In EDS ansehen

Comparison of BlueRecording with existing tools

Gespeichert in:
Bibliographische Detailangaben
Titel: Comparison of BlueRecording with existing tools
Autoren: Joseph James Tharayil, Jorge Blanco Alonso, Silvia Farcito, Bryn Lloyd, Armando Romani, Elvis Boci, Antonino Cassara, Felix Schürmann, Esra Neufeld, Niels Kuster, Michael Reimann
Publikationsjahr: 2025
Schlagwörter: Biophysics, Cell Biology, Genetics, Neuroscience, Physiology, Biotechnology, Evolutionary Biology, Developmental Biology, Cancer, Space Science, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, standalone python code, sonata data format, rat somatosensory cortex, new avenues open, network simulations accessible, coreneuron computation engine, computational neuroscience grows, complex tissue anatomy, permit online calculation, signal information content, e ., non, simulate eeg recordings, enable efficient calculation, div >< p, dipolar current sources
Beschreibung: 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.
Publikationsart: dataset
Sprache: unknown
Relation: https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145
DOI: 10.1371/journal.pcbi.1013023.t004
Verfügbarkeit: https://doi.org/10.1371/journal.pcbi.1013023.t004
https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145
Rights: CC BY 4.0
Dokumentencode: edsbas.AC8CCBA
Datenbank: BASE
FullText Text:
  Availability: 0
CustomLinks:
  – Url: https://doi.org/10.1371/journal.pcbi.1013023.t004#
    Name: EDS - BASE (s4221598)
    Category: fullText
    Text: View record from BASE
  – Url: https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=EBSCO&SrcAuth=EBSCO&DestApp=WOS&ServiceName=TransferToWoS&DestLinkType=GeneralSearchSummary&Func=Links&author=Tharayil%20JJ
    Name: ISI
    Category: fullText
    Text: Nájsť tento článok vo Web of Science
    Icon: https://imagesrvr.epnet.com/ls/20docs.gif
    MouseOverText: Nájsť tento článok vo Web of Science
Header DbId: edsbas
DbLabel: BASE
An: edsbas.AC8CCBA
RelevancyScore: 919
AccessLevel: 3
PubType:
PubTypeId: unknown
PreciseRelevancyScore: 918.707275390625
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Comparison of BlueRecording with existing tools
– Name: Author
  Label: Authors
  Group: Au
  Data: &lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Joseph+James+Tharayil%22&quot;&gt;Joseph James Tharayil&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Jorge+Blanco+Alonso%22&quot;&gt;Jorge Blanco Alonso&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Silvia+Farcito%22&quot;&gt;Silvia Farcito&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Bryn+Lloyd%22&quot;&gt;Bryn Lloyd&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Armando+Romani%22&quot;&gt;Armando Romani&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Elvis+Boci%22&quot;&gt;Elvis Boci&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Antonino+Cassara%22&quot;&gt;Antonino Cassara&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Felix+Sch&#252;rmann%22&quot;&gt;Felix Sch&#252;rmann&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Esra+Neufeld%22&quot;&gt;Esra Neufeld&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Niels+Kuster%22&quot;&gt;Niels Kuster&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Michael+Reimann%22&quot;&gt;Michael Reimann&lt;/searchLink&gt;
– Name: DatePubCY
  Label: Publication Year
  Group: Date
  Data: 2025
– Name: Subject
  Label: Subject Terms
  Group: Su
  Data: &lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Biophysics%22&quot;&gt;Biophysics&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Cell+Biology%22&quot;&gt;Cell Biology&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Genetics%22&quot;&gt;Genetics&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Neuroscience%22&quot;&gt;Neuroscience&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Physiology%22&quot;&gt;Physiology&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Biotechnology%22&quot;&gt;Biotechnology&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Evolutionary+Biology%22&quot;&gt;Evolutionary Biology&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Developmental+Biology%22&quot;&gt;Developmental Biology&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Cancer%22&quot;&gt;Cancer&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Space+Science%22&quot;&gt;Space Science&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Biological+Sciences+not+elsewhere+classified%22&quot;&gt;Biological Sciences not elsewhere classified&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Mathematical+Sciences+not+elsewhere+classified%22&quot;&gt;Mathematical Sciences not elsewhere classified&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Chemical+Sciences+not+elsewhere+classified%22&quot;&gt;Chemical Sciences not elsewhere classified&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Information+Systems+not+elsewhere+classified%22&quot;&gt;Information Systems not elsewhere classified&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22standalone+python+code%22&quot;&gt;standalone python code&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22sonata+data+format%22&quot;&gt;sonata data format&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22rat+somatosensory+cortex%22&quot;&gt;rat somatosensory cortex&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22new+avenues+open%22&quot;&gt;new avenues open&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22network+simulations+accessible%22&quot;&gt;network simulations accessible&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22coreneuron+computation+engine%22&quot;&gt;coreneuron computation engine&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22computational+neuroscience+grows%22&quot;&gt;computational neuroscience grows&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22complex+tissue+anatomy%22&quot;&gt;complex tissue anatomy&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22permit+online+calculation%22&quot;&gt;permit online calculation&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22signal+information+content%22&quot;&gt;signal information content&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22e+%2E%22&quot;&gt;e .&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22non%22&quot;&gt;non&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22simulate+eeg+recordings%22&quot;&gt;simulate eeg recordings&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22enable+efficient+calculation%22&quot;&gt;enable efficient calculation&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22div+&gt;&lt;+p%22&quot;&gt;div &gt;&lt; p&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22dipolar+current+sources%22&quot;&gt;dipolar current sources&lt;/searchLink&gt;
– Name: Abstract
  Label: Description
  Group: Ab
  Data: 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.
– Name: TypeDocument
  Label: Document Type
  Group: TypDoc
  Data: dataset
– Name: Language
  Label: Language
  Group: Lang
  Data: unknown
– Name: NoteTitleSource
  Label: Relation
  Group: SrcInfo
  Data: https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145
– Name: DOI
  Label: DOI
  Group: ID
  Data: 10.1371/journal.pcbi.1013023.t004
– Name: URL
  Label: Availability
  Group: URL
  Data: https://doi.org/10.1371/journal.pcbi.1013023.t004&lt;br /&gt;https://figshare.com/articles/dataset/Comparison_of_BlueRecording_with_existing_tools/29138145
– Name: Copyright
  Label: Rights
  Group: Cpyrght
  Data: CC BY 4.0
– Name: AN
  Label: Accession Number
  Group: ID
  Data: edsbas.AC8CCBA
PLink https://erproxy.cvtisr.sk/sfx/access?url=https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=edsbas&AN=edsbas.AC8CCBA
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1371/journal.pcbi.1013023.t004
    Languages:
      – Text: unknown
    Subjects:
      – SubjectFull: Biophysics
        Type: general
      – SubjectFull: Cell Biology
        Type: general
      – SubjectFull: Genetics
        Type: general
      – SubjectFull: Neuroscience
        Type: general
      – SubjectFull: Physiology
        Type: general
      – SubjectFull: Biotechnology
        Type: general
      – SubjectFull: Evolutionary Biology
        Type: general
      – SubjectFull: Developmental Biology
        Type: general
      – SubjectFull: Cancer
        Type: general
      – SubjectFull: Space Science
        Type: general
      – SubjectFull: Biological Sciences not elsewhere classified
        Type: general
      – SubjectFull: Mathematical Sciences not elsewhere classified
        Type: general
      – SubjectFull: Chemical Sciences not elsewhere classified
        Type: general
      – SubjectFull: Information Systems not elsewhere classified
        Type: general
      – SubjectFull: standalone python code
        Type: general
      – SubjectFull: sonata data format
        Type: general
      – SubjectFull: rat somatosensory cortex
        Type: general
      – SubjectFull: new avenues open
        Type: general
      – SubjectFull: network simulations accessible
        Type: general
      – SubjectFull: coreneuron computation engine
        Type: general
      – SubjectFull: computational neuroscience grows
        Type: general
      – SubjectFull: complex tissue anatomy
        Type: general
      – SubjectFull: permit online calculation
        Type: general
      – SubjectFull: signal information content
        Type: general
      – SubjectFull: e .
        Type: general
      – SubjectFull: non
        Type: general
      – SubjectFull: simulate eeg recordings
        Type: general
      – SubjectFull: enable efficient calculation
        Type: general
      – SubjectFull: div >< p
        Type: general
      – SubjectFull: dipolar current sources
        Type: general
    Titles:
      – TitleFull: Comparison of BlueRecording with existing tools
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Joseph James Tharayil
      – PersonEntity:
          Name:
            NameFull: Jorge Blanco Alonso
      – PersonEntity:
          Name:
            NameFull: Silvia Farcito
      – PersonEntity:
          Name:
            NameFull: Bryn Lloyd
      – PersonEntity:
          Name:
            NameFull: Armando Romani
      – PersonEntity:
          Name:
            NameFull: Elvis Boci
      – PersonEntity:
          Name:
            NameFull: Antonino Cassara
      – PersonEntity:
          Name:
            NameFull: Felix Schürmann
      – PersonEntity:
          Name:
            NameFull: Esra Neufeld
      – PersonEntity:
          Name:
            NameFull: Niels Kuster
      – PersonEntity:
          Name:
            NameFull: Michael Reimann
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 01
              Type: published
              Y: 2025
          Identifiers:
            – Type: issn-locals
              Value: edsbas
            – Type: issn-locals
              Value: edsbas.oa
ResultId 1