A digital slide scanning apparatus comprising: a stage configured to support a glass slide comprising a sample; a high-resolution camera; a first lens defining a macro image optical path to the high-resolution camera, wherein the first lens is configured to provide a field of view to the high-resolution camera, and wherein the field of view of the high-resolution camera is wide enough to capture substantially the entire width of the glass slide; a first illumination system optically coupled with the first lens and configured to provide transmission-mode illumination of the field of view from below the glass slide on the stage; a second illumination system optically coupled with the first lens and configured to provide reflection-mode illumination of the field of view at an angle from above the glass slide on the stage, wherein the first illumination system, the second illumination system and the high-resolution camera are aligned such that substantially all of the illumination light from the second illumination system that is reflected from the slide, the sample, and elements of the first illumination system is directed away from the macro image optical path to the high-resolution camera; and at least one processor configured to, while the stage is supporting the glass slide: capture a first macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the first illumination system, capture a second macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the second illumination system, identify image artifacts in the second macro image, and based on the identified image artifacts in the second macro image, correct the first macro image to generate a modified first macro image. a stage configured to support a glass slide comprising a sample; a high-resolution camera; a first lens defining a macro image optical path to the high-resolution camera, wherein the first lens is configured to provide a field of view to the high-resolution camera, and wherein the field of view of the high-resolution camera is wide enough to capture substantially the entire width of the glass slide; a first illumination system optically coupled with the first lens and configured to provide transmission-mode illumination of the field of view from below the glass slide on the stage; a second illumination system optically coupled with the first lens and configured to provide reflection-mode illumination of the field of view at an angle from above the glass slide on the stage, wherein the first illumination system, the second illumination system and the high-resolution camera are aligned such that substantially all of the illumination light from the second illumination system that is reflected from the slide, the sample, and elements of the first illumination system is directed away from the macro image optical path to the high-resolution camera; and at least one processor configured to, while the stage is supporting the glass slide: capture a first macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the first illumination system, capture a second macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the second illumination system, identify image artifacts in the second macro image, and based on the identified image artifacts in the second macro image, correct the first macro image to generate a modified first macro image. capture a first macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the first illumination system, capture a second macro image of the sample on the glass slide using the high-resolution camera while the glass slide is under the first lens while the field of view is illuminated by the second illumination system, identify image artifacts in the second macro image, and based on the identified image artifacts in the second macro image, correct the first macro image to generate a modified first macro image.