A method and system for generating material decomposition images from plural-energy x-ray based imaging, the method comprising: modelling spatial relationships and spectral relationships among the plurality of images by learning features from the plurality of images in combination and one or more of the plurality of images individually with a deep learning neural network; generating one or more basis material images employing the spatial relationships and the spectral relationships; and generating one or more material specific or material decomposition images from the basis material images. The neural network has an encoder-decoder structure and includes a plurality of encoder branches; each of one or more of the plurality of encoder branches encodes two or more images of the plurality of images in combination; and each of one or more of the plurality of encoder branches encodes a respective individual image of the plurality of images.