The current genome-sequencing projects provide [`]word indices' of the book of life. A central post-genomic question will be how these words are three-dimensionally deployed in the generation of organism form. Gene expression studies of developing organisms contribute an increasing wealth of snapshot data on the activation of individual genes at selected locations and single moments in the developmental process. However, a comprehensive understanding of the dynamic activation of multiple genes and their functional role in controlling the 3D processes of collective cell behaviour, pattern formation and morphogenesis, requires special tools for a systematic description of spatio-temporal patterns of gene activation and the ensuing phenotypic effects. This article concentrates on new, computer-based tools for the 3D analysis of gene expression patterns in embryonic development and their use for the systematic establishment of comprehensive gene expression maps.