Get Ready for JUMP-CP: Tools to Help You Leverage the Largest Public Cell Painting Dataset

The Joint Undertaking in Morphological Profiling (JUMP) Cell Painting (CP) Consortium, spearheaded by the Broad Institute, was established to generate a large public reference Cell Painting dataset. Scheduled to be released on Nov 1st, 2022, this will give researchers access to image-derived morphological profiles for over 140,000 reference small molecules, CRISPRs and ORFs. This reference dataset will allow scientists to use a data-driven approach to accelerate their drug discovery projects. This will help to determine a potential therapeutic’s mechanism of action, predict its activity or toxicity, and more. All based on imaging data.

The JUMP-CP dataset promises to be a valuable resource for drug discovery research. The complexity and size of the dataset, however, poses a challenge for scientists outside of the consortium. Here, we will present a robust and iterative data analytics workflow that we have used to evaluate the JUMP-CP pilot dataset, and share some of the results.
Furthermore, we will focus on “getting ready for JUMP-CP!”: how to help ensure your data is aligned and comparable with the JUMP-CP dataset. Specifically, we will discuss how a set of reference compounds can be used for Cell Painting assay development and validation.

During this webinar, you will learn:
- About JUMP-CP and how it can help your research.
- How we used our data analytics tool StratoMineR to analyze the JUMP-CP pilot data.
- How you can ensure your Cell Painting data is comparable to the JUMP-CP data.

Background

What is Cell Painting?
Cell Painting (CP) is a high-content, image-based morphological profiling assay. For the assay, six fluorescent dyes are used, revealing up to eight cellular components or organelles. Combined with sophisticated image analysis tools, this approach allows the user to obtain detailed cellular profiles, consisting of hundreds or even thousands of morphological features —measures of intensity, size, shape, spatial relationships, amongst many others. The amount of detail in these morphological profiles makes this assay sensitive to subtle cellular changes, and therefore a valuable tool to assess cellular responses to drugs or genetic perturbations.

What is the JUMP-CP consortium?
The Joint Undertaking in Morphological Profiling (JUMP) Cell Painting (CP) consortium, spearheaded by the Broad Institute of MIT and Harvard, is a collaboration between non-profit and industry partners. The consortium’s aim is to create an unprecedented public Cell Painting dataset. For this purpose, the consortium developed a standardized Cell Painting protocol, which was used to obtain the phenotypic profiles of over one billion cells responding to over 140.000 small molecules and genetic perturbations. The dataset will be released on Nov 1st,2022.
The consortium’s ultimate goal is “to make cell images as computable as genomes and transcriptomes".

Read more on the JUMP-CP website: jump-cellpainting.broadinstitute.org

Please note that Core Life Analytics is not a JUMP-CP Consortium partner. We are following the developments closely, as we see the obvious potential of this resource, but we also see the challenges that scientists face in accessing and leveraging it. We hope to contribute to making the dataset more accessible to anyone who is interested.

References:
We used the dataset cpg0000 (Chandrasekaran et al., 2022a), available from the Cell Painting Gallery on the Registry of Open Data on AWS (https://registry.opendata.aws/cellpainting-gallery/).