MASQOTSeg is a tool for segmentation and quality control of two-channel microarray data. All of the steps in MASQOTSeg are designed to be performed in a batch-wise fashion and require a minimal amount of user interaction. It supports segmentation using the seeded region growing algorithm (Adams and Bischof, 1994) based on spot coordinates from MASQOTGrid or GPR files.
MASQOTSeg implements the MASQOT methodology for multivariate spot quality control and support data export in native (tab-delimited text) or GPR file formats. By utilizing the MASQOT quality control score, all physical spot properties will jointly contribute to the final quality assessment based on a weighted sum.
Overview images of the segmentation, color-coded according to the quality assessments, are outputted if requested by the user. The main purpose of the overview images is to detect distinct regions of the slide that are of undesirably low quality.