Science Pool

In-depth Cellular Analysis using Cell Painting

Cell Painting sounds like art for biologists, and indeed it is a tool that leads to colourful and often very aesthetic images. However, it is a serious and, above all, very useful technology. It provides researchers with a multi-parameter, image-based description of the cell response to any condition that perturbs the cell, e.g. the treatment with a compound, a silencing via siRNA, or CRISPR engineering.

Basically, it ( 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 multi-well plates, exposed to the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Next, automated image analysis can be used to identify individual cells and to measure up to 1,700 morphological features (size, shape, texture, intensity, etc) to produce a rich profile that enables the detection of subtle phenotypes.

Profiles of cells treated with different methods or compounds can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic changes, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. The assay offers single-cell resolution and is complementary to the Connectivity Map (, which characterizes cell population responses to perturbation using transcriptomics.

Evotec has implemented a robust Cell Painting workflow to allow for the study of several thousands of compounds, using automated process for cell treatment and labelling, image analysis, data processing and quality control. The Company now uses Cell Painting to support hit triage at the end of a High Throughput Screening in order to select series with optimised phenotypic characteristics, for example to avoid major off-target effect or keep some degree of biological diversity.

To further improve sensitivity of the assay, Evotec is currently testing different approaches:

  • Use new combinations of markers, including multiplexing
  • Replace well level by cell level analysis
  • Use artificial intelligence for image analysis