A method for atlas-based volumetric registration with surface constraints for optical bioluminescence tomography in small animal imaging

Atlases are normalized representations of anatomy that can provide a standard coordinate system for in vivo imaging studies. For Optical Bioluminescence Tomography (OBT) in small animals, the animal's surface topography can be reconstructed from structured light measurements, but internal anatomy is unavailable unless additional CT or MR images are acquired. We present a novel method for estimating the internal organ structure of a mouse by warping a labeled 3D volumetric mouse atlas with the constraint that the surfaces of the two should match. Surface-constrained harmonic maps used for this bijective warping are computed by minimizing the covariant harmonic energy. We demonstrate the application of this warping scheme in OBT, where scattering and absorption coefficients of tissue are functions of the internal anatomy and hence, better estimates of the organ structures can lead to a more accurate forward model resulting in improved source localization. We first estimated the subject's internal geometry using the atlas-based warping scheme. Then the mouse was tessellated and optical properties were assigned based on the estimated organ structure. Bioluminescent sources were simulated, an optical forward model was computed using a finite-element solver, and multispectral data were simulated. We evaluate the accuracy of the forward model computed using the warped atlas against that assuming a homogeneous mouse model. This is done by comparing each model against a 'true' optical forward model where the anatomy of the mouse is assumed known. We also evaluate the impact of anatomical alignment on bioluminescence source localization.