RxRx3: Phenomics Map of Biology

The combination of modern genetic perturbation techniques with high content screening has enabled genome-scale cell microscopy experiments that can be leveraged to construct maps of biology. These are built by processing microscopy images to produce readouts in unified and relatable representation space to capture known biological relationships and discover new ones. To further enable the scientific community to develop methods and insights from map-scale data, here we release RxRx3, the first ever public high-content screening dataset combining genome-scale CRISPR knockouts with multiple-concentration screening of small molecules (a set of FDA approved and commercially available bioactive compounds). The dataset contains 6-channel fluorescent microscopy images and associated deep learning embeddings from over 2.2 million wells that span 17,063 CRISPR knockouts and 1,674 compounds at 8 doses each. RxRx3 is one of the largest collections of cellular screening data, and as far as we know, the largest generated consistently via a common experimental protocol within a single laboratory. Our goal in releasing RxRx3 is to demonstrate the benefits of generating consistent data, enable the development of the machine learning methods on this scale of data and to foster research, methods development, and collaboration. For more information about RxRx3 please visit RxRx.ai/rxrx3