1. A method of calibrating an imaging system for analyzing a plurality of molecular species in a sample, said method comprising: acquiring a plurality of images of the sample with an image acquisition device at a plurality of different wavelengths by scanning the image at a plurality of different wavelengths, each scan producing a displacement factor in a first and second direction, the displacement factor defining the difference in displacement between a region of interest of an image taken with respect to one wavelength and a region of interest of an image taken with respect to a different wavelength; comparing a region of interest associated with at least one of the images acquired at one respective wavelength to a region of interest associated with at least one of the images acquired at a different wavelength to determine the displacement factors among the images; and aligning the plurality of images using the displacement factors such that the region of interest associated with at least one of the images acquired at one respective wavelength corresponds to the region of interest associated with the at least one of the images acquired at the different wavelength.