A method of detecting clouds in an acquired aerial image includes determining a region of a reference aerial image corresponding to a region of an acquired aerial image. For each of a plurality of locations over the region of the acquired aerial image and corresponding to a plurality of locations over the region of the reference aerial image, the mutual information of one or more variables associated with the location in the acquired aerial image and one or more variables associated with the corresponding location in the reference aerial image is calculated. Using the mutual information calculated for each of the plurality of locations over the region of the acquired aerial image, it is determined when the acquired aerial image displays a cloud at the location in the region of the acquired aerial image.