Multi-Domain Translation between Single-Cell Imaging and Sequencing Data using Autoencoders

Abstract

The development of single-cell methods for capturing different data modalities including imaging and sequencing have revolutionized our ability to identify heterogeneous cell states. While various methods have been proposed to integrate different sequencing data modalities, coupling imaging and sequencing has been an open challenge. We here present an approach for integrating vastly different modalities by learning a probabilistic coupling between the different data modalities using autoencoders to map to a shared latent space. We validate this approach by integrating single-cell RNA-seq and chromatin images to identify distinct sub-populations of human naive CD4+ T-cells that are poised for activation. Collectively, our approach provides a framework to integrate and translate between data modalities that cannot yet be measured within the same cell for diverse applications in biomedical discovery.