title: Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model.
abstract: Brain surface profile is essential for brain studies, including registration, segmentation of brain structure and drawing neuronal circuits. Recent advances in high-throughput imaging techniques enable imaging whole mouse brain at micron spatial resolution and provide a basis for more fine quantitative studies in neuroscience. However, reconstructing micron resolution brain surface from newly produced neuronal dataset still faces challenges. Most current methods apply global analysis, which are neither applicable to a large imaging dataset nor to a brain surface with an inhomogeneous signal intensity. Here, we proposed a resampling-based variational model for this purpose. In this model, the movement directions of the initial boundary elements are fixed, the final positions of the initial boundary elements that form the brain surface are determined by the local signal intensity. These features assure an effective reconstruction of the brain surface from a new brain dataset. Compared with conventional typical methods, such as level set based method and active contour method, our method significantly increases the recall and precision rates above 97% and is approximately hundreds-fold faster. We demonstrated a fast reconstruction at micron level of the whole brain surface from a large dataset of hundreds of GB in size within 6 hours.
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.|School of Mathematics and Statistics, Hubei University of Education, Wuhan 430205, China.
authors.forename: Tingwei
authors.initials: T
authors.lastname: Quan
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Li
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Qingming
authors.initials: Q
authors.lastname: Luo
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Gong
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology- Wuhan National Laboratory for Optoelectronics, Wuhan 430074, China.|Key Laboratory of Biomedical Photonics of Ministry of Education, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Shaoqun
authors.initials: S
authors.lastname: Zeng
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D016208:Databases, Factual; D021621:Imaging, Three-Dimensional; D051379:Mice