The invention is directed to a preserved serial set of sequential, iterative, and ordered thin sections of a specimen block, and a catalog of images taken from one or more sub-series of the set of sections and organized so as to create a three-dimensional profile of the microscopic structures of the specimen block. The serial set of sequential, iterative, and ordered thin sections are prepared from the specimen block by cutting and imaging thin sections of that specimen block so that the thin sections remain strictly in the sequential, iterative, order in which they are cut from the specimen block. A spatial index is created from the cataloged three-dimensional images which is searchable by local content-based image retrieval (LCBIR). The LCBIR query is used to locate, within the three-dimensional index, microscopic structural features, thereby making that portion of the specimen available for further analysis and/or for extraction.