1. A microscopy system, comprising: a surgical microscope having a first field of view configured to acquire images of a sample within the first field of view when the sample is exposed to infrared radiation; a confocal endomicroscope having a second field of view configured to acquire images of the sample within the second field of view; a navigation sub-system configured to monitor a location of the second microscope; and a display sub-system in communication with the first microscope, the second microscope and the navigation sub-system, wherein: the surgical microscope has a field of view having an area of 1 cm 2 or more; the area of the field of view of the confocal endomicroscope is 1 mm 2 or less; and during operation of the microscopy system the display sub-system displays information about a relative location of one or more images acquired using the confocal microscope relative to the field of view of the surgical microscope based on information from the navigation sub-system.