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Gutzen R, De Bonis G, De Luca C, Pastorelli E, Capone C, Allegra Mascaro AL, Resta F, Manasanch A, Pavone FS, Sanchez-Vives MV, Mattia M, Grün S, Paolucci PS, Denker M. A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets. CELL REPORTS METHODS 2024; 4:100681. [PMID: 38183979 PMCID: PMC10831958 DOI: 10.1016/j.crmeth.2023.100681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/11/2023] [Accepted: 12/11/2023] [Indexed: 01/08/2024]
Abstract
Neuroscience is moving toward a more integrative discipline where understanding brain function requires consolidating the accumulated evidence seen across experiments, species, and measurement techniques. A remaining challenge on that path is integrating such heterogeneous data into analysis workflows such that consistent and comparable conclusions can be distilled as an experimental basis for models and theories. Here, we propose a solution in the context of slow-wave activity (<1 Hz), which occurs during unconscious brain states like sleep and general anesthesia and is observed across diverse experimental approaches. We address the issue of integrating and comparing heterogeneous data by conceptualizing a general pipeline design that is adaptable to a variety of inputs and applications. Furthermore, we present the Collaborative Brain Wave Analysis Pipeline (Cobrawap) as a concrete, reusable software implementation to perform broad, detailed, and rigorous comparisons of slow-wave characteristics across multiple, openly available electrocorticography (ECoG) and calcium imaging datasets.
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Affiliation(s)
- Robin Gutzen
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany.
| | - Giulia De Bonis
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Chiara De Luca
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Elena Pastorelli
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Cristiano Capone
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy
| | - Anna Letizia Allegra Mascaro
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy
| | - Francesco Resta
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Arnau Manasanch
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy; National Institute of Optics, National Research Council, Sesto Fiorentino, Italy
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maurizio Mattia
- National Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Sonja Grün
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany
| | | | - Michael Denker
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany
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