A microscopy imaging system and method acquires digital images of a microscope specimen using a computer-controlled microscope and digital camera. A specimen on a microscope slide is placed within the microscope. The method comprises the steps of determining whether an area of the specimen contained within a microscope field of view has a thickness, and, if so, capturing digital images of the field of view at a plurality of depths of focus. In a preferred embodiment, the step of determining whether an area of the specimen contained within a microscope field of view has a thickness comprises the steps of: capturing a digital image of the field of view at two or more depths of focus; comparing the captured digital images, and determining that the specimen has a thickness, if the comparing step finds that the images are different. The method may be implemented in the form of a computer program.