Strategies for recovering exact structure of neural circuits with broadly targeted fluorescent connectivity probes

We present a framework for reconstructing structure of complete neural circuits in the brain using collections of independent measurements of connectivity performed with existing anatomical or functional fluorescent probes, and designed to provide complementary information about neural circuit’s structure by targeting slightly different its parts either in deterministic or stochastic succession. We discuss specific implementation of this procedure using synaptic fluorescent marker GRASP and Cre/Lox system Brainbow to collect ensemble of observations of the sets of synapses between stochastically labeled samples of neurons. By representing such measurements mathematically as weak constraints on circuit’s connectivity matrix and by solving a constrained optimization problem, we are able to exactly deduce the wiring diagram in C. Elegans in an in-silico experiment from only ~10,000 measurements. This offers possibility for routinely reconstructing complete connectivity in smaller organisms, such as C. Elegans, using exclusively light microscopy instruments over the span of single weeks.