Abstract: Extraction of quantitative information on gene expression from confocal images requires the precise detection of boundaries of the individual cells. In addition, the cell shape analysis is essential for understanding morphogenetic processes such as tissue stretching, contraction and folding. Drosophila eye imaginal disc is a widely used model system illustrating such processes. In this work, we developed a number of methods for quantitative analysis of the eye disc cellular structure based on the fluorescent tissue labeling with different markers. All image processing procedures are implemented in the ProStack package developed by the authors. The methods described here can be adapted for cell shape quantification and gene expression analysis in other epithelial tissues.