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 coexpression 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.

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