Abstract: The following concerns a method for co-localization of microscopy or histology stains by the assembly of a virtual image from one or more imaging operations. In particular, the method decreases the time required to obtain multiple labeled antigen or protein histology images of a biological sample. The method includes imaging the tissue as it is sliced by a microtome with a knife edge scanning microscope and spatially aligning the samples by the generated images. The spatial alignment of samples enabled by the method allows a panel of different antigen or protein secondary or functional stains to be compared across different sample slices, thereby allowing concurrent secondary stains of tissues and cells.