Registering Drosophila embryos at cellular resolution to build a quantitative 3D atlas of gene expression patterns and morphology

The Berkeley Drosophila Transcription Network Project is developing a suite of methods to convert volumetric data generated by confocal fluorescence microscopy into numerical three dimensional representations of gene expression at cellular resolution. One key difficulty is that fluorescence microscopy can only capture expression levels for a few gene products in a given animal. We report on a method for registering 3D expression data from different Drosophila embryos stained for overlapping subsets of gene products in order to build a composite atlas, ultimately containing co-expression information for thousands of genes. Our techniques have also allowed the discovery of a complex pattern of cell density across the blastula that changes over time and may play a role in gastrulation.