The recent advent of tools for manipulating and monitoring gene expression calls for efficient ways to document, access and analyse these gene expression patterns. Although a number of databases and gene expression atlases have been compiled in recent years, many of them are limited with regards to their content and utility. Here, Chris Doe and colleagues develop new software that overcomes these limitations (p. 2524). This new ‘atlas-builder’ software can be used to create an atlas of gene expression in any tissue in any organism with stereotyped cell positions. Importantly, they report, the atlases generated by this software are three-dimensional, allow for the registration of an infinite number of markers, are searchable and are open-ended; additional markers can be added by users. To validate the software and to help demonstrate its advantages, the authors generated an ‘eNeuro’ atlas of the Drosophila embryonic CNS. The authors initially populated the atlas with eight transcription factors that mark the major CNS cell types. The atlas was subsequently expanded to include data from 75 Gal4 lines expressed in sparse patterns, thereby allowing the identification of molecularly distinct subsets of interneurons and revealing unexpected diversity among motor neurons. The ‘atlas-builder’ software and the eNeuro atlas, both of which have been made publicly available, promise to be valuable resources for the developmental biology community.