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Background  The Drosophila pupal eye has become a popular paradigm for understanding morphogenesis and tissue patterning. Correct rearrangement of cells between ommatidia is required to organize the ommatidial array across the eye field. This requires cell movement, cell death, changes to cell-cell adhesion, signaling and fate specification.    Methodology  We describe a method to quantitatively assess mis-patterning of the Drosophila pupal eye and objectively calculate a ‘mis-patterning score’ characteristic of a specific genotype. This entails step-by-step scoring of specific traits observed in pupal eyes dissected 40–42 hours after puparium formation and subsequent statistical analysis of this data.    Significance  This method provides an unbiased quantitative score of mis-patterning severity that can be used to compare the impact of different genetic mutations on tissue patterning.

A Quantitative Method to Analyze Drosophila Pupal Eye Patterning