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Current data management approaches can easily handle the relatively simple requirements for molecular biology research but not the more varied and sophisticated microscopy imaging data in neuroscience research. We developed a project-oriented experimental imaging data management system through integration of the object-relational Oracle DBMS (database management system) and a distributed file management system, the storage resource broker (SRB). The data model we developed on Oracle9i supports semantic and analytical queries and image content mining. The MIDM provides comprehensive descriptive, structural, spatial and administrative information on microscopy image datasets. The current MIDM is web accessible at http://ncmir.ucsd.edu/CCDB. This paper describes the MIDM architecture and data mode in MIDM.