In this paper, segmenting and classifying low contrast defects on flat panel display is one of the key problems for automatic inspection system in practice. Problems become more complicated when the quality of acquired image is degraded by the illumination irregularity. Many algorithms are developed and implemented successfully for the defects segmentation. However, vision algorithms are inherently prone to be dependent on parameters to be set manually. In this paper, one morphological segmentation algorithm is chosen and a technique using frequency domain analysis of input images is developed for automatically selection the morphological parameter. An extensive statistical performance analysis is performed to compare the developed algorithms.