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Abstract A separable covariance model can describe the among-row and among-column correlations of a random matrix and permits likelihood-based inference with a very small sample size. However, if the assumption of separability is not met, data analysis with a separable model may misrepresent important dependence patterns in the data. As a compromise between separable and unstructured covariance estimation, we decompose a covariance matrix into a separable component and a complementary ‘core’ covariance matrix. This decomposition defines a new covariance matrix decomposition that makes use of the parsimony and interpretability of a separable covariance model, yet fully describes covariance matrices that are non-separable. This decomposition motivates a new type of shrinkage estimator, obtained by appropriately shrinking the core of the sample covariance matrix, that adapts to the degree of separability of the population covariance matrix.