The microscopic imaging apparatus includes a system controlling unit for obtaining a VD time setting value, and for obtaining the number of electric charge subtracting pulses, a synchronization signal generating unit for generating a vertical synchronization signal on the basis of the VD time setting value output from the system controlling unit and the horizontal synchronization signal, and a timing generating unit for extracting the electric charge of the imaging device by supplying the horizontal synchronization signal by the number of electric charge subtracting pulses to the imaging device as the electric charge subtracting pulses, and for generating a read pulse synchronous with the vertical synchronization signal in order to stop the accumulation of the electric charge of the imaging device after exposure is started.