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Optimizing the Cell Painting assay for image-based profiling.

Beth A Cimini1, Srinivas Niranj Chandrasekaran1, Maria Kost-Alimova2

  • 1Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Nature Protocols
|June 21, 2023
PubMed
Summary
This summary is machine-generated.

The Cell Painting assay, a popular method for image-based profiling, has been updated to version 3. This enhanced protocol simplifies steps and reduces costs while maintaining robust detection of cellular morphology for research and drug discovery.

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Area of Science:

  • Cellular imaging
  • High-content screening
  • Morphological profiling

Background:

  • Image-based profiling extracts thousands of cellular features from microscopy images.
  • Applications include clustering perturbations, identifying disease phenotypes, and predicting assay outcomes.
  • Cell Painting is a widely used assay for image-based profiling.

Purpose of the Study:

  • To provide an updated protocol for the Cell Painting assay (version 3).
  • To quantitatively optimize the assay for improved detection of morphological phenotypes and perturbation grouping.
  • To simplify assay steps and reduce costs.

Main Methods:

  • The Cell Painting assay uses six stains across five channels to label eight cellular components.
  • The protocol was quantitatively optimized by the Joint Undertaking for Morphological Profiling Cell Painting Consortium.
  • Version 3 simplifies steps and reduces stain concentrations.

Main Results:

  • The updated Cell Painting assay (version 3) is robust to protocol variations.
  • Two vendors' dyes perform equivalently.
  • Simplified steps and reduced stain concentrations lead to cost savings.

Conclusions:

  • Cell Painting version 3 offers a simplified, cost-effective, and robust method for image-based profiling.
  • The assay effectively detects morphological phenotypes and groups similar perturbations.
  • This updated protocol supports basic research and drug discovery applications.