Median-modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing.

Denoising is a fundamental early stage in 2-DE image analysis strongly influencing spot detection or pixel-based methods. A novel nonlinear adaptive spatial filter (median-modified Wiener filter, MMWF), is here compared with five well-established denoising techniques (Median, Wiener, Gaussian, and Polynomial-Savitzky-Golay filters; wavelet denoising) to suggest, by means of fuzzy sets evaluation, the best denoising approach to use in practice. Although median filter and wavelet achieved the best performance in spike and Gaussian denoising respectively, they are unsuitable for contemporary removal of different types of noise, because their best setting is noise-dependent. Vice versa, MMWF that arrived second in each single denoising category, was evaluated as the best filter for global denoising, being its best setting invariant of the type of noise. In addition, median filter eroded the edge of isolated spots and filled the space between close-set spots, whereas MMWF because of a novel filter effect (drop-off-effect) does not suffer from erosion problem, preserves the morphology of close-set spots, and avoids spot and spike fuzzyfication, an aberration encountered for Wiener filter. In our tests, MMWF was assessed as the best choice when the goal is to minimize spot edge aberrations while removing spike and Gaussian noise.