Digital three-dimensional models, besides representing helpful didactic tools, play an important role in the analysis of brain function and development. The fundamental idea of this approach is that patterns of neural connectivity and activity, pathological lesions, or gene expression are transferred into a single in silico structure: the digital atlas model. This article focuses on recent and ongoing work to build digital models of the developing Drosophila brain, which is formed by an invariant set of approximately 100 neural lineages. Lineages represent key elements in the emerging models of the fly brain: aside from their common origin, which is reflected in the shared expression of numerous developmental control genes, neurons belonging to a given lineage share many morphological characters, including axonal projection and dendritic arborization.