An autofocus microscope, comprising: at least one image capture device configured to capture images of a sample located on a stage, wherein the at least one image capture device includes a lens; a focus actuator configured to adjust a distance between the sample and a focal plane of the at least one image capture device; an illumination assembly including a plurality of light sources to illuminate the sample from any of a plurality of illumination angles; and at least one controller programmed to: cause the illumination assembly to illuminate the sample from a first illumination angle; acquire, from the at least one image capture device, a first image of the sample illuminated from the first illumination angle; cause the illumination assembly to illuminate the sample from a second illumination angle different from the first illumination angle; acquire, from the at least one image capture device, a second image of the sample illuminated from the second illumination angle; determine an amount of shift between one or more image features present in the first image of the sample and a corresponding one or more image features present in the second image of the sample; and where the amount of determined shift is non-zero, cause the focus actuator to change the distance between the sample and the focal plane. at least one image capture device configured to capture images of a sample located on a stage, wherein the at least one image capture device includes a lens; a focus actuator configured to adjust a distance between the sample and a focal plane of the at least one image capture device; an illumination assembly including a plurality of light sources to illuminate the sample from any of a plurality of illumination angles; and at least one controller programmed to: cause the illumination assembly to illuminate the sample from a first illumination angle; acquire, from the at least one image capture device, a first image of the sample illuminated from the first illumination angle; cause the illumination assembly to illuminate the sample from a second illumination angle different from the first illumination angle; acquire, from the at least one image capture device, a second image of the sample illuminated from the second illumination angle; determine an amount of shift between one or more image features present in the first image of the sample and a corresponding one or more image features present in the second image of the sample; and where the amount of determined shift is non-zero, cause the focus actuator to change the distance between the sample and the focal plane. cause the illumination assembly to illuminate the sample from a first illumination angle; acquire, from the at least one image capture device, a first image of the sample illuminated from the first illumination angle; cause the illumination assembly to illuminate the sample from a second illumination angle different from the first illumination angle; acquire, from the at least one image capture device, a second image of the sample illuminated from the second illumination angle; determine an amount of shift between one or more image features present in the first image of the sample and a corresponding one or more image features present in the second image of the sample; and where the amount of determined shift is non-zero, cause the focus actuator to change the distance between the sample and the focal plane.