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This paper presents color enhancement of low exposure images using histogram specification and its application to the p re-processing of a multiple color-filter aperture (MCA) camera which can estimate depth information of objects at different distances and perform multifocusing. Insufficient amount of exposure is the fundamental problem of the M CA camera because of the fixed and finite-sized apertures. The image acquired by the MCA camera cannot avoid the low-exposure and low-contrast degradation. The proposed color enhancement algorithm analyzes the low exposure phenomenon of a particular aperture, and improves the contrast and performance of the registration process in the MCA camera system. The proposed method can enhance the contrast of any low-exposure color images acquired by a conventional camera, and it can also be used to improve the image registration performance of the MCA camera. As a result, it can be incorporated into multifocusing, extended depth of field (EDoF) systems, and real-time 3D reconstruction.