title: DigiWarp: a method for deformable mouse atlas warping to surface topographic data.
abstract: For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L(2) pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.
authors.affiliation: Laboratory of Neuro Imaging, UCLA School of Medicine, Los Angeles, CA 90095, USA. anand.joshi@loni.ucla.edu
authors.forename: Anand A
authors.initials: AA
authors.lastname: Joshi
authors.forename: Abhijit J
authors.initials: AJ
authors.lastname: Chaudhari
authors.forename: Changqing
authors.initials: C
authors.lastname: Li
authors.forename: Joyita
authors.initials: J
authors.lastname: Dutta
authors.forename: Simon R
authors.initials: SR
authors.lastname: Cherry
authors.forename: David W
authors.initials: DW
authors.lastname: Shattuck
authors.forename: Arthur W
authors.initials: AW
authors.lastname: Toga
authors.forename: Richard M
authors.initials: RM
authors.lastname: Leahy
mesh_terms: D000716:Anatomy, Artistic; D000818:Animals; D001271:Atlases as Topic; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging; D008297:Male; D051379:Mice; D011187:Posture; D011786:Quality Control; D012886:Skull / Q000000981:diagnostic imaging; D013499:Surface Properties; D055114:X-Ray Microtomography