When water is removed from the paper during paper making, a dimensional change occurs in which the paper shrinks in the direction perpendicular to the direction of processing. The dimensional changes vary across the web and influence, e.g., the surface and compression properties of the paper; they also complicate the control of the paper machine. In this article, a robust method for estimating the relative shrinkage profile is presented. The method is based on a one-dimensional recording of the imprints from the forming fabric, using a fluorescence technique. The recording is transformed into a time-frequency spectrum, on which three different frequency estimators have been evaluated. In simulations on synthetic data and measurements on paper profiles the estimator that maximizes the correlation energy showed the most robust and accurate performance of the methods evaluated, even at a low signal-to-noise ratio.