Literature DB >> 25528614

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology.

Joshua H Siegle1, Gregory J Hale2, Jonathan P Newman2, Jakob Voigts2.   

Abstract

One often-overlooked factor when selecting a platform for large-scale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's schematics and source code are available to end users. Open systems have a reputation for being difficult to acquire, poorly documented, and hard to maintain. With the arrival of more powerful and compact integrated circuits, rapid prototyping services, and web-based tools for collaborative development, these stereotypes must be reconsidered. We discuss some of the reasons why multichannel extracellular electrophysiology could benefit from open-source approaches and describe examples of successful community-driven tool development within this field. In order to promote the adoption of open-source hardware and to reduce the need for redundant development efforts, we advocate a move toward standardized interfaces that connect each element of the data processing pipeline. This will give researchers the flexibility to modify their tools when necessary, while allowing them to continue to benefit from the high-quality products and expertise provided by commercial vendors.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 25528614      PMCID: PMC4447530          DOI: 10.1016/j.conb.2014.11.004

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


  42 in total

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2.  Klusters, NeuroScope, NDManager: a free software suite for neurophysiological data processing and visualization.

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Review 3.  Measuring and interpreting neuronal correlations.

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4.  Dynamics of the hippocampal ensemble code for space.

Authors:  M A Wilson; B L McNaughton
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5.  Quantitative measures of cluster quality for use in extracellular recordings.

Authors:  N Schmitzer-Torbert; J Jackson; D Henze; K Harris; A D Redish
Journal:  Neuroscience       Date:  2005       Impact factor: 3.590

6.  nSTAT: open-source neural spike train analysis toolbox for Matlab.

Authors:  I Cajigas; W Q Malik; E N Brown
Journal:  J Neurosci Methods       Date:  2012-09-05       Impact factor: 2.390

Review 7.  Targeting neurons and photons for optogenetics.

Authors:  Adam M Packer; Botond Roska; Michael Häusser
Journal:  Nat Neurosci       Date:  2013-06-25       Impact factor: 24.884

8.  The flexDrive: an ultra-light implant for optical control and highly parallel chronic recording of neuronal ensembles in freely moving mice.

Authors:  Jakob Voigts; Joshua H Siegle; Dominique L Pritchett; Christopher I Moore
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Authors:  Thomas A Pologruto; Bernardo L Sabatini; Karel Svoboda
Journal:  Biomed Eng Online       Date:  2003-05-17       Impact factor: 2.819

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  15 in total

1.  Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording.

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Journal:  J Neural Eng       Date:  2017-03-07       Impact factor: 5.379

2.  Brain activity mapping at multiple scales with silicon microprobes containing 1,024 electrodes.

Authors:  Justin L Shobe; Leslie D Claar; Sepideh Parhami; Konstantin I Bakhurin; Sotiris C Masmanidis
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3.  A Sparse Probabilistic Code Underlies the Limits of Behavioral Discrimination.

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Journal:  Cereb Cortex       Date:  2020-03-14       Impact factor: 5.357

4.  A low-cost, scalable, current-sensing digital headstage for high channel count μECoG.

Authors:  Michael Trumpis; Michele Insanally; Jialin Zou; Ashraf Elsharif; Ali Ghomashchi; N Sertac Artan; Robert C Froemke; Jonathan Viventi
Journal:  J Neural Eng       Date:  2017-01-19       Impact factor: 5.379

5.  Open source silicon microprobes for high throughput neural recording.

Authors:  Long Yang; Kwang Lee; Jomar Villagracia; Sotiris C Masmanidis
Journal:  J Neural Eng       Date:  2020-01-24       Impact factor: 5.379

6.  Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments.

Authors:  Kateryna Voitiuk; Jinghui Geng; Matthew G Keefe; David F Parks; Sebastian E Sanso; Nico Hawthorne; Daniel B Freeman; Rob Currie; Mohammed A Mostajo-Radji; Alex A Pollen; Tomasz J Nowakowski; Sofie R Salama; Mircea Teodorescu; David Haussler
Journal:  J Neural Eng       Date:  2021-11-12       Impact factor: 5.379

7.  A High-Resolution Opto-Electrophysiology System With a Miniature Integrated Headstage.

Authors:  Adam E Mendrela; Kanghwan Kim; Daniel English; Sam McKenzie; John P Seymour; Gyorgy Buzsaki; Euisik Yoon
Journal:  IEEE Trans Biomed Circuits Syst       Date:  2018-07-16       Impact factor: 3.833

8.  Experimental Directory Structure (Exdir): An Alternative to HDF5 Without Introducing a New File Format.

Authors:  Svenn-Arne Dragly; Milad Hobbi Mobarhan; Mikkel E Lepperød; Simen Tennøe; Marianne Fyhn; Torkel Hafting; Anders Malthe-Sørenssen
Journal:  Front Neuroinform       Date:  2018-04-13       Impact factor: 4.081

9.  Long Term Recordings with Immobile Silicon Probes in the Mouse Cortex.

Authors:  Michael Okun; Armin Lak; Matteo Carandini; Kenneth D Harris
Journal:  PLoS One       Date:  2016-03-09       Impact factor: 3.240

10.  Artefactual origin of biphasic cortical spike-LFP correlation.

Authors:  Michael Okun
Journal:  J Comput Neurosci       Date:  2016-09-14       Impact factor: 1.621

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