The expression levels of rod opsin and glial fibrillary acidic protein (GFAP) capture important structural changes in the retina during injury and recovery. Quantitatively measuring these expression levels in confocal micrographs requires identifying the retinal layer boundaries and spatially corresponding the layers across different images. In this paper, a method to segment the retinal layers using a parametric active contour model is presented. Then spatially aligned expression levels across different images are determined by thresholding the solution to a Dirichlet boundary value problem. Our analysis provides quantitative metrics of retinal restructuring that are needed for improving retinal therapies after injury.