The Sedeen viewer already provides the functionality needed to manually align multiple images. It is possible to create transparent overlays and to drag and rotate one image relative to another in real time. This can be done at any magnification and it is possible to refine the alignment of 2 images across multiple scales. The rigid transformations are then saved automatically and can be reapplied when the image is reloaded. The plugin and viewer framework will be further extended to include functions that allow transformations calculated from the image data to be applied to regions of interest. This will allow regions or labels defined in one reference frame to be projected onto another co-registered reference frame. Functions to store transformations, to apply deformations to images and to store the reformatted results will also be added to the plugin framework. We will integrate additional functionality developed in the Martel lab that will allow the automatic registration of histology sections to other 2D images including grossing images, blockface images and radiological images.