Abstract
Systems and methods according to embodiments of the present invention facilitate imaging and sectioning of a thick specimen that allow for 3D image reconstruction. An example embodiment employs a laser scanning microscope and sectioning device, where the specimen, and optionally, the sectioning device are affixed to respective programmable stages. The stage normally used for aligning the specimen with the microscope objective is used as an integral component for sectioning the specimen. A specimen is imaged such that the imaging depth is less than the sectioning depth to produce overlap in contiguous sets of images; both acts are repeated until the imaging is completed. A substantially or completely seamless 3D image of the specimen is reconstructed by collecting sets of 2D images and aligning imaged features of structures in overlapping images or portions thereof. Specimen may be from a human, animal, or plant.