title: An automated three-dimensional detection and segmentation method for touching cells by integrating concave points clustering and random walker algorithm.
abstract: Characterizing cytoarchitecture is crucial for understanding brain functions and neural diseases. In neuroanatomy, it is an important task to accurately extract cell populations' centroids and contours. Recent advances have permitted imaging at single cell resolution for an entire mouse brain using the Nissl staining method. However, it is difficult to precisely segment numerous cells, especially those cells touching each other. As presented herein, we have developed an automated three-dimensional detection and segmentation method applied to the Nissl staining data, with the following two key steps: 1) concave points clustering to determine the seed points of touching cells; and 2) random walker segmentation to obtain cell contours. Also, we have evaluated the performance of our proposed method with several mouse brain datasets, which were captured with the micro-optical sectioning tomography imaging system, and the datasets include closely touching cells. Comparing with traditional detection and segmentation methods, our approach shows promising detection accuracy and high robustness.
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: He
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Meng
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 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, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Shangbin
authors.initials: S
authors.lastname: Chen
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Wenxiang
authors.initials: W
authors.lastname: Ding
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, 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, Huazhong University of Science and Technology-Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei, China; MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, China.
authors.forename: Anan
authors.initials: A
authors.lastname: Li
mesh_terms: D000465:Algorithms; D000818:Animals; D001331:Automation; D001921:Brain / Q000166:cytology*; D016000:Cluster Analysis; D021621:Imaging, Three-Dimensional / Q000379:methods*; D051379:Mice; D008810:Mice, Inbred C57BL; D015203:Reproducibility of Results
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