Effective and efficient neural networks for spike inference from in vivo calcium imaging

Calcium imaging provides advantages in monitoring large populations of neuronal activities simultaneously. However, it lacks the signal quality provided by neural spike recording in traditional electrophysiology. To address this issue, we developed a supervised data-driven approach to extract spike information from calcium signals. We propose the ENS² (effective and efficient neural networks for spike inference from calcium signals) system for spike-rate and spike-event predictions using ΔF/F calcium inputs based on a U-Net deep neural network. When testing on a large, ground-truth public database, it consistently outperformed state-of-the-art algorithms in both spike-rate and spike-event predictions with reduced computational load. We further demonstrated that ENS² can be applied to analyses of orientation selectivity in primary visual cortex neurons. We conclude that it would be a versatile inference system that may benefit diverse neuroscience studies.