Peripheral artery disease is a relatively common disease, normally caused by reduced blood flow to the limbs due to atherosclerosis in the arteries supplying them. Peripheral arteries’ anatomy, including collateral circulation, and flow information enable disease status assessment. We developed pCafe to semi-automatically trace peripheral arteries from 3D magnetic resonance angiography and measure both morphometry (anatomy) and intensity features (velocity). pCafe was validated on subjects with, and without peripheral artery occlusion, showing excellent agreement with human reviewer’s measurement (intra-class coefficient of 0.998). pCafe may be a useful tool to quantitatively characterize peripheral vascular structures in peripheral artery disease research.