System for combined three-dimensional morphological and molecular analysis of thick tissue specimens

We present a new system for simultaneous morphological and molecular analysis of thick tissue samples. The system is composed of a computer-assisted microscope and a JAVA-based image display, analysis, and visualization program that allows acquisition, annotation, meaningful storage, three-dimensional reconstruction, and analysis of structures of interest in thick sectioned tissue specimens. We describe the system in detail and illustrate its use by imaging, reconstructing, and analyzing two complete tissue blocks that were differently processed and stained. One block was obtained from a ductal carcinoma in situ (DCIS) lumpectomy specimen and stained alternatively with Hematoxilyn and Eosin (H&E), and with a counterstain and fluorescence in situ hybridization (FISH) to the ERB-B2 gene. The second block contained a fully sectioned mammary gland of a mouse, stained for histology with H&E. We show how the system greatly reduces the amount of interaction required for the acquisition and analysis and is, therefore, suitable for studies that require morphologically driven, wide-scale (e.g., whole gland) analysis of complex tissue samples or cultures.