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GTree: an Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population

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Abstract

Recent technological advancements have facilitated the imaging of specific neuronal populations at the single-axon level across the mouse brain. However, the digital reconstruction of neurons from a large dataset requires months of manual effort using the currently available software. In this study, we develop an open-source software called GTree (global tree reconstruction system) to overcome the above-mentioned problem. GTree offers an error-screening system for the fast localization of submicron errors in densely packed neurites and along with long projections across the whole brain, thus achieving reconstruction close to the ground truth. Moreover, GTree integrates a series of our previous algorithms to significantly reduce manual interference and achieve high-level automation. When applied to an entire mouse brain dataset, GTree is shown to be five times faster than widely used commercial software. Finally, using GTree, we demonstrate the reconstruction of 35 long-projection neurons around one injection site of a mouse brain. GTree is also applicable to large datasets (10 TB or higher) from various light microscopes.

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Acknowledgements

We thank Drs. Yunyun Han, Pavel Osten and Arun Narasimhan for providing testing datasets. We also thank the Optical Bioimaging Core Facility of WNLO-HUST for the support in data acquisition, and the Analytical and Testing Center of HUST for spectral measurements. We thank the help from Li Jing and Su Lei in the design of the software tool. We thank Li Shoucheng, Li Yingfei, Zhao Ming, Wang Hao, Chen Cheng, Zhao Yu, Huang Lu, Kong Xinyi, Li Hanying, Zhou Wuxian, Tian Tian, He Sijie, Wang Danni and Gong Yaqiong for their efforts in testing the software and in tracing neurons.

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  1. Hang Zhou, Shiwei Li and Anan Li equally contributed to this work.

Authors and Affiliations

  1. Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong, University of Science and Technology, Hubei, Wuhan, 430074, China

    Hang Zhou, Shiwei Li, Anan Li, Qing Huang, Feng Xiong, Ning Li, Jiacheng Han, Hongtao Kang, Yijun Chen, Yun Li, Huimin Lin, Yu-Hui Zhang, Xiaohua Lv, Xiuli Liu, Hui Gong, Qingming Luo, Shaoqun Zeng & Tingwei Quan

  2. MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Hubei, Wuhan, 430074, China

    Hang Zhou, Shiwei Li, Anan Li, Qing Huang, Feng Xiong, Ning Li, Jiacheng Han, Hongtao Kang, Yijun Chen, Yun Li, Huimin Lin, Yu-Hui Zhang, Xiaohua Lv, Xiuli Liu, Hui Gong, Qingming Luo, Shaoqun Zeng & Tingwei Quan

  3. School of Mathematics and Economics, Hubei University of Education, 430205, Wuhan, Hubei, China

    Tingwei Quan

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  1. Hang Zhou
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Zhou, H., Li, S., Li, A. et al. GTree: an Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population. Neuroinform 19, 305–317 (2021). https://doi.org/10.1007/s12021-020-09484-6

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