Orthogonal polarization spectroscopy (OPS) is a technique for taking images to finally characterise microcirculation. Current image analysis algorithms have limitations when applied to image sequences obtained from the liver. We developed an automatic analysis tool which enables detection of liver vessels, measurement of vessel diameters, and determination of blood flow velocities with sparse user interactions. For validation purpose, data was analysed with our proposed algorithm and compared with manual results by experienced users. Related to commercial products, the needed time for analysis is reduced from more than 30 minutes to less than 2 minutes with comparable results for accuracy.