Macroscopic imaging data, such as from a CT, MR, PET, or SPECT scanner, is obtained. Microscopic imaging data of at least a portion of the same tissue is obtained. To align the microscopic imaging data with the macroscopic imaging data, intermediate data is also obtained. For example, photographic data is acquired at an intermediary stage of a process of preparing tissue for microscopic scan. The macroscopic and microscopic data are registered to the intermediary photographic data. Once registered to the intermediary data, the spatial relationship between the macroscopic and microscopic data is known and may be used for imaging or quantification.