An autofocus system includes an imaging device, a lens system and a focus control actuator that is configured to change a focus position of the imaging device in relation to a stage. The electronic control unit is configured to control the focus control actuator to a plurality of predetermined focus positions, and activate the imaging device to obtain an image at predetermined positions and then apply a spatial filter to the obtained images. This generates a filtered image for the obtained images. The control unit determines a focus score for the filtered images such that the focus score corresponds to a degree of focus in the obtained images. The control unit identifies a best focus position by comparing the focus score of the filtered images, and controls the focus control actuator to the best focus position corresponding to the highest focus score.