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 L2 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 6197-6214 |
| Number of pages | 18 |
| Journal | Physics in Medicine and Biology |
| Volume | 55 |
| Issue number | 20 |
| DOIs | |
| State | Published - Oct 21 2010 |
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ASJC Scopus subject areas
- Radiology Nuclear Medicine and imaging
- Radiological and Ultrasound Technology
Cite this
DigiWarp : A method for deformable mouse atlas warping to surface topographic data. / Joshi, Anand A.; Chaudhari, Abhijit; Li, Changqing; Dutta, Joyita; Cherry, Simon R; Shattuck, David W.; Toga, Arthur W.; Leahy, Richard M.
In: Physics in Medicine and Biology, Vol. 55, No. 20, 21.10.2010, p. 6197-6214.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - DigiWarp
T2 - A method for deformable mouse atlas warping to surface topographic data
AU - Joshi, Anand A.
AU - Chaudhari, Abhijit
AU - Li, Changqing
AU - Dutta, Joyita
AU - Cherry, Simon R
AU - Shattuck, David W.
AU - Toga, Arthur W.
AU - Leahy, Richard M.
PY - 2010/10/21
Y1 - 2010/10/21
N2 - 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 L2 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.
AB - 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 L2 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.
UR - http://www.scopus.com/inward/record.url?scp=78149335624&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=78149335624&partnerID=8YFLogxK
U2 - 10.1088/0031-9155/55/20/011
DO - 10.1088/0031-9155/55/20/011
M3 - Article
C2 - 20885019
AN - SCOPUS:78149335624
VL - 55
SP - 6197
EP - 6214
JO - Physics in Medicine and Biology
JF - Physics in Medicine and Biology
SN - 0031-9155
IS - 20
ER -