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Cell Painting, an image-based assay for morphological profiling

Mark-Anthony Bray, Shantanu Singh, Han Han, Chadwick T. Davis, Blake Borgeson, Cathy Hartland, Maria Kost-Alimova, Sigrun M. Gustafsdottir, Christopher C. Gibson, Anne E. Carpenter
doi: https://doi.org/10.1101/049817
Mark-Anthony Bray
1Imaging Platform, Broad Institute of Harvard and MIT, Cambridge USA
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Shantanu Singh
1Imaging Platform, Broad Institute of Harvard and MIT, Cambridge USA
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Han Han
2Recursion Pharmaceuticals, Salt Lake City USA
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Chadwick T. Davis
2Recursion Pharmaceuticals, Salt Lake City USA
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Blake Borgeson
2Recursion Pharmaceuticals, Salt Lake City USA
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Cathy Hartland
3Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge USA
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Maria Kost-Alimova
3Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge USA
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Sigrun M. Gustafsdottir
3Center for the Science of Therapeutics, Broad Institute of Harvard and MIT, Cambridge USA
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Christopher C. Gibson
2Recursion Pharmaceuticals, Salt Lake City USA
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Anne E. Carpenter
1Imaging Platform, Broad Institute of Harvard and MIT, Cambridge USA
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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, 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 28, 2016.
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Cell Painting, an image-based assay for morphological profiling
Mark-Anthony Bray, Shantanu Singh, Han Han, Chadwick T. Davis, Blake Borgeson, Cathy Hartland, Maria Kost-Alimova, Sigrun M. Gustafsdottir, Christopher C. Gibson, Anne E. Carpenter
bioRxiv 049817; doi: https://doi.org/10.1101/049817
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Cell Painting, an image-based assay for morphological profiling
Mark-Anthony Bray, Shantanu Singh, Han Han, Chadwick T. Davis, Blake Borgeson, Cathy Hartland, Maria Kost-Alimova, Sigrun M. Gustafsdottir, Christopher C. Gibson, Anne E. Carpenter
bioRxiv 049817; doi: https://doi.org/10.1101/049817

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