Literature DB >> 25982977

Open source tools for large-scale neuroscience.

Jeremy Freeman1.   

Abstract

New technologies for monitoring and manipulating the nervous system promise exciting biology but pose challenges for analysis and computation. Solutions can be found in the form of modern approaches to distributed computing, machine learning, and interactive visualization. But embracing these new technologies will require a cultural shift: away from independent efforts and proprietary methods and toward an open source and collaborative neuroscience.
Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Mesh:

Year:  2015        PMID: 25982977     DOI: 10.1016/j.conb.2015.04.002

Source DB:  PubMed          Journal:  Curr Opin Neurobiol        ISSN: 0959-4388            Impact factor:   6.627


  17 in total

1.  The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services.

Authors:  Paolo Avesani; Brent McPherson; Soichi Hayashi; Cesar F Caiafa; Robert Henschel; Eleftherios Garyfallidis; Lindsey Kitchell; Daniel Bullock; Andrew Patterson; Emanuele Olivetti; Olaf Sporns; Andrew J Saykin; Lei Wang; Ivo Dinov; David Hancock; Bradley Caron; Yiming Qian; Franco Pestilli
Journal:  Sci Data       Date:  2019-05-23       Impact factor: 6.444

2.  Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.

Authors:  Philipp Berens; Jeremy Freeman; Thomas Deneux; Nikolay Chenkov; Thomas McColgan; Artur Speiser; Jakob H Macke; Srinivas C Turaga; Patrick Mineault; Peter Rupprecht; Stephan Gerhard; Rainer W Friedrich; Johannes Friedrich; Liam Paninski; Marius Pachitariu; Kenneth D Harris; Ben Bolte; Timothy A Machado; Dario Ringach; Jasmine Stone; Luke E Rogerson; Nicolas J Sofroniew; Jacob Reimer; Emmanouil Froudarakis; Thomas Euler; Miroslav Román Rosón; Lucas Theis; Andreas S Tolias; Matthias Bethge
Journal:  PLoS Comput Biol       Date:  2018-05-21       Impact factor: 4.475

3.  A Distributed Computing Platform for fMRI Big Data Analytics.

Authors:  Milad Makkie; Xiang Li; Shannon Quinn; Binbin Lin; Jieping Ye; Geoffrey Mon; Tianming Liu
Journal:  IEEE Trans Big Data       Date:  2018-03-06

4.  Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis.

Authors:  Taiga Abe; Ian Kinsella; Shreya Saxena; E Kelly Buchanan; Joao Couto; John Briggs; Sian Lee Kitt; Ryan Glassman; John Zhou; Liam Paninski; John P Cunningham
Journal:  Neuron       Date:  2022-07-22       Impact factor: 18.688

5.  Minian, an open-source miniscope analysis pipeline.

Authors:  Zhe Dong; William Mau; Yu Feng; Zachary T Pennington; Lingxuan Chen; Yosif Zaki; Kanaka Rajan; Tristan Shuman; Daniel Aharoni; Denise J Cai
Journal:  Elife       Date:  2022-06-01       Impact factor: 8.713

6.  Lessons from a catalogue of 6674 brain recordings.

Authors:  Alexis D J Makin; John Tyson-Carr; Giulia Rampone; Yiovanna Derpsch; Damien Wright; Marco Bertamini
Journal:  Elife       Date:  2022-06-15       Impact factor: 8.713

7.  Recommender-as-a-Service with Chatbot Guided Domain-science Knowledge Discovery in a Science Gateway.

Authors:  Komal Vekaria; Prasad Calyam; Sai Swathi Sivarathri; Songjie Wang; Yuanxun Zhang; Ashish Pandey; Cong Chen; Dong Xu; Trupti Joshi; Satish Nair
Journal:  Concurr Comput       Date:  2020-11-11       Impact factor: 1.831

8.  SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function.

Authors:  Raju Tomer; Matthew Lovett-Barron; Isaac Kauvar; Aaron Andalman; Vanessa M Burns; Sethuraman Sankaran; Logan Grosenick; Michael Broxton; Samuel Yang; Karl Deisseroth
Journal:  Cell       Date:  2015-12-17       Impact factor: 41.582

Review 9.  Improving scalability in systems neuroscience.

Authors:  Zhe Sage Chen; Bijan Pesaran
Journal:  Neuron       Date:  2021-04-07       Impact factor: 18.688

10.  Neuroscience education and research in Cameroon: Current status and future direction.

Authors:  Ngala Elvis Mbiydzenyuy; Constant Anatole Pieme; Richard E Brown; Carine Nguemeni
Journal:  IBRO Neurosci Rep       Date:  2021-03-05
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