A functional connectivity atlas of $\textit{C. elegans}$ measured by neural activation

Neural processing and dynamics are governed by the details of how neural signals propagate from one neuron to the next through the brain. We systematically measured functional properties of neural connections in the head of the nematode $\textit{Caenorhabditis elegans}$ by direct optogenetic activation and simultaneous calcium imaging of 10438 neuron pairs. By measuring responses to neural activation, we extracted the strength, sign, temporal properties, and direction of information flow between neurons in order to create an atlas of causal functional connectivity. We find that functional connectivity differs from predictions based on anatomy, in part, because of extrasynaptic signaling. Our measurements show that neurons such as RID signal extrasynaptically to other neurons for which there are no direct wired connections. We show that functional connectivity better predicts spontaneous activity than anatomy, suggesting that functional connectivity captures properties of the network that are critical for interpreting neural function.