1. A computer-implemented method for registering images, comprising: acquiring a first set of images of a sample on a slide positioned on a stage, wherein each image is taken at a different field of view; generating a global transformation matrix by registering the images of the first set to one another to form a composite image; acquiring a subset of images of the sample on the slide after the slide is removed from and replaced on the stage, wherein the subset of images is less than the number of images in the first set; registering each image of the subset with a corresponding image of the first set of images to determine a translation, a rotation, and a scale factor; acquiring a second set of images of the sample at the same respective fields of view used to acquire the first set of images; rotating and scaling each image of the second set of images using the rotation and the scale factor determined for the subset of images; and registering the rotated and scaled images of the second set to the corresponding images of the first set.