This invention relates to a method and apparatus for image processing, and more particularly, this invention relates to a method and apparatus for processing image data generated by bioanalytical devices, such as DNA sequencers. An object of the present invention is to remove artifacts such as noise, blur, background, non-uniform illumination, lack of registration, and extract pixel signals back to DNA-beads in a way that de-mixes pixels that contain contributions from nearby beads. In one aspect of the present invention, a system for optimizing an image comprises means for receiving an initial image which includes a plurality of microparticles with different intensities; a computing device, comprising a processor executing instructions to perform: generating an initial function denoting each microparticle's location and intensity in the initial image; determining an image processing operator adapted to determine an extent of point spread and blurriness in the initial image; computing an optimum function denoting each microparticle's location and intensity in an optimizing image; and producing the optimizing image with enhanced accuracy and density of the microparticles.