The compound eye ofDrosophila melanogasterhas long been a model for studying genetics, development, neurodegeneration, and heterochromatin. Imaging and morphometry of adultDrosophilaand other insects is hampered by the low throughput, narrow focal plane, and small image sensors typical of stereomicroscope cameras. In educational environments, where data collection may be distributed among many individuals over extended time periods, these limitations are compounded by inter-operator variability in lighting, sample positioning, focus, and post-acquisition processing. Our goal was to develop an affordable and student-friendly method for multiplexed quantitative analysis of adultDrosophilaphenotypes. Here we report a system for efficient data collection and analysis of up to 60 adult flies in a single image with standardized conditions that eliminate inter-operator variability and enable precise quantitative comparison of adult morphological phenotypes. Semi-automated data analysis using ImageJ and R reduces image manipulations, facilitates reproducibility, and can be adapted to emerging automated segmentation methods. This collection of classroom-friendly methods doubles as a hands-on introduction to imaging, data visualization, and statistical analysis for students