Automated ROI detection allows rapid quantification of synaptic activity across tens of thousands of synapses in cell culture.

Synapses are the basic unit of information transfer between neurons. Their dysfunction is a common trigger of cognitive diseases and disorders. However, high-throughput analysis methods to assess synaptic function and dysfunction are lacking. Calcium imaging in cultured neurons in the absence of Mg2+ and presence of TTX allows visualization of NMDAR-dependent spontaneous synaptic calcium transients, which report pre and postsynaptic function. Here, we introduce a high-throughput automated analysis pipeline that combines Suite2p ROI detection and Python scripts to analyze tens of thousands of synapses and quantify changes in presynaptic vesicle fusion rates (frequency), postsynaptic function (amplitude), and the number of functional synapses. We use this pipeline to test known NMDAR agonists (glycine) and antagonists (ketamine, memantine, APV), presynaptic function modulating compounds (PDBu), and encephalitis patient-derived NMDAR auto-antibodies, where our pipeline proved more sensitive in detecting dysfunction at the single-synapse level than other methods. The ability to detect, track, and quantify activity across tens of thousands of synapses and millions of synaptic calcium transients using this pipeline will aid drug discovery of compounds that protect synapse function.