Abstract
Mouse lung models facilitate the study of the pathogenesis of various pulmonary diseases such as infections and inflammatory diseases. The co-registration of ex vivo histological data and pre-excised magnetic resonance imaging (MRI) in preclinical mouse models would allow for determination and validation of imaging signatures for different pathobiologies within the lung. While slice-based co-registration could be used, this approach assumes that (a) slice correspondences between the two different modalities exist, and (b) finding slice correspondences often requires the intervention of an expert and is time consuming. A more practical approach is to first reconstruct the 3D histological volume from individual slices, then perform 3D registration with the MR volume. Before the histological reconstruction, image registration is required to compensate for geometric differences between slices. Pairwise algorithms work by registering pairs of successive slices. However, even if successive slices are registered reasonably well, the propagation of registration errors over slices can yield a distorted volumetric reconstruction significantly different in shape from the shape of the true specimen. Groupwise registration can reduce the error propagation by considering more than two successive images during the registration, but existing algorithms are computationally expensive. In this paper, we present an efficient groupwise registration approach, which yields consistent volumetric reconstruction and yet runs equally fast as pairwise registration. The improvements are based on 1) natural gradient which speeds up the transform warping procedure and 2) efficient optimization of the cost function of our groupwise registration. The strength of the natural gradient technique is that it could help mitigate the impact of the uncertainties of the gradient direction across multiple template slices. Experiments on two mouse lung datasets show that compared to pairwise registration, our groupwise approach runs faster in terms of registration convergence, and yields globally more consistent reconstruction.
| Original language | English |
|---|---|
| Title of host publication | Medical Imaging 2013: Image Processing |
| Volume | 8669 |
| DOIs | |
| Publication status | Published - 2013 |
| Externally published | Yes |
| Event | Medical Imaging 2013: Image Processing - Lake Buena Vista, FL, United States Duration: 10 Feb 2013 → 12 Feb 2013 |
Conference
| Conference | Medical Imaging 2013: Image Processing |
|---|---|
| Country | United States |
| City | Lake Buena Vista, FL |
| Period | 10.2.13 → 12.2.13 |
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ASJC Scopus subject areas
- Atomic and Molecular Physics, and Optics
- Electronic, Optical and Magnetic Materials
- Biomaterials
- Radiology Nuclear Medicine and imaging
Cite this
Mouse lung volume reconstruction from efficient groupwise registration of individual histological slices with natural gradient@case.edu. / Wang, Haibo; Rusu, Mirabela; Golden, Thea; Gow, Andrew; Madabhushi, Anant.
Medical Imaging 2013: Image Processing. Vol. 8669 2013. 866914.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Mouse lung volume reconstruction from efficient groupwise registration of individual histological slices with natural gradient@case.edu
AU - Wang, Haibo
AU - Rusu, Mirabela
AU - Golden, Thea
AU - Gow, Andrew
AU - Madabhushi, Anant
PY - 2013
Y1 - 2013
N2 - Mouse lung models facilitate the study of the pathogenesis of various pulmonary diseases such as infections and inflammatory diseases. The co-registration of ex vivo histological data and pre-excised magnetic resonance imaging (MRI) in preclinical mouse models would allow for determination and validation of imaging signatures for different pathobiologies within the lung. While slice-based co-registration could be used, this approach assumes that (a) slice correspondences between the two different modalities exist, and (b) finding slice correspondences often requires the intervention of an expert and is time consuming. A more practical approach is to first reconstruct the 3D histological volume from individual slices, then perform 3D registration with the MR volume. Before the histological reconstruction, image registration is required to compensate for geometric differences between slices. Pairwise algorithms work by registering pairs of successive slices. However, even if successive slices are registered reasonably well, the propagation of registration errors over slices can yield a distorted volumetric reconstruction significantly different in shape from the shape of the true specimen. Groupwise registration can reduce the error propagation by considering more than two successive images during the registration, but existing algorithms are computationally expensive. In this paper, we present an efficient groupwise registration approach, which yields consistent volumetric reconstruction and yet runs equally fast as pairwise registration. The improvements are based on 1) natural gradient which speeds up the transform warping procedure and 2) efficient optimization of the cost function of our groupwise registration. The strength of the natural gradient technique is that it could help mitigate the impact of the uncertainties of the gradient direction across multiple template slices. Experiments on two mouse lung datasets show that compared to pairwise registration, our groupwise approach runs faster in terms of registration convergence, and yields globally more consistent reconstruction.
AB - Mouse lung models facilitate the study of the pathogenesis of various pulmonary diseases such as infections and inflammatory diseases. The co-registration of ex vivo histological data and pre-excised magnetic resonance imaging (MRI) in preclinical mouse models would allow for determination and validation of imaging signatures for different pathobiologies within the lung. While slice-based co-registration could be used, this approach assumes that (a) slice correspondences between the two different modalities exist, and (b) finding slice correspondences often requires the intervention of an expert and is time consuming. A more practical approach is to first reconstruct the 3D histological volume from individual slices, then perform 3D registration with the MR volume. Before the histological reconstruction, image registration is required to compensate for geometric differences between slices. Pairwise algorithms work by registering pairs of successive slices. However, even if successive slices are registered reasonably well, the propagation of registration errors over slices can yield a distorted volumetric reconstruction significantly different in shape from the shape of the true specimen. Groupwise registration can reduce the error propagation by considering more than two successive images during the registration, but existing algorithms are computationally expensive. In this paper, we present an efficient groupwise registration approach, which yields consistent volumetric reconstruction and yet runs equally fast as pairwise registration. The improvements are based on 1) natural gradient which speeds up the transform warping procedure and 2) efficient optimization of the cost function of our groupwise registration. The strength of the natural gradient technique is that it could help mitigate the impact of the uncertainties of the gradient direction across multiple template slices. Experiments on two mouse lung datasets show that compared to pairwise registration, our groupwise approach runs faster in terms of registration convergence, and yields globally more consistent reconstruction.
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U2 - 10.1117/12.2006860
DO - 10.1117/12.2006860
M3 - Conference contribution
SN - 9780819494436
VL - 8669
BT - Medical Imaging 2013: Image Processing
ER -