A method for quantifying caries, executed at least in part on data processing hardware, the method comprising generating a digital image of a tooth, the image comprising intensity values for a region of pixels corresponding to the tooth, gum, and background; extracting a lesion area from sound tooth regions by identifying tooth regions, extracting suspicious lesion areas, and removing false positives; identifying an adjacent sound region that is adjacent to the extracted lesion area; reconstructing intensity values for tooth tissue within the lesion area according to values in the adjacent sound region; and quantifying the condition of the caries using the reconstructed intensity values and intensity values from the lesion area.