Cytoarchitecture is a basic principle of microstructural brain parcellation. We introduce Julich-Brain, a three-dimensional atlas containing cytoarchitectonic maps of cortical areas and subcortical nuclei. The atlas is probabilistic, which enables it to account for variations between individual brains. Building such an atlas was highly data- and labor-intensive and required the development of nested, interdependent workflows for detecting borders between brain areas, data processing, provenance tracking, and flexible execution of processing chains to handle large amounts of data at different spatial scales. Full cortical coverage was achieved by the inclusion of gap maps to complement cortical maps. The atlas is dynamic and will be adapted as mapping progresses; it is openly available to support neuroimaging studies as well as modeling and simulation; and it is interoperable, enabling connection to other atlases and resources.