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

Zhou, Hang; Li, Shiwei; Li, Anan; Huang, Qing; Xiong, Feng; Li, Ning; Han, Jiacheng; Kang, Huifang; Chen, Yijun; Li, Yun; Lin, Hsuan-Yin; Zhang, Yuhui; Li, Xiaohua; Liu, Xiuli; Gong, Hui; Luo, Qingming; Zeng, Shaoqun; Quan, Tingwei

doi:10.1007/s12021-020-09484-6

Cited by 39 publications

(33 citation statements)

References 44 publications

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“…Quantization of the neuronal image is regarded as the bridge from imaging datasets to knowledge discovery. Many tools ( Peng et al, 2010 ; Wang et al, 2011 ; Quan et al, 2013 ; Feng et al, 2015 ; Zhou et al, 2020 ) have been proposed for this purpose. Due to the complexity and diversity of neuronal images, most of the quantitative tools behave well on some specific datasets.…”

Section: Discussionmentioning

confidence: 99%

“…Due to the complexity of neuronal structure in large-scale, the differences in sample preparation and imaging procedure, the neuronal images become huge, diverse and complicated. A large number of software tools ( Rodriguez et al, 2009 ; Peng et al, 2010 ; Wang et al, 2011 ; Quan et al, 2013 ; Gala et al, 2014 ; Feng et al, 2015 ; Fürth et al, 2018 ) have been developed to quantify these challenging datasets, including soma localization ( Quan et al, 2013 ; Yan et al, 2013 ; Frasconi et al, 2014 ; Ozcan et al, 2015 ; Kayasandik and Labate, 2016 ; He et al, 2018 ) and neurite tracing ( Peng et al, 2010 , 2011 ; Wang et al, 2011 ; Quan et al, 2013 ; Li R. et al, 2019 ; Winnubst et al, 2019 ; Zhou et al, 2020 ). However, most of these tools behave well on some specific datasets and experience the difficulties to deal with various neuronal images ( Meijering et al, 2016 ; Fürth et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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Foreground Estimation in Neuronal Images With a Sparse-Smooth Model for Robust Quantification

et al. 2021

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3D volume imaging has been regarded as a basic tool to explore the organization and function of the neuronal system. Foreground estimation from neuronal image is essential in the quantification and analysis of neuronal image such as soma counting, neurite tracing and neuron reconstruction. However, the complexity of neuronal structure itself and differences in the imaging procedure, including different optical systems and biological labeling methods, result in various and complex neuronal images, which greatly challenge foreground estimation from neuronal image. In this study, we propose a robust sparse-smooth model (RSSM) to separate the foreground and the background of neuronal image. The model combines the different smoothness levels of the foreground and the background, and the sparsity of the foreground. These prior constraints together contribute to the robustness of foreground estimation from a variety of neuronal images. We demonstrate the proposed RSSM method could promote some best available tools to trace neurites or locate somas from neuronal images with their default parameters, and the quantified results are similar or superior to the results that generated from the original images. The proposed method is proved to be robust in the foreground estimation from different neuronal images, and helps to improve the usability of current quantitative tools on various neuronal images with several applications.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Foreground Estimation in Neuronal Images With a Sparse-Smooth Model for Robust Quantification

et al. 2021

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“…Initially, a skeleton of the blood vessels of each data block was developed using an automatic reconstruction method ( Quan et al, 2016 ). Then tracking was refined manually to acquire the final vascular tracking results ( Zhou et al, 2020 ). The tracked skeleton of blood vessels was then analyzed using the shape reconstruction algorithm to obtain the radius information of each skeletal point ( Li et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Dl-3-N-Butylphthalide Promotes Angiogenesis in an Optimized Model of Transient Ischemic Attack in C57BL/6 Mice

Wang

et al. 2021

Front. Pharmacol.

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Transient ischemic attack (TIA) has been widely regarded as a clinical entity. Even though magnetic resonance imaging (MRI) results of TIA patients are negative, potential neurovascular damage might be present, and may account for long-term cognitive impairment. Animal models that simulate human diseases are essential tools for in-depth study of TIA. Previous studies have clarified that Dl-3-N-butylphthalide (NBP) promotes angiogenesis after stroke. However, the effects of NBP on TIA remain unknown. This study aims to develop an optimized TIA model in C57BL/6 mice to explore the microscopic evidence of ischemic injury after TIA, and investigate the therapeutic effects of NBP on TIA. C57BL/6 mice underwent varying durations (7, 8, 9 or 10 min) of middle cerebral artery occlusion (MCAO). Cerebral artery occlusion and reperfusion were assessed by laser speckle contrast imaging. TIA and ischemic stroke were distinguished by neurological testing and MRI examination at 24 h post-operation. Neuronal apoptosis was examined by TUNEL staining. Images of submicron cerebrovascular networks were obtained via micro-optical sectioning tomography. Subsequently, the mice were randomly assigned to a sham-operated group, a vehicle-treated TIA group or an NBP-treated TIA group. Vascular density was determined by immunofluorescent staining and fluorescein isothiocyanate method, and the expression of angiogenic growth factors were detected by western blot analysis. We found that an 8-min or shorter period of ischemia induced neither permanent neurological deficits nor MRI detectable brain lesions in C57BL/6 mice, but histologically caused neuronal apoptosis and cerebral vasculature abnormalities. NBP treatment increased the number of CD31+ microvessels and perfused microvessels after TIA. NBP also up-regulated the expression of VEGF, Ang-1 and Ang-2 and improved the cerebrovascular network. In conclusion, 8 min or shorter cerebral ischemia induced by the suture MCAO method is an appropriate TIA model in C57BL/6 mice, which conforms to the definition of human TIA, but causes microscopic neurovascular impairment. NBP treatment increased the expression of angiogenic growth factors, promoted angiogenesis and improved cerebral microvessels after TIA. Our study provides new insights on the pathogenesis and potential treatments of TIA.

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“…Recent advances in high-resolution light microscopy [1][2][3][4][5][6] , tissue clearing 7-13 , sparse labeling techniques 2,14-17 and full morphology neuron tracing methods [18][19][20][21] now make it feasible to map the mammalian whole-brain at single cell resolution [22][23][24] . Large international efforts such as the BRAIN Initiative Cell Census Network (BICCN) 25 , MouseLight project 19 , Allen Mouse Brain Connectivity Atlas 26 and Mouse Connectome project [27][28][29] , are engaged in cell typing, mapping long-range axonal projection and microcircuit connection analyses.…”

Section: Introductionmentioning

confidence: 99%

Cross-Modality Coherent Registration of Whole Mouse Brains

Peng

et al. 2021

Preprint

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Recent whole brain mapping projects are collecting large-scale 3D images using powerful and informative modalities, such as STPT, fMOST, VISoR, or MRI. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modality image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulted from different sample preparation methods and imaging modalities. We introduced a cross-modality registration method, called mBrainAligner, which uses coherent landmark mapping as well as deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We also built a single cell resolution atlas using the fMOST modality, and used our method to generate whole brain map of 3D full single neuron morphology and neuron cell types.

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

Cited by 39 publications

References 44 publications

Foreground Estimation in Neuronal Images With a Sparse-Smooth Model for Robust Quantification

Foreground Estimation in Neuronal Images With a Sparse-Smooth Model for Robust Quantification

Dl-3-N-Butylphthalide Promotes Angiogenesis in an Optimized Model of Transient Ischemic Attack in C57BL/6 Mice

Cross-Modality Coherent Registration of Whole Mouse Brains

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