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In this paper we present a new auto-microscope system controlled by microcomputer for image processing. The microstructure of objects can be observed and processed. A charge-coupled device (CCD) array is used as the photoelectric detector. This auto-microscope system can complete autofocusing, recognizing or screening out pattern in the field of view and automatic measuring for photomicrographing by the light intensity information sampling by CCD array. For this auto-microscope system we designed the scanning mechanism of microscope stage, adjustable holder of CCD in 5-Dimention, autofocusing mechanism and a auto-photomicrograph camera with large cassette. The autofocusing discrimination function constructed by means of self entropy is better suitable for low contrast image produced by microscope system. The geometrical features of the microscope image are selected for composing the discrimination function and this discrimination function is used for classifing the patterns in the microscope field of view by training samples. Automatically measuring light for photomicrograph is realized by the same CCD array and the controlling circuit, interface circuit and other circuits of this system are developed. Some experiments results: autofocusing, auto-screening the cell pattern in the microscope field of view are given.