1. A system for imaging a tissue sample comprising: a light source for producing excitation light and providing at least two photons onto the region of interest; a scanning microscope optically coupled to the light source such that light is coupled through a lens of the scanning microscope onto the region of interest within a biological sample, the scanning microscope being operated in response to microscope scan parameters; a controlled stage to support the biological sample to be sectioned into a plurality of layers from the biological sample after imaging of each layer in sequence, the controlled stage being operated in response to selected stage scan parameters; an x-y scanner to scan the region of interest; an image sensor that receives light from the biological sample through the lens to detect fluorescence images of the region of interest within each of the plurality of layers; and a data processor that processes the plurality of images to produce stored electronic image data of the region of interest, the data processor being programmed to control imaging resolution of the plurality of layers of the biological sample.