COSMOS: A Platform for real-time morphology-based, label-free cell sorting using deep learning (targeted RNA-Seq)

Cells are the singular building blocks of life, and comprehensive understanding of morphology among other properties is crucial to assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without need for biomarker labels and stains/dyes. We demonstrate COSMOS capabilities with multiple human cell lines and tissue samples. These early results suggest that our neural networks embedding space can capture and recapitulate deep visual characteristics and can be used to efficiently purify unlabeled viable cells with desired morphological traits. Our approach resolves a technical gap in ability to perform real-time deep learning assessment and sorting of cells based on high-resolution brightfield images. Overall design: Transcriptome profiling by single cell target immune response panel with the BD Rhapsody system on pre-sorted and COSMOS-sorted peripheral blood mononuclear cells (PBMCs).