1. A method for imaging a biological specimen, the method comprising: embedding the specimen to set a molecular arrangement therein; thinly slicing the embedded specimen to provide a multitude of thin physical slices, having respective slice thicknesses defined between upper and lower surfaces of the respective slices of the specimen; serially arranging and fixing the physical slices in an array on a microscopy slide, therein forming an array of a multitude of slices; applying a stain to the physical slices; collecting image data from the slices on the slide, the image data including imaged portions of the specimen extending from the upper surface to the lower surface of each slice; using the image data and a known serial arrangement of the physical slices to combine image data from different slices to construct a three-dimensional image of the specimen; and after collecting image data, eluting the slices on the slide and repeating the steps of applying a stain and collecting image data with the eluted slices, wherein using the image data and a known serial arrangement of the slices to combine image data from different slices to construct a three-dimensional image of the specimen includes using image data from the slices before and after elution.