MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts three independent applications (MASQOTGrid, MASQOTSeg and MASQOTView) for this purpose with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology (Bylesjö, et al., BMC Bioinformatics, 2005). MASQOT-GUI is Java-based and licensed under the GNU Lesser General Public License (LGPL), which implies that the source code is freely available. Additional documentation and pre-compiled installation tools for the Windows and Linux platforms are available for download here.
MASQOTGrid is an application for gridding (addressing) of two-channel microarray data.
MASQOTSeg is an application for segmentation of microarray spots featuring integrated multivariate spot quality control assessment. The program uses spot locations (from MASQOTGrid or from other gridding applications) and outputs a set of common spot properties along with the MASQOT quality score.
MASQOTView is an application for viewing and re-flagging microarray spots. Selected spots, filtered based on the MASQOT quality control score, will be cropped and scaled and can subsequently be visually inspected.