BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models.
As the size and complexity of network simulations accessible to computational neuroscience grows, new avenues open for research into extracellularly recorded electric signals. Biophysically detailed simulations permit the identification of the biological origins of the different components of record...
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| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1013023 |
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| author | Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito Bryn Lloyd Armando Romani Elvis Boci Antonino Cassara Felix Schürmann Esra Neufeld Niels Kuster Michael Reimann |
| author_facet | Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito Bryn Lloyd Armando Romani Elvis Boci Antonino Cassara Felix Schürmann Esra Neufeld Niels Kuster Michael Reimann |
| author_sort | Joseph James Tharayil |
| collection | DOAJ |
| description | As the size and complexity of network simulations accessible to computational neuroscience grows, new avenues open for research into extracellularly recorded electric signals. Biophysically detailed simulations permit the identification of the biological origins of the different components of recorded signals, the evaluation of signal sensitivity to different anatomical, physiological, and geometric factors, and selection of recording parameters to maximize the signal information content. Simultaneously, virtual extracellular signals produced by these networks may become important metrics for neuro-simulation validation. To enable efficient calculation of extracellular signals from large neural network simulations, we have developed BlueRecording, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. In particular, we implement a general form of the reciprocity theorem, which is capable of handling non-dipolar current sources, such as may be found in long axons and recordings close to the current source, as well as complex tissue anatomy, dielectric heterogeneity, and electrode geometries. To our knowledge, this is the first application of this generalized (i.e., non-dipolar) reciprocity-based approach to simulate EEG recordings. We use these tools to calculate extracellular signals from an in silico model of the rat somatosensory cortex and hippocampus and to study signal contribution differences between regions and cell types. |
| format | Article |
| id | doaj-art-e09c239920c64c139fa42cae1b61598c |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-e09c239920c64c139fa42cae1b61598c2025-08-20T02:17:08ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582025-05-01215e101302310.1371/journal.pcbi.1013023BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models.Joseph James TharayilJorge Blanco AlonsoSilvia FarcitoBryn LloydArmando RomaniElvis BociAntonino CassaraFelix SchürmannEsra NeufeldNiels KusterMichael ReimannAs the size and complexity of network simulations accessible to computational neuroscience grows, new avenues open for research into extracellularly recorded electric signals. Biophysically detailed simulations permit the identification of the biological origins of the different components of recorded signals, the evaluation of signal sensitivity to different anatomical, physiological, and geometric factors, and selection of recording parameters to maximize the signal information content. Simultaneously, virtual extracellular signals produced by these networks may become important metrics for neuro-simulation validation. To enable efficient calculation of extracellular signals from large neural network simulations, we have developed BlueRecording, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. In particular, we implement a general form of the reciprocity theorem, which is capable of handling non-dipolar current sources, such as may be found in long axons and recordings close to the current source, as well as complex tissue anatomy, dielectric heterogeneity, and electrode geometries. To our knowledge, this is the first application of this generalized (i.e., non-dipolar) reciprocity-based approach to simulate EEG recordings. We use these tools to calculate extracellular signals from an in silico model of the rat somatosensory cortex and hippocampus and to study signal contribution differences between regions and cell types.https://doi.org/10.1371/journal.pcbi.1013023 |
| spellingShingle | Joseph James Tharayil Jorge Blanco Alonso Silvia Farcito Bryn Lloyd Armando Romani Elvis Boci Antonino Cassara Felix Schürmann Esra Neufeld Niels Kuster Michael Reimann BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. PLoS Computational Biology |
| title | BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. |
| title_full | BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. |
| title_fullStr | BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. |
| title_full_unstemmed | BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. |
| title_short | BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models. |
| title_sort | bluerecording a pipeline for the efficient calculation of extracellular recordings in large scale neural circuit models |
| url | https://doi.org/10.1371/journal.pcbi.1013023 |
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