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Motivated by the study of micro-vascular disease, we have been investigating the relationship between the structure of capillary networks and the resulting blood perfusion through the muscular walls of the heart. In order to derive equations describing effective fluid transport, we employ an averaging technique called homogenisation, based on a separation of length scales. We find that the tissue-scale flow is governed by Darcy's Law, whose coefficients we are able to explicitly calculate by averaging the solution of the microscopic capillary-scale equations. By sampling from available data acquired via high-resolution imaging of the coronary capillaries, we automatically construct physiologically-realistic vessel networks on which we then numerically solve our capillary-scale equations. By validating against the explicit solution of Poiseuille flow in a discrete network of vessels, we show that our homogenisation method is indeed able to efficiently capture the averaged flow properties.