A new micro-particle induced X-ray emission-computed tomography (PIXE-CT) system was developed at Takasaki Ion Accelerators for Advanced Radiation Application in Japan Atomic Energy Agency. In this system, scanning transmission ion microscopy-CT was performed as well as PIXE-CT for three-dimensional (3D) measurement of major elements' distributions, which are required for corrections of X-ray yields due to energy losses of projectiles and absorption of X-rays. Moreover, maximum likelihood expectation maximization algorithm has been introduced to image reconstruction because higher spatial resolution can be obtained even with less X-ray yields. Consequently, 3D distribution of trace elements in a minute biological cell less than 100 μm has been successfully obtained.