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Boundary elements provide an attractive method for image-guided multi-modality near infrared spectroscopy in three dimensions using only surface discretization. This method operates under the assumption that the underlying tissue contains piece-wise constant domains whose boundaries are known a priori from an alternative imaging modality such as MRI or microCT. This significantly simplifies the meshing process providing both speed-up and accuracy in the forward solution. Challenges with this method are in solving dense matrices, and working with complex heterogeneous domains. Solutions to these problems are presented here, with applications in breast cancer imaging and small - animal molecular imaging.