The basic medical science research and clinical diagnosis and treatment have strongly benefited from the development of various noninvasive biomedical imaging techniques, e.g. magnetic resonance imaging (MRI) and computed tomography (CT). The mathematical tools provide many different ways to analyze these valuable images. In this talk, we will give examples of morphology and connectome study of human brains, the shape analysis of ciliary muscle of human eyes, and the estimate of oxygen transport in tissue transfer.