title: Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling.
abstract: Digital reconstruction of three-dimensional (3D) neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM) challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST) system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Ming
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Anan
authors.initials: A
authors.lastname: Li
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Jingpeng
authors.initials: J
authors.lastname: Wu
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Yan
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 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, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, 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, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Shaoqun
authors.initials: S
authors.lastname: Zeng
authors.affiliation: Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology - Wuhan National Laboratory for Optoelectronics, Wuhan, China ; MoE Key Laboratory of Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Liu
mesh_terms: D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008027:Light; D051379:Mice; D008853:Microscopy / Q000379:methods*; D009434:Neural Pathways / Q000033:anatomy & histology*; D009474:Neurons / Q000166:cytology*; D012984:Software