Literature DB >> 32283996

Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics.

Adam S Charles1,2, Benjamin Falk1, Nicholas Turner3, Talmo D Pereira4, Daniel Tward1, Benjamin D Pedigo1, Jaewon Chung1, Randal Burns1, Satrajit S Ghosh5,6, Justus M Kebschull1,7, William Silversmith4, Joshua T Vogelstein1,2.   

Abstract

As acquiring bigger data becomes easier in experimental brain science, computational and statistical brain science must achieve similar advances to fully capitalize on these data. Tackling these problems will benefit from a more explicit and concerted effort to work together. Specifically, brain science can be further democratized by harnessing the power of community-driven tools, which both are built by and benefit from many different people with different backgrounds and expertise. This perspective can be applied across modalities and scales and enables collaborations across previously siloed communities.

Entities:  

Keywords:  computational; infrastructure; reference data; statistics

Mesh:

Year:  2020        PMID: 32283996      PMCID: PMC9119703          DOI: 10.1146/annurev-neuro-100119-110036

Source DB:  PubMed          Journal:  Annu Rev Neurosci        ISSN: 0147-006X            Impact factor:   15.553


  71 in total

1.  Elastic volume reconstruction from series of ultra-thin microscopy sections.

Authors:  Stephan Saalfeld; Richard Fetter; Albert Cardona; Pavel Tomancak
Journal:  Nat Methods       Date:  2012-06-10       Impact factor: 28.547

2.  ITK-SNAP: An interactive tool for semi-automatic segmentation of multi-modality biomedical images.

Authors:  Paul A Yushkevich; Guido Gerig
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2016-08

3.  Connectomic reconstruction of the inner plexiform layer in the mouse retina.

Authors:  Moritz Helmstaedter; Kevin L Briggman; Srinivas C Turaga; Viren Jain; H Sebastian Seung; Winfried Denk
Journal:  Nature       Date:  2013-08-08       Impact factor: 49.962

4.  Whole-brain serial-section electron microscopy in larval zebrafish.

Authors:  David Grant Colburn Hildebrand; Marcelo Cicconet; Russel Miguel Torres; Woohyuk Choi; Tran Minh Quan; Jungmin Moon; Arthur Willis Wetzel; Andrew Scott Champion; Brett Jesse Graham; Owen Randlett; George Scott Plummer; Ruben Portugues; Isaac Henry Bianco; Stephan Saalfeld; Alexander David Baden; Kunal Lillaney; Randal Burns; Joshua Tzvi Vogelstein; Alexander Franz Schier; Wei-Chung Allen Lee; Won-Ki Jeong; Jeff William Lichtman; Florian Engert
Journal:  Nature       Date:  2017-05-10       Impact factor: 49.962

5.  Dimensions of deprivation and threat, psychopathology, and potential mediators: A multi-year longitudinal analysis.

Authors:  Adam Bryant Miller; Margaret A Sheridan; Jamie L Hanson; Katie A McLaughlin; John E Bates; Jennifer E Lansford; Gregory S Pettit; Kenneth A Dodge
Journal:  J Abnorm Psychol       Date:  2018-02

6.  Discovering and deciphering relationships across disparate data modalities.

Authors:  Joshua T Vogelstein; Eric W Bridgeford; Qing Wang; Carey E Priebe; Mauro Maggioni; Cencheng Shen
Journal:  Elife       Date:  2019-01-15       Impact factor: 8.140

7.  Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism.

Authors:  Yongsoo Kim; Guangyu Robert Yang; Kith Pradhan; Kannan Umadevi Venkataraju; Mihail Bota; Luis Carlos García Del Molino; Greg Fitzgerald; Keerthi Ram; Miao He; Jesse Maurica Levine; Partha Mitra; Z Josh Huang; Xiao-Jing Wang; Pavel Osten
Journal:  Cell       Date:  2017-10-05       Impact factor: 41.582

8.  Network anatomy and in vivo physiology of visual cortical neurons.

Authors:  Davi D Bock; Wei-Chung Allen Lee; Aaron M Kerlin; Mark L Andermann; Greg Hood; Arthur W Wetzel; Sergey Yurgenson; Edward R Soucy; Hyon Suk Kim; R Clay Reid
Journal:  Nature       Date:  2011-03-10       Impact factor: 49.962

9.  Dipy, a library for the analysis of diffusion MRI data.

Authors:  Eleftherios Garyfallidis; Matthew Brett; Bagrat Amirbekian; Ariel Rokem; Stefan van der Walt; Maxime Descoteaux; Ian Nimmo-Smith
Journal:  Front Neuroinform       Date:  2014-02-21       Impact factor: 4.081

10.  A platform for brain-wide imaging and reconstruction of individual neurons.

Authors:  Michael N Economo; Nathan G Clack; Luke D Lavis; Charles R Gerfen; Karel Svoboda; Eugene W Myers; Jayaram Chandrashekar
Journal:  Elife       Date:  2016-01-20       Impact factor: 8.140

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  5 in total

1.  Standardized and reproducible measurement of decision-making in mice.

Authors:  Valeria Aguillon-Rodriguez; Dora Angelaki; Hannah Bayer; Niccolo Bonacchi; Matteo Carandini; Fanny Cazettes; Gaelle Chapuis; Anne K Churchland; Yang Dan; Eric Dewitt; Mayo Faulkner; Hamish Forrest; Laura Haetzel; Michael Häusser; Sonja B Hofer; Fei Hu; Anup Khanal; Christopher Krasniak; Ines Laranjeira; Zachary F Mainen; Guido Meijer; Nathaniel J Miska; Thomas D Mrsic-Flogel; Masayoshi Murakami; Jean-Paul Noel; Alejandro Pan-Vazquez; Cyrille Rossant; Joshua Sanders; Karolina Socha; Rebecca Terry; Anne E Urai; Hernando Vergara; Miles Wells; Christian J Wilson; Ilana B Witten; Lauren E Wool; Anthony M Zador
Journal:  Elife       Date:  2021-05-20       Impact factor: 8.713

2.  RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations.

Authors:  Jingpeng Wu; Nicholas Turner; J Alexander Bae; Ashwin Vishwanathan; H Sebastian Seung
Journal:  Front Neuroinform       Date:  2022-03-02       Impact factor: 4.081

3.  Recommendations for repositories and scientific gateways from a neuroscience perspective.

Authors:  Malin Sandström; Mathew Abrams; Jan G Bjaalie; Mona Hicks; David N Kennedy; Arvind Kumar; Jean-Baptiste Poline; Prasun K Roy; Paul Tiesinga; Thomas Wachtler; Wojtek J Goscinski
Journal:  Sci Data       Date:  2022-05-16       Impact factor: 6.444

Review 4.  Review of data processing of functional optical microscopy for neuroscience.

Authors:  Hadas Benisty; Alexander Song; Gal Mishne; Adam S Charles
Journal:  Neurophotonics       Date:  2022-08-04       Impact factor: 4.212

5.  Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data.

Authors:  Jean-Baptiste Poline; David N Kennedy; Friedrich T Sommer; Giorgio A Ascoli; David C Van Essen; Adam R Ferguson; Jeffrey S Grethe; Michael J Hawrylycz; Paul M Thompson; Russell A Poldrack; Satrajit S Ghosh; David B Keator; Thomas L Athey; Joshua T Vogelstein; Helen S Mayberg; Maryann E Martone
Journal:  Neuroinformatics       Date:  2022-01-21
  5 in total

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