Medium-Throughput Processing of Whole Mount In Situ Hybridisation Experiments into Gene Expression Domains

(A) Data acquisition consists of the following steps. First, gene expression patterns of interest are visualised using enzymatic (colorimetric) whole-mount in situ hybridisation (WMISH). Second, embryos are imaged using a compound wide-field microscope, and third, this results in a set of four images that serve as the basis for further processing. (B) Data processing consists of (1) distinguishing the embryo from the background (image segmentation), (2) extracting gene expression profiles along the A–P axis, and (3) determining the boundaries of gene expression domains using spline approximations. The resulting data, metadata, and processing parameters are stored in a database. Median boundary positions define an integrated data set of gene expression. Measured boundary profiles and positions are used to analyse variability and spatio-temporal dynamics of gene expression.