My group drives technological innovations in microfluidics and bioimaging for holistic profiling of complex biological systems. Microfluidics enables high throughput analysis of individual cells, viruses, and molecules while imaging probes the spatial architecture of cellular and molecular landscapes. Using the new platforms, we aim to establish a mechanistic understanding of how individual biological components (viruses or cells) drive systems of high complexity. In the first part of the talk, I will introduce the new microfluidic tools we have developed to achieve single virus/microbe genomics. Using the new tools, we aim to pioneer single virus genomics for comprehensive profiling of the mutational landscape and quantitative assessment of the key processes impacting virus evolution. In the later part of the talk, I will discuss our efforts to expand the scope of the current in situ single cell transcriptomics technology using various chemical approaches and a new analysis tool that extracts the colocalization pattern of genes.