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; 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; and aligning the plurality of images 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.