Presented herein are systems and methods for tomographic imaging of a region of interest in a subject using short-wave infrared light to provide for accurate reconstruction of absorption maps within the region of interest. The reconstructed absorption maps are representations of the spatial variation in tissue absorption within the region of interest. The reconstructed absorption maps can themselves be used to analyze anatomical properties and biological processes within the region of interest, and/or be used as input information about anatomical properties in order to facilitate data processing used to obtain images of the region of interest via other imaging modalities. For example, the reconstructed absorption maps may be incorporated into forward models that are used in tomographic reconstruction processing in fluorescence and other contrast-based tomographic imaging modalities. Incorporating reconstructed absorption maps into other tomographic reconstruction processing algorithms in this manner improves the accuracy of the resultant reconstructions.