CellXpress.ai: Machine learning powered system for automation of complex 2D and 3D cell culture workflows

Attrition in the therapeutic pipeline can often be attributed to a lack of translational efficacy from pre-clinical to clinical phases. Organoids show great promise as a game-changer in disease modeling and drug screening, as they better resemble tissue structure and functionality, and show more predictive responses to drugs. However, challenges associated with the practical adoption of organoids, such as assay complexity, reproducibility, and scalability, have limited their widespread adoption as a primary screening method in drug discovery. To alleviate the bottlenecks that come with labor-intensive manual protocols, we developed a cell culture automation solution called the CellXpress.ai® Automated Cell Culture System. The instrument enables automation of the entire organoid culture for prolonged complex workflows. The CellXpress.ai system provides media exchanges, cell plating, passaging and monitoring, endpoint assays, and complex image analysis. The instrument contains functional components, including an automated imager, a liquid handler, and an incubator, connected by one unified software. Development of cell cultures is monitored by periodic imaging and AI-powered image analysis, which can trigger automatic decisions to initiate passaging, endpoint assay, or troubleshooting steps. Here we present methods and results from automation of several commonly used complex biological workflows, including maintenance and culture of iPSC, automated maintenance and expansion of 3D organoids in matrix domes, and formation, culture, and assays for 3D spheroids in the low attachment plates. Cell culture process automation powered by imaging and AI -controlled decision making has great potential to bring 3D biology to another level, allowing to increase throughput and productivity, and enabling a variety of drug discovery and precision medicine applications.