Time series measured from real-world systems are generally noisy, complex and display statistical properties that evolve continuously over time. Here, we present a method that combines wavelet analysis and non-stationary surrogates to detect short-lived spatial coherent patterns from multivariate time-series. In contrast with standard methods, the surrogate data proposed here are realisations of a non-stationary stochastic process, preserving both the amplitude and time-frequency distributions of original data. We evaluate this framework on synthetic and real-world time series, and we show that it can provide useful insights into the time-resolved structure of spatially extended systems.