatively gene expression domains from 3D confocal images at the tissue and organ level, which can be applied to shoot meristems and other organs and tissues.