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The study of animal colouration addresses fundamental and applied aspects relevant to a wide range of fields, including behavioural ecology, environmental adaptation and visual ecology. Although a variety of methods are available to measure animal colours, only few focus on chromatophores (specialized cells containing pigments) and pigment migration. Here, we illustrate a freely available and user-friendly method to quantify pigment cover (PiC) with high precision and low effort using digital images, where the foreground (i.e. pigments in chromatophores) can be detected and separated from the background. Images of the brown shrimp, Crangon crangon , were used to compare PiC with the traditional Chromatophore Index (CI). Results indicate that PiC outcompetes CI for pigment detection and transparency measures in terms of speed, accuracy and precision. The proposed methodology provides researchers with a useful tool to answer essential physiological, behavioural and evolutionary questions on animal colouration in a wide range of species., (© The Author 2017. Published by Oxford University Press.)