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Background  Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly  Drosophila melanogaster  is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom.  In the sea anemone  Nematostella vectensis  the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans.  Nematostella  is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques.    Findings  Our new quantification method produces standardized gene expression profiles from raw or annotated  Nematostella in situ  hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation.    Conclusions  We created a standard format for gene expression data, which enables quantitative analysis of  in situ  hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar  Nematostella  morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.

Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis