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Recently, three-dimensional (3D) object reconstruction using photon counting integral imaging (PCII) based on grayscale elemental images has been reported. In this paper, we present a multispectral PCII system using Bayer elemental images for multispectral visualization of photon limited 3D scenes. We measure the accuracy as well as the speed of demosaicing algorithms to estimate multispectral 3D scenes at low light levels. Experimental results demonstrate that the gradient corrected linear interpolation technique achieves better performance in terms of peak-to-SNR (PSNR) and faster computation.