1. A system for imaging a tissue sample comprising: a multiphoton light source that emits excitation light to illuminate a region of interest; a microscope optically coupled to the light source such that light is coupled through a lens of the microscope onto the region of interest within a biological sample at a plurality of focal locations, the 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; a scanner to scan a plurality of focal locations within the region of interest; an imaging device that receives light from the plurality of focal locations within the biological sample 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.