Removal of background signal from in situ data on the expression of segmentation genes in Drosophila

Here we present a method for the removal of nonspecific background signal from fluorescently localized expression patterns of Drosophila segmentation genes. Our algorithm for removal of background signal brings the data to a common standard form with zero background and removes systematic error in gene expression levels caused by the presence of background. The method is based on the discovery, reported here, that background is well fit by a very broad two-dimensional paraboloid. The paraboloid is determined from the area of the embryo in which a given gene is not expressed and the whole pattern is then normalized by this paraboloid to remove background from the entire embryo. The software implementing this algorithm is available from the authors.