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In this paper,we report a novel measurement system based on the development of Fudan Scanning Proton Microscopy (SPM) facility.By using Si-PIN diode (Hamamatsu S1223-01) detector,scanning transmission ion microscopy (STIM) measurement system has been set up.It can provide density and structural images with high probing efficiency and non-destruction by utilizing the energy loss of high energy (MeV) and focused ions penetrating through a thin sample.STIM measurement is able to map the density distribution of organic elements which mostly compose biology materials,such information can not be detected by using conventional Be-windowed Si (Li) X-ray detector in Particle Induced X-ray Emission (PIXE) technique.The spatial resolution capability of STIM is higher than PIXE technique at same accelerator status.As a result of STIM measurement,paramecium attached on the top of Kapton tube was measured by STIM.