Literature DB >> 26595210

NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites.

Tingwei Quan1,2,3,4, Hang Zhou1,2,3, Jing Li1,2,3, Shiwei Li1,2,3, Anan Li1,2,3, Yuxin Li1,2,3, Xiaohua Lv1,2,3, Qingming Luo1,2,3, Hui Gong1,2,3, Shaoqun Zeng1,2,3.   

Abstract

The reconstruction of neuronal populations, a key step in understanding neural circuits, remains a challenge in the presence of densely packed neurites. Here we achieved automatic reconstruction of neuronal populations by partially mimicking human strategies to separate individual neurons. For populations not resolvable by other methods, we obtained recall and precision rates of approximately 80%. We also demonstrate the reconstruction of 960 neurons within 3 h.

Entities:  

Mesh:

Year:  2015        PMID: 26595210     DOI: 10.1038/nmeth.3662

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  25 in total

1.  The DIADEM metric: comparing multiple reconstructions of the same neuron.

Authors:  Todd A Gillette; Kerry M Brown; Giorgio A Ascoli
Journal:  Neuroinformatics       Date:  2011-09

Review 2.  The big and the small: challenges of imaging the brain's circuits.

Authors:  Jeff W Lichtman; Winfried Denk
Journal:  Science       Date:  2011-11-04       Impact factor: 47.728

3.  Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain.

Authors:  Anan Li; Hui Gong; Bin Zhang; Qingdi Wang; Cheng Yan; Jingpeng Wu; Qian Liu; Shaoqun Zeng; Qingming Luo
Journal:  Science       Date:  2010-11-04       Impact factor: 47.728

4.  New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales.

Authors:  S L Wearne; A Rodriguez; D B Ehlenberger; A B Rocher; S C Henderson; P R Hof
Journal:  Neuroscience       Date:  2005       Impact factor: 3.590

5.  A broadly applicable 3-D neuron tracing method based on open-curve snake.

Authors:  Yu Wang; Arunachalam Narayanaswamy; Chia-Ling Tsai; Badrinath Roysam
Journal:  Neuroinformatics       Date:  2011-09

6.  Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors.

Authors:  Engin Türetken; Germán González; Christian Blum; Pascal Fua
Journal:  Neuroinformatics       Date:  2011-09

Review 7.  Computational methods and challenges for large-scale circuit mapping.

Authors:  Moritz Helmstaedter; Partha P Mitra
Journal:  Curr Opin Neurobiol       Date:  2012-01-03       Impact factor: 6.627

Review 8.  The DIADEM data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions.

Authors:  Kerry M Brown; Germán Barrionuevo; Alison J Canty; Vincenzo De Paola; Judith A Hirsch; Gregory S X E Jefferis; Ju Lu; Marjolein Snippe; Izumi Sugihara; Giorgio A Ascoli
Journal:  Neuroinformatics       Date:  2011-09

9.  Active learning of neuron morphology for accurate automated tracing of neurites.

Authors:  Rohan Gala; Julio Chapeton; Jayant Jitesh; Chintan Bhavsar; Armen Stepanyants
Journal:  Front Neuroanat       Date:  2014-05-19       Impact factor: 3.856

10.  Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging.

Authors:  Hanqing Xiong; Zhenqiao Zhou; Mingqiang Zhu; Xiaohua Lv; Anan Li; Shiwei Li; Longhui Li; Tao Yang; Siming Wang; Zhongqin Yang; Tonghui Xu; Qingming Luo; Hui Gong; Shaoqun Zeng
Journal:  Nat Commun       Date:  2014-06-02       Impact factor: 14.919

View more
  32 in total

1.  Brain-Wide Shape Reconstruction of a Traced Neuron Using the Convex Image Segmentation Method.

Authors:  Shiwei Li; Tingwei Quan; Hang Zhou; Qing Huang; Tao Guan; Yijun Chen; Cheng Xu; Hongtao Kang; Anan Li; Ling Fu; Qingming Luo; Hui Gong; Shaoqun Zeng
Journal:  Neuroinformatics       Date:  2020-04

2.  Chemical reactivation of resin-embedded pHuji adds red for simultaneous two-color imaging with EGFP.

Authors:  Wenyan Guo; Xiuli Liu; Yurong Liu; Yadong Gang; Xiaobin He; Yao Jia; Fangfang Yin; Pei Li; Fei Huang; Hongfu Zhou; Xiaojun Wang; Hui Gong; Qingming Luo; Fuqiang Xu; Shaoqun Zeng
Journal:  Biomed Opt Express       Date:  2017-06-15       Impact factor: 3.732

3.  SparseTracer: the Reconstruction of Discontinuous Neuronal Morphology in Noisy Images.

Authors:  Shiwei Li; Hang Zhou; Tingwei Quan; Jing Li; Yuxin Li; Anan Li; Qingming Luo; Hui Gong; Shaoqun Zeng
Journal:  Neuroinformatics       Date:  2017-04

4.  An interactive framework for whole-brain maps at cellular resolution.

Authors:  Daniel Fürth; Thomas Vaissière; Ourania Tzortzi; Yang Xuan; Antje Märtin; Iakovos Lazaridis; Giada Spigolon; Gilberto Fisone; Raju Tomer; Karl Deisseroth; Marie Carlén; Courtney A Miller; Gavin Rumbaugh; Konstantinos Meletis
Journal:  Nat Neurosci       Date:  2017-12-04       Impact factor: 24.884

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

Authors:  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
Journal:  Neuroinformatics       Date:  2021-04

6.  Plastic embedding immunolabeled large-volume samples for three-dimensional high-resolution imaging.

Authors:  Yadong Gang; Xiuli Liu; Xiaojun Wang; Qi Zhang; Hongfu Zhou; Ruixi Chen; Ling Liu; Yao Jia; Fangfang Yin; Gong Rao; Jiadong Chen; Shaoqun Zeng
Journal:  Biomed Opt Express       Date:  2017-07-10       Impact factor: 3.732

7.  Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network.

Authors:  Drew Friedmann; Albert Pun; Eliza L Adams; Jan H Lui; Justus M Kebschull; Sophie M Grutzner; Caitlin Castagnola; Marc Tessier-Lavigne; Liqun Luo
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-01       Impact factor: 11.205

8.  TISSUE CLEARING.

Authors:  Douglas S Richardson; Webster Guan; Katsuhiko Matsumoto; Chenchen Pan; Kwanghun Chung; Ali Ertürk; Hiroki R Ueda; Jeff W Lichtman
Journal:  Nat Rev Methods Primers       Date:  2021-12-16

9.  Divergent Projection Patterns Revealed by Reconstruction of Individual Neurons in Orbitofrontal Cortex.

Authors:  Junjun Wang; Pei Sun; Xiaohua Lv; Sen Jin; Anan Li; Jianxia Kuang; Ning Li; Yadong Gang; Rui Guo; Shaoqun Zeng; Fuqiang Xu; Yu-Hui Zhang
Journal:  Neurosci Bull       Date:  2020-12-29       Impact factor: 5.203

10.  A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.

Authors:  Hao Jia; Sung-Joon Park; Kenta Nakai
Journal:  BMC Bioinformatics       Date:  2021-06-02       Impact factor: 3.307

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.