The photon counting image system is able to detect the ultra-weak bioluminescence of the macro image of organisms. To study the luminescence of cell or molecules, the microscopic photon counting image system is necessary. The difference of two systems is that the microscopic photon counting image system is a noise limited system. The light source of radioisotope 14C is used for examination the state to ensure the limit detect of microscopic photon counting image system. The fundamental capability of the system is to measure the distribution and function of extremely small amounts of biomolecules, to realise real time visualisation of oxyradical burst activities, continuous observation of the calcium ion wave moving, and monitoring of gene expression etc. It will be an important development of transform from photon to molecule and from image of histology to image of function, promising for applications in the field of biology and medical science.