Abstract: A system and method for acquiring images of objects distributed within a specimen affixed to a surface of a slide, the specimen having an uneven height relative to the slide surface using a camera having an objective lens with an optical axis that forms a non-orthogonal angle with the surface of the slide, the method including acquiring a first plurality of images of a first linear portion of the specimen; evaluating a focus of objects within the linear portion of the specimen captured in the first plurality of images; and acquiring a second plurality of images of the first linear portion or of a second linear portion of the specimen different from the first, wherein a height of the objective lens relative to the slide surface is varied during acquisition of the second plurality of images based on the evaluated focus of the objects captured in the first plurality of images.