1. A method for registering a digital image with a reference, comprising: (a) accessing a reference image and a registration image, the registration image being segmented into at least 2 hierarchical levels; (b) receiving a user selection of a segmentation level; (c) displaying at least one segmented element of the reference image in accordance with the selected segmentation level; (d) receiving a user selection of a segmented element at the selected level; (e) receiving user input for alteration of the registration image by modification of the selected element; and (f) storing the altered registration image including the modified selected element.