A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets

Cell Reports Methods, vol. 4, pp. 100681

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.

Authors 14

1. Robin Gutzen corresponding Aachen Theoretical Systems Neurobiology

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

   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. Electronic address: r.gutzen@fz-juelich.de

   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

2. G. De Bonis

   Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy

3. Chiara De Luca

   Istituto Nazionale di Fisica Nucleare · University of Zurich · ETH Zurich · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I · Institute of Neuroinformatics

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy; Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland

   Institute of Neuroinformatics, University of Zürich and ETH Zürich, Zürich, Switzerland

   Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy

4. Elena Pastorelli

   Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy

5. Cristiano Capone

   Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy

6. Anna Letizia Allegra Mascaro

   European Laboratory for Non-Linear Spectroscopy · Neuroscience Institute · National Research Council · University of Florence

   Affiliation as printed

   European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Neuroscience Institute, National Research Council, Pisa, Italy

   European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy

   Neuroscience Institute, National Research Council, Pisa, Italy

7. Francesco Resta

   European Laboratory for Non-Linear Spectroscopy · University of Florence

   Affiliation as printed

   European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy; Department of Physics and Astronomy, University of Florence, Florence, Italy

   Department of Physics and Astronomy, University of Florence, Florence, Italy

   European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy

8. Arnau Manasanch

   Consorci Institut D'Investigacions Biomediques August Pi I Sunyer

   Affiliation as printed

   Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain

9. Francesco Saverio Pavone

   European Laboratory for Non-Linear Spectroscopy · National Institute of Optics · National Research Council · University of Florence

   Affiliation as printed

   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

   Department of Physics and Astronomy, University of Florence, Florence, Italy

   European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Florence, Italy

   National Institute of Optics, National Research Council, Sesto Fiorentino, Italy

10. Maria Victoria Sanchez-Vives

    Institució Catalana de Recerca i Estudis Avançats · Consorci Institut D'Investigacions Biomediques August Pi I Sunyer

    Affiliation as printed

    Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain

11. Maurizio Mattia

    Istituto Superiore di Sanità

    Affiliation as printed

    National Center for Radiation Protection and Computational Physics, Istituto Superiore di Sanità (ISS), Rome, Italy

12. Sonja Grün Aachen Theoretical Systems Neurobiology

    Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

    Affiliation as printed

    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

    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

13. Pier Stanislao Paolucci

    Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

    Affiliation as printed

    Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma, Rome, Italy

14. Michael Denker

    Forschungszentrum Jülich · Jülich Aachen Research Alliance

    Affiliation as printed

    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