A scalable, all-optical method for mapping synaptic connectivity with cell-type specificity

Single-cell transcriptomics has uncovered the vast heterogeneity of cell types that compose each region of the mammalian brain, but describing how such diverse types connect to form functional circuits has remained challenging. Current methods for measuring the presence and strength of synaptic connections principally rely on low-throughput whole-cell recording approaches. However, the development of optical tools for perturbing and observing neural activity--now notably including genetically encoded voltage indicators--presents an exciting opportunity to vastly increase the throughput of physiological connectivity mapping. Here, we combine massively parallel optical measurements of synaptic strength with a novel pipeline for thick-tissue spatial transcriptomics to assay synaptic connectivity motifs with high sensitivity, high throughput, and cell-type specificity. We apply this approach in the motor cortex to describe new cell-type-specific synaptic innervation patterns for long-range thalamic and contralateral input onto more than 1000 motor cortical neurons.