Ultrastructural readout of in vivo synaptic activity for functional connectomics.
Large-volume ultrastructural mapping approaches yield detailed circuit wiring diagrams but lack an integrated synaptic activity readout which is essential for functional interpretation of the connectome. Here we resolve this limitation by combining functional synaptic labelling in vivo with focused ion-beam scanning electron microscopy (FIBSEM) and machine learning-based segmentation. Our approach generates high-resolution near-isotropic three-dimensional readouts of activated vesicle pools across large populations of individual synapses in a volume of tissue, opening the way for detailed functional connectomics studies. We apply this method to measure presynaptic activity in an ultrastructural context in synapses activated by sensory input in primary visual cortex in awake head-fixed mice, showing that the numbers of recycling and non-recycling vesicles approximate to a lognormal distribution across a large number of synapses. We also demonstrate that neighbouring boutons of the same axon, which share the same spiking activity, can differ greatly in their presynaptic release probability.