title: Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.
abstract: 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, which is a morphological profiling assay that multiplexes six fluorescent dyes, imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Cells are plated in multiwell plates, perturbed with the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Next, an automated image analysis software identifies individual cells and measures ∼1,500 morphological features (various measures of size, shape, texture, intensity, and so on) to produce a rich profile that is suitable for the detection of 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.
authors: Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Mark-Anthony
authors: 0000-0002-9748-3592
authors: MA
authors: Bray
authors: Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Shantanu
authors: S
authors: Singh
authors: Recursion Pharmaceuticals, Salt Lake City, Utah, USA.
authors: Han
authors: H
authors: Han
authors: Recursion Pharmaceuticals, Salt Lake City, Utah, USA.
authors: Chadwick T
authors: CT
authors: Davis
authors: Recursion Pharmaceuticals, Salt Lake City, Utah, USA.
authors: Blake
authors: B
authors: Borgeson
authors: Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Cathy
authors: C
authors: Hartland
authors: Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Maria
authors: M
authors: Kost-Alimova
authors: Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Sigrun M
authors: SM
authors: Gustafsdottir
authors: Recursion Pharmaceuticals, Salt Lake City, Utah, USA.
authors: Christopher C
authors: CC
authors: Gibson
authors: Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
authors: Anne E
authors: AE
authors: Carpenter
mesh_terms: D045744:Cell Line, Tumor; D048430:Cell Shape; D048429:Cell Size; D005456:Fluorescent Dyes / Q000378:metabolism*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D057054:Molecular Imaging / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes