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Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.

Mark-Anthony Bray1, Shantanu Singh1, Han Han2

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Summary

This study details Cell Painting, a morphological profiling assay using fluorescent dyes to analyze cellular features from microscopy images. It enables the detection of subtle phenotypes for applications in drug discovery and disease research.

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Area of Science:

  • Cellular imaging and high-content screening
  • Quantitative biology and phenotypic analysis

Background:

  • Morphological profiling quantifies cellular phenotypes from microscopy images.
  • Identifying biological similarities and differences requires rich cellular profiles.

Purpose of the Study:

  • To describe the Cell Painting assay protocol for morphological profiling.
  • To enable the detection of subtle cellular phenotypes.
  • To facilitate comparison of cell populations under various perturbations.

Main Methods:

  • Cell Painting assay uses six fluorescent dyes across five channels.
  • Cells are cultured, perturbed, stained, fixed, and imaged using high-throughput microscopy.
  • Automated image analysis extracts ~1,500 morphological features per cell.

Main Results:

  • Generates rich cell profiles detailing size, shape, texture, and intensity.
  • Enables detection of subtle phenotypic changes.
  • Profiles can be compared to identify functional pathways and disease signatures.

Conclusions:

  • Cell Painting provides a robust method for detailed morphological profiling.
  • The assay supports diverse applications including drug discovery and disease research.
  • Experimental execution and data analysis are time-efficient, taking 2-4 weeks.