Recent technological advances in microscopy have enabled cell-based whole genome screens, but the analysis of the vast amount of image data generated by such screens usually proves to be rate limiting. In this study, we performed a whole genome RNA interference (RNAi) screen to uncover genes that affect spreading of Drosophila melanogaster S2 cells using several computational methods for analyzing the image data in an automated manner. Expected genes in the Scar-Arp2/3 actin nucleation pathway were identified as well as casein kinase I, which had a similar morphological RNAi signature. A distinct nonspreading morphological phenotype was identified for genes involved in membrane secretion or synthesis. In this group, we identified a new secretory peptide and investigated the functions of two poorly characterized endoplasmic reticulum proteins that have roles in secretion. Thus, this genome-wide screen succeeded in identifying known and unexpected proteins that are important for cell spreading, and the computational tools developed in this study should prove useful for other types of automated whole genome screens.