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Cell Painting

What is cell painting?

Cell painting is a type of phenotypic assay and a powerful application of high-content screening. Cells are "painted" by staining specific cellular compartments with different fluorescent bioprobes simultaneously, followed by imaging and analysis to extract hundreds to thousands of features in order to phenotypically profile the cells and elucidate their behaviour.

Origin of cell painting technique

The first iteration of cell painting, without naming it as such, was published in a 2013 paper by Gustafsdottir and colleagues at the Broad Institute of Harvard and MIT. The assay was then slightly modified into its current configuration by Bray and colleagues, who coined the term "Cell Painting”, in a 2016 publication that describes the process in detail.

The cell painting process

The cell painting process is dependent on the use of known reference compounds to "train" image analysis algorithms to generate multiparametric data that is subsequently filtered using machine learning approaches to reduce the overall complexity of the multidimensional data. The highly-dimensional data is displayed using tools such as PCA (Principal Component Analysis) or t-SNE (t-Distributed Stochastic Neighbor Embedding) that allow for clustering of similar phenotypic profiles that may "suggest" a mechanism or mode of action (MOA) for unknown compounds by comparison with reference compounds of known MOA.

At a high-level, the process of cell painting incorporates high-throughput robotics and automation to seed cells and deliver compounds to microplates, the use of multiple fluorescent bioprobes to stain cell compartments, acquisition of images, image analysis, and machine and deep learning data analysis tools to enrich and summarize findings of complex multidimensional data.

Cell painting for phenotypic drug discovery

With cell painting, computational and cell biology combine to provide a deeper understanding of the impact of genetic or exogenous perturbagens, with the aim of identifying therapeutics, investigating human gene function, or assessing environmental toxicants.

Since the first publications describing the technique, cell painting has been rapidly adopted for phenotypic drug discovery and basic research. Implementing the assay comes with some challenges, ranging from the choice of cell model, appropriate labeling reagents, and optimizing instrumentation for detection, to making sense of the thousands of features that can be generated during data analysis.

References:

  1. Gustafsdottir, S.M., et al., Multiplex cytological profiling assay to measure diverse cellular states. PLoS One, 2013. 8(12): p. e80999.
  2. Bray, M.A., et al., Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc, 2016. 11(9): p. 1757-74.

For research use only. Not for use in diagnostic procedures.

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PhenoVue cell painting kits

PhenoVue™ cell painting kits comprise 6 validated, pre-optimized fluorescent probes to stain the actin cytoskeleton, nucleoli, nucleus, plasma membranes, ER and Golgi and apparatus, together with a stain diluent, to streamline the cell painting workflow. We are proud to be supporting partners of the Joint Undertaking in Morphological Profiling-Cell Painting (JUMP-CP) consortium, providing our PhenoVue Cell Painting JUMP kits to the Consortium to create the world’s largest, public cell painting dataset.

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PhenoVue™ cell painting kits comprise 6 validated, pre-optimized fluorescent probes to stain the actin cytoskeleton, nucleoli, nucleus, plasma membranes, ER and Golgi and apparatus, together with a stain diluent, to streamline the cell painting workflow. We are proud to be supporting partners of the Joint Undertaking in Morphological Profiling-Cell Painting (JUMP-CP) consortium, providing our PhenoVue Cell Painting JUMP kits to the Consortium to create the world’s largest, public cell painting dataset.

Learn More

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HCS/HCA instruments

Opera Phenix® Plus high-content screening system offers fast acquisition for multiplexing experiments by combining multi-camera technology with our proprietary automated high NA water immersion objectives that allow acquisition of images with shorter exposure times and higher resolution. Synchrony™ Optics combine a pinhole disk with a microlens-enhanced Nipkow disk to capture the illuminating light for a strong excitation of fluorophores and delivers high quality confocality. Optional high-power lasers minimize exposure times further and help to increase throughput of your cell painting screen.

Opera Phenix® Plus high-content screening system offers fast acquisition for multiplexing experiments by combining multi-camera technology with our proprietary automated high NA water immersion objectives that allow acquisition of images with shorter exposure times and higher resolution. Synchrony™ Optics combine a pinhole disk with a microlens-enhanced Nipkow disk to capture the illuminating light for a strong excitation of fluorophores and delivers high quality confocality. Optional high-power lasers minimize exposure times further and help to increase throughput of your cell painting screen.

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PhenoPlate microplates

PhenoPlate™ (formerly CellCarrier™ Ultra) microplates have been engineered to deliver superior images and the highest quality data for high-content applications. The excellent flatness of the plate bottom provides optimal clarity and fast autofocusing, while the high optical quality of the cyclic olefin imaging surface ensures superior image quality.

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PhenoPlate™ (formerly CellCarrier™ Ultra) microplates have been engineered to deliver superior images and the highest quality data for high-content applications. The excellent flatness of the plate bottom provides optimal clarity and fast autofocusing, while the high optical quality of the cyclic olefin imaging surface ensures superior image quality.

Learn More

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Powerful software

Harmony® imaging and analysis software offers all the tools needed to extract the multitude of cellular parameters in an easy and straightforward way. With its building block approach to image analysis, as few as four building blocks are needed to set up the analysis sequence.

Signals Image Artist™ image analysis and management platform for high-content screening and cell imaging data allows you to quickly process, analyze, share, and store the vast volumes of data generated by high-content screening and cellular imaging, including 3D imaging, phenotypic screening, and cell painting – so you get answers sooner.

Signals VitroVivo data analysis and management software offers tools for quality control, data visualization and hit detection.

Learn More

Harmony® imaging and analysis software offers all the tools needed to extract the multitude of cellular parameters in an easy and straightforward way. With its building block approach to image analysis, as few as four building blocks are needed to set up the analysis sequence.

Signals Image Artist™ image analysis and management platform for high-content screening and cell imaging data allows you to quickly process, analyze, share, and store the vast volumes of data generated by high-content screening and cellular imaging, including 3D imaging, phenotypic screening, and cell painting – so you get answers sooner.

Signals VitroVivo data analysis and management software offers tools for quality control, data visualization and hit detection.

Learn More

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explorer G3 customized cell painting workstation

explorer™ G3 customized cell painting workstation provides an integrated, turn-key solution to automate cell painting assays using our PhenoVue Cell Painting Kits with image acquisition on our Opera Phenix Plus high content imager.

explorer™ G3 customized cell painting workstation provides an integrated, turn-key solution to automate cell painting assays using our PhenoVue Cell Painting Kits with image acquisition on our Opera Phenix Plus high content imager.