To understand how cells develop or function, it is important to study equivalent cells across individuals. Comparing a cell's fate between mutant and wild-type individuals can reveal how a gene regulates development. Similarly, combining information about a neuron's structure from one animal with functional recordings of its activity in another can reveal that neuron's contribution to a circuit. Comparing information across animals requires identifying cells by some combination of cell shape, position, gene expression and lineage. However, methods to identify cell fates in complex tissues are simplex, focusing on one or a small number of cell types at a time, making it hard to assess the behavior of the full population. We propose to develop multiplexed 3D multicolor fluorescent labeling and associated hardware and software to automate cell identification in live animals. In Aim 1 we will develop this approach in the nematode C. elegans because its invariant developmental lineage and known wiring of every neuron provides a powerful platform on which to build, test and validate this approach. In Aim 2 we will apply this to understand patterns of fate transformations across the entire organism in developmental mutants. Finally in Aim 3, we will use our labeling method to identify all neurons in the adult nerve ring (brain), and combine this with whole-brain imaging methods to map for the first time activity of every neuron onto the wiring diagram.

Animal nervous systems are incredible tissues, made of diverse collection of nerve cells (neurons) with different functions, all wired together to enable complex behaviors. We propose to study how nervous systems are formed and how the activity of the individual cells function to produce these behaviors using one of the best models for these processes is the nematode C. elegans, which has a simple and well-characterized nervous system and patterns of development yet develops and functions through the same conserved mechanisms seen in more complex organisms. This project will develop the tools to identify all of the cells in C. elegans embryos and adult nervous systems, allowing for the first time a complete description of the development and function of nervous systems.