A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo
In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2018-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/34518 |
| _version_ | 1818027034325024768 |
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| author | Pierre Yger Giulia LB Spampinato Elric Esposito Baptiste Lefebvre Stéphane Deny Christophe Gardella Marcel Stimberg Florian Jetter Guenther Zeck Serge Picaud Jens Duebel Olivier Marre |
| author_facet | Pierre Yger Giulia LB Spampinato Elric Esposito Baptiste Lefebvre Stéphane Deny Christophe Gardella Marcel Stimberg Florian Jetter Guenther Zeck Serge Picaud Jens Duebel Olivier Marre |
| author_sort | Pierre Yger |
| collection | DOAJ |
| description | In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain ‘ground truth’ data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes. |
| first_indexed | 2024-12-10T04:41:29Z |
| format | Article |
| id | doaj.art-075978833acf4f7488d2c63e3e551e5c |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-12-10T04:41:29Z |
| publishDate | 2018-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-075978833acf4f7488d2c63e3e551e5c2022-12-22T02:01:52ZengeLife Sciences Publications LtdeLife2050-084X2018-03-01710.7554/eLife.34518A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivoPierre Yger0https://orcid.org/0000-0003-1376-5240Giulia LB Spampinato1Elric Esposito2Baptiste Lefebvre3Stéphane Deny4Christophe Gardella5https://orcid.org/0000-0003-3204-9012Marcel Stimberg6https://orcid.org/0000-0002-2648-4790Florian Jetter7Guenther Zeck8Serge Picaud9Jens Duebel10Olivier Marre11https://orcid.org/0000-0002-0090-6190Institut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, France; Laboratoire de Physique Statistique, CNRS, ENS, UPMC, 75005, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceNMI, Neurophysics Group, Reutlingen, GermanyNMI, Neurophysics Group, Reutlingen, GermanyInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceInstitut de la Vision, INSERM UMRS 968, UPMC UM 80, Paris, FranceIn recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain ‘ground truth’ data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes.https://elifesciences.org/articles/34518electrophysiologysilicon probepopulation recordingspike sortingneural ensemble |
| spellingShingle | Pierre Yger Giulia LB Spampinato Elric Esposito Baptiste Lefebvre Stéphane Deny Christophe Gardella Marcel Stimberg Florian Jetter Guenther Zeck Serge Picaud Jens Duebel Olivier Marre A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo eLife electrophysiology silicon probe population recording spike sorting neural ensemble |
| title | A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| title_full | A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| title_fullStr | A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| title_full_unstemmed | A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| title_short | A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| title_sort | spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo |
| topic | electrophysiology silicon probe population recording spike sorting neural ensemble |
| url | https://elifesciences.org/articles/34518 |
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