The single cell is the fundamental unit of biology. Understanding how the identity of individual cells in multicellular organisms contribute to their function remains a key question in Biology. Traditionally, most observations of cells were made through imaging-based techniques. Today, advances in Next Generation Sequencing have led to the widespread adoption of sequencing-based techniques for investigating the genotype and phenotype at single-cell resolution. Microfluidics, including droplet-based microfluidics, have been instrumental in the most successful commercial single-cell genomics platforms.

Integrating sequencing and imaging techniques will provide additional information than either of the techniques alone. Both single-cell imaging and genomics techniques measure orthogonal targets, and when combined reveal additional insights into cellular function. However, when performing sequential single-cell assays, there currently exists a tradeoff between throughput and information content. This dissertation will describe progress made towards reducing that gap. I will describe novel microfluidic platforms and techniques and applications involving integrating single-cell sequencing and optical measurements at high throughput. The microfluidics tools that will be discussed in this Dissertation aim to be a platform for performing single-cell multi-parameter and multi-omics techniques that will help further our understanding of cellular identity and how genotype informs phenotype at the single-cell level.