PolNet is a software tool for the computer simulation of blood flow in realistic microvascular networks imaged with a wide variety of microscopy and clinical imaging techniques. To date, PolNet has contributed to: a) uncovering the relationship between blood flow and blood vessel biology and its importance for correct vascularisation of tissues, and b) developing ways of predicting retinal vascular damage in diabetic retinopathy patients. PolNet facilitates the adoption of cutting-edge computer simulation technology by non-experts in the Biosciences.