Abstract: The present invention provides a method to clarify and contrast stain intact biological tissue samples for microscopic analysis. Biological specimens are prepared for visual analysis by depigmenting specimen, staining the specimen non-specifically with fluorescent dye, and equilibrating the depigmented, non-specifically stained specimen in a clearing solution, wherein the refractive index of the clearing solution approximates that of the specimen. Visual analysis of the specimen can include, for example, determination of distribution, quantity and size of foreign material in the biological specimen. Also, the morphology of tissue surrounding foreign material can be assessed.