1. A system for imaging a biological sample comprising: a light source that emits excitation light having a wavelength in a range of 650 nm-1200 nm, the light source being optically coupled with an optical system onto a region of interest positioned below a surface of the biological sample; a scanning device optically coupled to the light source such that light is scanned into the region of interest, the scanning device being connected to a controller that operates the scanning device in response to light 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 wherein each layer includes at least one region of interest to be scanned, the controlled stage being operated in response to selected stage scan parameters; a sectioning device connected to the controller such that relative movement of the controlled stage and the sectioning device in response to control signals is operative to section the biological sample into the plurality of layers; an imaging device that receives light from the biological sample to detect light from within the region of interest that is positioned below a surface of each of the plurality of layers prior to sectioning; and a data processor that is connected to the imaging device and a memory to process the plurality of images and generate stored electronic image data of the region of interest in each of the plurality of layers.