Method and system for imaging tissue, including (i) causing a macroscopic image of a tissue surface to be displayed on a visual display; (ii) receiving a selection of at least one portion of the macroscopic image; (iii) causing a plurality of confocal images captured by a confocal imager at different depths in a portion of the tissue to be displayed; (iv) receiving a selection of at least one target depth image; and (v) for each selected target depth image, instructing the confocal imager to capture a plurality of additional images at different locations and at a common depth with the target depth image. A system for imaging tissue having a macroscopic display module; a first selection module; a confocal display module; a second selection module; and an instruction module for instructing a confocal imager to capture a plurality of images at different locations over a selected region of the tissue.