The Cell Painting Assay as a Screening Tool for the Discovery of Bioactivities in New Chemical Matter

  • Axel Pahl
  • Sonja SieversEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1888)


Multiparametric phenotypic screening based on cellular morphology interrogates many biological pathways simultaneously and is therefore a valuable screening tool for the discovery of new biological activities. The cell painting assay stains various cellular features using six different dyes in one well. By automated image analysis, hundreds of parameters are calculated from the images which deliver a phenotypic profile of the cell. It has been shown that compounds with similar modes of action deliver similar phenotypic profiles. Using a reference set of compounds with known modes of action, it is possible to assign probable modes of action to new compounds and to discover compounds with potentially new modes of action.

Here we describe the cell painting assay as a screening tool using a hit identification workflow which has been implemented using open-source software.

Key words

Cell painting assay Phenotypic profile Screening Hit identification Morphological profiling 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Max Planck Institute of Molecular PhysiologyDortmundGermany

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