Imaging the Transcriptome: Constructing Tissue Atlases with Massively Multiplexed RNA Imaging

Imaging-based approaches to single-cell transcriptomics are emerging as powerful complements to single-cell RNA-sequencing methods, in part, because these techniques preserve the native spatial context of RNAs within cells and tissues. I will describe multiplexed error robust fluorescence in situ hybridization (MERFISH)—a technique capable of imaging thousands of different RNAs simultaneously in fixed cells. This technique promises the ability to discover, identify, and map cell types in a wide variety of tissues and diseases states, and I will describe one recent application of this technique: its use to create a molecularly defined, functionally annotated cellular map of a portion of the mouse hypothalamus.