Disclosed herein, in certain embodiments, is a method of treating breast cancer characterized by the amplification of HER2 genes in a subject in need thereof, comprising: (a) isolating a tissue sample comprised of a plurality of breast tumor cells; (b) isolating a first section from said tissue sample; (c) isolating a second section from an adjacent portion of said tissue sample; (d) contacting the first section with a first stain; (e) contacting the second section with a probe; (f) imaging the first section following contact with the stain to produce a first image; (g) analyzing the first image for abnormal microscopic features; (h) identifying areas of interest in the first image that display abnormal microscopic features; (i) electronically annotating the first image to identify the areas of interest; (j) imaging the second section following contact with the probe; (k) aligning the first image and the second image; and (l) analyzing areas of interest in the second image that correspond to an area of interest identified in the first image; wherein the subject is administered an anti-HER2 antibody if HER2 is amplified or providing an alternative treatment if HER2 is not amplified.