An accurate 3D shape context based non-rigid registration method for mouse whole-body skeleton registration

Xiao, Di; Zahra, David; Bourgeat, Pierrick; Berghofer, Paula; Tamayo, Oscar Acosta; Wimberley, Catriona; Grégoire, Marie Claude; Salvado, Olivier

doi:10.1117/12.877915

Cited by 2 publications

(2 citation statements)

References 14 publications

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“…Khmelinskii et al proposed some articulated skeleton atlases which are better at whole-body posture alignment [57]. Xiao et al also developed a shape-context based non-rigid registration method which achieved posture alignment by piecewisely aligning the mouse skeleton [58], [59]. It could be a promising improvement if the statistical trunk atlas could be combined with articulated skeleton atlas or piecewise skeleton registration approach, to offer wider usability and better accuracy for mouse micro-CT image registration.…”

Section: Discussionmentioning

confidence: 99%

Estimation of Mouse Organ Locations Through Registration of a Statistical Mouse Atlas With Micro-CT Images

Wang

Stout²,

Chatziioannou³

2012

IEEE Trans. Med. Imaging

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Micro-CT is widely used in preclinical studies of small animals. Due to the low soft-tissue contrast in typical studies, segmentation of soft tissue organs from noncontrast enhanced micro-CT images is a challenging problem. Here, we propose an atlas-based approach for estimating the major organs in mouse micro-CT images. A statistical atlas of major trunk organs was constructed based on 45 training subjects. The statistical shape model technique was used to include inter-subject anatomical variations. The shape correlations between different organs were described using a conditional Gaussian model. For registration, first the high-contrast organs in micro-CT images were registered by fitting the statistical shape model, while the low-contrast organs were subsequently estimated from the high-contrast organs using the conditional Gaussian model. The registration accuracy was validated based on 23 noncontrast-enhanced and 45 contrast-enhanced micro-CT images. Three different accuracy metrics (Dice coefficient, organ volume recovery coefficient, and surface distance) were used for evaluation. The Dice coefficients vary from 0.45 ± 0.18 for the spleen to 0.90 ± 0.02 for the lungs, the volume recovery coefficients vary from for the liver to 1.30 ± 0.75 for the spleen, the surface distances vary from 0.18 ± 0.01 mm for the lungs to 0.72 ± 0.42 mm for the spleen. The registration accuracy of the statistical atlas was compared with two publicly available single-subject mouse atlases, i.e., the MOBY phantom and the DIGIMOUSE atlas, and the results proved that the statistical atlas is more accurate than the single atlases. To evaluate the influence of the training subject size, different numbers of training subjects were used for atlas construction and registration. The results showed an improvement of the registration accuracy when more training subjects were used for the atlas construction. The statistical atlas-based registration was also compared with the thin-plate spline based deformable registration, commonly used in mouse atlas registration. The results revealed that the statistical atlas has the advantage of improving the estimation of low-contrast organs.

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Section: Discussionmentioning

confidence: 99%

Estimation of Mouse Organ Locations Through Registration of a Statistical Mouse Atlas With Micro-CT Images

Wang

Stout²,

Chatziioannou³

2012

IEEE Trans. Med. Imaging

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“…Only few others have worked on personalization of full body models [20] [21]. Several approaches have been presented using mouse image data [22] [23].…”

Section: Modeling Techniques For Realistic Computational Human Phantomentioning

confidence: 99%

Advances in Computational Human Phantoms and Their Applications in Biomedical Engineering—A Topical Review

Kainz

Neufeld

Bolch

et al. 2019

IEEE Trans. Radiat. Plasma Med. Sci.

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Over the past decades, significant improvements have been made in the field of computational human phantoms (CHPs) and their applications in biomedical engineering. Their sophistication has dramatically increased. The very first CHPs were composed of simple geometric volumes, e.g., cylinders and spheres, while current CHPs have a high resolution, cover a substantial range of the patient population, have high anatomical accuracy, are poseable, morphable, and are augmented with various details to perform functionalized computations. Advances in imaging techniques and semi-automated segmentation tools allow fast and personalized development of CHPs. These advances open the door to quickly develop personalized CHPs, inherently including the disease of the patient. Because many of these CHPs are increasingly providing data for regulatory submissions of various medical devices, the validity, anatomical accuracy, and availability to cover the entire patient population is of utmost importance. The article is organized into two main sections: the first section reviews the different modeling techniques used to create CHPs, whereas the second section discusses various applications of CHPs in biomedical engineering. Each topic gives an overview, a brief history, recent developments, and an outlook into the future.

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An accurate 3D shape context based non-rigid registration method for mouse whole-body skeleton registration

Cited by 2 publications

References 14 publications

Estimation of Mouse Organ Locations Through Registration of a Statistical Mouse Atlas With Micro-CT Images

Estimation of Mouse Organ Locations Through Registration of a Statistical Mouse Atlas With Micro-CT Images

Advances in Computational Human Phantoms and Their Applications in Biomedical Engineering—A Topical Review

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