Microarray is a new class of biotechnologies able to help biologist researches to extrapolate new knowledge from biological experiments. Image Analysis is devoted to extrapolate, process and visualize image information. For this reason it has found application also in Microarray, where it is a crucial step of this technology. The Microarray Technology consists of different sequential phases that are shown in Figure 1. We propose a new advanced segmentation pipeline called MISP (Microarray Image Segmentation Pipeline). MISP steps and semantic segmentation regions discovered using the pipeline are showed in the figures below. The MISP Software Architecture (Figure 6) include Visualization, Segmentation, information and quality measure extraction. Preliminary results showed how the proposed pipeline is able to capture in a more reliable way the underlying signal distribution of input data.