A method of generating a composite image from multiple images captured for a subject is disclosed. In some embodiments, the method may include receiving, via an image capturing device, a plurality of sets of images of at least a portion of a subject. The images within a set of images may be captured at a plurality of vertical positions with respect to an associated fixed section of a horizontal plane. The method may further include generating a plurality of focus-stacked images corresponding to the plurality of sets of images, for example, by combining the images in the associated set of images. The method may further include aligning the plurality of focus-stacked images in the horizontal plane based on a horizontal coordinate transformation model to generate a composite image representing the subject.