Large volumes of neuroscience data comprise multiple, non-stationary electrophysiological or neuroimaging time series recorded from different brain regions. Estimating the dependence between such neural time series accurately is critical, since changes in the dependence structure are presumed to reflect functional interactions between neuronal populations. We propose a new method of wavelet coherence, derived from the new bivariate locally stationary wavelet (LSW) time series model. Since wavelets are localised in both time and scale, this approach leads to a natural, local and multiscale estimate of nonstationary dependence. Our methodology is illustrated by application to a simulated example, and to electrophysiological data relating to interactions between the rat hippocampus and prefrontal cortex during working memory and decision-making. We thereby demonstrate that this novel LSW model can be of use in systems neuroscience applications.