PT - JOURNAL ARTICLE AU - Mark-Anthony Bray AU - Shantanu Singh AU - Han Han AU - Chadwick T. Davis AU - Blake Borgeson AU - Cathy Hartland AU - Maria Kost-Alimova AU - Sigrun M. Gustafsdottir AU - Christopher C. Gibson AU - Anne E. Carpenter TI - Cell Painting, an image-based assay for morphological profiling AID - 10.1101/049817 DP - 2016 Jan 01 TA - bioRxiv PG - 049817 4099 - http://biorxiv.org/content/early/2016/04/28/049817.short 4100 - http://biorxiv.org/content/early/2016/04/28/049817.full AB - In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, a morphological profiling assay multiplexing six fluorescent dyes imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Automated image analysis software identifies individual cells and measures ~1,500 morphological features (various measures of size, shape, texture, intensity, etc.) to produce a rich profile suitable for detecting subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes 2 weeks; feature extraction and data analysis take an additional 1-2 weeks.