A microarray image gridding method based on image projection difference sequences analysis and local extrema searching

Microarray image gridding is one important step of microarray image analysis to determine 2D image coordinates of all array spots in the hybridized gene chip image. Accuracy of microarray image gridding will affect the reliability of gene-chip data extraction and even the final analysis results of gene-chip assays. However, in recent years, many new microarray image gridding methods presented have higher accuracy but have more computation complexity than those precedented ones. To promote gridding accuracy and decrease computation complexity simultaneously, we presented a novel and simple microarray image gridding method based on image projection sequences analysis and local extrema searching. Firstly we transformed 2D microarray image into vertical and horizontal 1D projection sequences, secondly utilized signal processing methods of low pass filtering and zero mean to filtered projection sequences, thirdly computed the first-order difference and second-order difference for the smoothed signals, and finally realized microarray image gridding according to the local extrema of difference sequences and span information of spots array on the microarray image. The subsequent gridding experiments showed that this method had met the requirements of computing accuracy and efficiency of microarray image gridding.