Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology
Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be diffi...
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Veröffentlicht in: | Journal of neural engineering 2017-08, Vol.14 (4), p.045003-045003 |
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creator | Siegle, Joshua H López, Aarón Cuevas Patel, Yogi A Abramov, Kirill Ohayon, Shay Voigts, Jakob |
description | Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research. |
doi_str_mv | 10.1088/1741-2552/aa5eea |
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Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.</description><identifier>ISSN: 1741-2560</identifier><identifier>EISSN: 1741-2552</identifier><identifier>DOI: 10.1088/1741-2552/aa5eea</identifier><identifier>PMID: 28169219</identifier><identifier>CODEN: JNEIEZ</identifier><language>eng</language><publisher>England: IOP Publishing</publisher><subject>Algorithms ; closed loop ; Electrophysiological Phenomena - physiology ; electrophysiology ; Equipment Design - instrumentation ; Equipment Design - methods ; Hippocampus - physiology ; Humans ; Neurosciences - instrumentation ; Neurosciences - methods ; open source ; software ; Software Design ; User-Computer Interface</subject><ispartof>Journal of neural engineering, 2017-08, Vol.14 (4), p.045003-045003</ispartof><rights>2017 IOP Publishing Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c410t-5cdce4b50d87d69275959d09023316539e51d4bd1cc21ed9fd2bc4a5b1e5e3433</citedby><cites>FETCH-LOGICAL-c410t-5cdce4b50d87d69275959d09023316539e51d4bd1cc21ed9fd2bc4a5b1e5e3433</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://iopscience.iop.org/article/10.1088/1741-2552/aa5eea/pdf$$EPDF$$P50$$Giop$$Hfree_for_read</linktopdf><link.rule.ids>314,778,782,27911,27912,53833,53880</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28169219$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Siegle, Joshua H</creatorcontrib><creatorcontrib>López, Aarón Cuevas</creatorcontrib><creatorcontrib>Patel, Yogi A</creatorcontrib><creatorcontrib>Abramov, Kirill</creatorcontrib><creatorcontrib>Ohayon, Shay</creatorcontrib><creatorcontrib>Voigts, Jakob</creatorcontrib><title>Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology</title><title>Journal of neural engineering</title><addtitle>JNE</addtitle><addtitle>J. Neural Eng</addtitle><description>Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.</description><subject>Algorithms</subject><subject>closed loop</subject><subject>Electrophysiological Phenomena - physiology</subject><subject>electrophysiology</subject><subject>Equipment Design - instrumentation</subject><subject>Equipment Design - methods</subject><subject>Hippocampus - physiology</subject><subject>Humans</subject><subject>Neurosciences - instrumentation</subject><subject>Neurosciences - methods</subject><subject>open source</subject><subject>software</subject><subject>Software Design</subject><subject>User-Computer Interface</subject><issn>1741-2560</issn><issn>1741-2552</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>O3W</sourceid><sourceid>EIF</sourceid><recordid>eNp9kT1PwzAQhi0EoqWwM6FsMDTUl9hpzIaq8iFV6lJmy7EvbaokDnEy9N_jqKUTYrF91nuPzo8JuQf6DDRNZzBnEEacRzOlOKK6IOPz1eX5nNARuXFuT2kMc0GvyShKIRERiDHZrBusg2WzO7iXQNWB9WXobN9qnAZN2W-LOsyUQ-ML1eW2rQK_BFVfdoXeqbrGMsASddfagVHY0m4Pt-QqV6XDu9M-IV9vy83iI1yt3z8Xr6tQM6BdyLXRyDJOTTo3fp45F1wYKmgUx5DwWCAHwzIDWkeARuQmyjRTPAPkGLM4npCnI7dp7XePrpNV4TSWparR9k5CmvAUROKBE0KPUd1a51rMZdMWlWoPEqgcXMpBlhzEyaNL3_JwovdZhebc8CvPB6bHQGEbuffOav_Y_3iPf8T3NUpgkknKuP8g2Zg8_gHdZIwQ</recordid><startdate>20170801</startdate><enddate>20170801</enddate><creator>Siegle, Joshua H</creator><creator>López, Aarón Cuevas</creator><creator>Patel, Yogi A</creator><creator>Abramov, Kirill</creator><creator>Ohayon, Shay</creator><creator>Voigts, Jakob</creator><general>IOP Publishing</general><scope>O3W</scope><scope>TSCCA</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20170801</creationdate><title>Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology</title><author>Siegle, Joshua H ; López, Aarón Cuevas ; Patel, Yogi A ; Abramov, Kirill ; Ohayon, Shay ; Voigts, Jakob</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c410t-5cdce4b50d87d69275959d09023316539e51d4bd1cc21ed9fd2bc4a5b1e5e3433</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Algorithms</topic><topic>closed loop</topic><topic>Electrophysiological Phenomena - physiology</topic><topic>electrophysiology</topic><topic>Equipment Design - instrumentation</topic><topic>Equipment Design - methods</topic><topic>Hippocampus - physiology</topic><topic>Humans</topic><topic>Neurosciences - instrumentation</topic><topic>Neurosciences - methods</topic><topic>open source</topic><topic>software</topic><topic>Software Design</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Siegle, Joshua H</creatorcontrib><creatorcontrib>López, Aarón Cuevas</creatorcontrib><creatorcontrib>Patel, Yogi A</creatorcontrib><creatorcontrib>Abramov, Kirill</creatorcontrib><creatorcontrib>Ohayon, Shay</creatorcontrib><creatorcontrib>Voigts, Jakob</creatorcontrib><collection>IOP Publishing Free Content</collection><collection>IOPscience (Open Access)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of neural engineering</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Siegle, Joshua H</au><au>López, Aarón Cuevas</au><au>Patel, Yogi A</au><au>Abramov, Kirill</au><au>Ohayon, Shay</au><au>Voigts, Jakob</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology</atitle><jtitle>Journal of neural engineering</jtitle><stitle>JNE</stitle><addtitle>J. Neural Eng</addtitle><date>2017-08-01</date><risdate>2017</risdate><volume>14</volume><issue>4</issue><spage>045003</spage><epage>045003</epage><pages>045003-045003</pages><issn>1741-2560</issn><eissn>1741-2552</eissn><coden>JNEIEZ</coden><abstract>Objective. Closed-loop experiments, in which causal interventions are conditioned on the state of the system under investigation, have become increasingly common in neuroscience. Such experiments can have a high degree of explanatory power, but they require a precise implementation that can be difficult to replicate across laboratories. We sought to overcome this limitation by building open-source software that makes it easier to develop and share algorithms for closed-loop control. Approach. We created the Open Ephys GUI, an open-source platform for multichannel electrophysiology experiments. In addition to the standard 'open-loop' visualization and recording functionality, the GUI also includes modules for delivering feedback in response to events detected in the incoming data stream. Importantly, these modules can be built and shared as plugins, which makes it possible for users to extend the functionality of the GUI through a simple API, without having to understand the inner workings of the entire application. Main results. In combination with low-cost, open-source hardware for amplifying and digitizing neural signals, the GUI has been used for closed-loop experiments that perturb the hippocampal theta rhythm in a phase-specific manner. Significance. The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time feedback into their research.</abstract><cop>England</cop><pub>IOP Publishing</pub><pmid>28169219</pmid><doi>10.1088/1741-2552/aa5eea</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Algorithms closed loop Electrophysiological Phenomena - physiology electrophysiology Equipment Design - instrumentation Equipment Design - methods Hippocampus - physiology Humans Neurosciences - instrumentation Neurosciences - methods open source software Software Design User-Computer Interface |
title | Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology |
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