title: A Novel Mouse Segmentation Method Based on Dynamic Contrast Enhanced Micro-CT Images.
abstract: With the development of hybrid imaging scanners, micro-CT is widely used in locating abnormalities, studying drug metabolism, and providing structural priors to aid image reconstruction in functional imaging. Due to the low contrast of soft tissues, segmentation of soft tissue organs from mouse micro-CT images is a challenging problem. In this paper, we propose a mouse segmentation scheme based on dynamic contrast enhanced micro-CT images. With a homemade fast scanning micro-CT scanner, dynamic contrast enhanced images were acquired before and after injection of non-ionic iodinated contrast agents (iohexol). Then the feature vector of each voxel was extracted from the signal intensities at different time points. Based on these features, the heart, liver, spleen, lung, and kidney could be classified into different categories and extracted from separate categories by morphological processing. The bone structure was segmented using a thresholding method. Our method was validated on seven BALB/c mice using two different classifiers: a support vector machine classifier with a radial basis function kernel and a random forest classifier. The results were compared to manual segmentation, and the performance was assessed using the Dice similarity coefficient, false positive ratio, and false negative ratio. The results showed high accuracy with the Dice similarity coefficient ranging from 0.709 ± 0.078 for the spleen to 0.929 ± 0.006 for the kidney.
authors.affiliation: Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Dongmei
authors.initials: D
authors.lastname: Yan
authors.affiliation: Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Luo
authors.affiliation: Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Xiaoquan
authors.initials: X
authors.lastname: Yang
mesh_terms: D000818:Animals; D003287:Contrast Media; D005260:Female; D007091:Image Processing, Computer-Assisted; D051379:Mice; D011856:Radiographic Image Enhancement; D015203:Reproducibility of Results; D060388:Support Vector Machine; D036542:Tomography, Spiral Computed; D055114:X-Ray Microtomography / Q000379:methods*
chemical_list: D003287:Contrast Media