Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

Here we describe a suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology at cellular resolution in whole embryos. A database containing information derived from 1,282 embryos is released that describes the mRNA expression of 22 genes at multiple time points in the Drosophila blastoderm. We demonstrate that our methods are sufficiently accurate to detect previously undescribed features of morphology and gene expression. The cellular blastoderm is shown to have an intricate morphology of nuclear density patterns and apical/basal displacements that correlate with later well-known morphological features. Pair rule gene expression stripes, generally considered to specify patterning only along the anterior/posterior body axis, are shown to have complex changes in stripe location, stripe curvature, and expression level along the dorsal/ventral axis. Pair rule genes are also found to not always maintain the same register to each other.The application of these quantitative methods to other developmental systems will likely reveal many other previously unknown features and provide a more rigorous understanding of developmental regulatory networks.Animal embryos can be thought of as dynamic three-dimensional arrays of cells expressing gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. Although developmental biologists most commonly analyze gene expression and morphology by visual inspection of photographic images, it has been increasingly recognized that a rigorous understanding of developmental processes requires automated methods that quantitatively record and analyze these phenomenally complex spatio-temporal patterns at cellular resolution. Different imaging and image analysis methods have been used to provide one-, two-, or three-dimensional descriptions of parts or all of a developing animal at various levels of detail (for example, [1-9]). Yet,