{
  "abstract": "Scientific progress depends on reliable and reproducible results. Progress can be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data involve bespoke formats and software that make replication and reuse of data difficult. To address these challenges, we created Spyglass, an open-source data management and analysis framework written in Python. Spyglass provides reproducible pipelines for common neuroscience analyses and sharing of raw data, intermediate analyses, and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for spectral filtering, spike sorting, pose tracking, and neural decoding. Spyglass can be extended to apply existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data. New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c: https://spyglass.hhmi.2i2c.cloud/.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Physiology, University of California, San Francisco, San Francisco, United States",
    "Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States",
    "Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, United States",
    "Scientific Data Division, Lawrence Berkeley National Laboratory, Berkeley, United States",
    "Center for Computational Mathematics, Flatiron Institute, New York, United States",
    "Graduate Program in Neural and Behavioral Sciences, University of Tübingen, Tübingen, Germany",
    "UCSF-UC Berkeley Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, United States",
    "Medical Scientist Training Program, University of California, San Francisco, San Francisco, United States",
    "Department of Neurology, University of California, San Francisco, San Francisco, United States",
    "Sainsbury Wellcome Centre, University College London, London, United Kingdom",
    "DataJoint, Houston, United States",
    "Department of Electrical and Computer Engineering, Rice University, Houston, United States",
    "Centre de Recherche en Neuroscience de Lyon, CNRS, Bron, France",
    "Allen Institute for Brain Science, Seattle, United States"
  ],
  "article_type": "tools resources",
  "arxiv": null,
  "author_total": 29,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Kyu Hyun Lee",
      "orcid": "0000-0001-6483-9444"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Eric L Denovellis",
      "orcid": "0000-0003-4606-087X"
    },
    {
      "affs": [
        3
      ],
      "name": "Ryan Ly",
      "orcid": "0000-0001-9238-0642"
    },
    {
      "affs": [
        4
      ],
      "name": "Jeremy Magland",
      "orcid": "0000-0002-5286-4375"
    },
    {
      "affs": [
        4
      ],
      "name": "Jeff Soules"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Alison E Comrie"
    },
    {
      "affs": [
        5
      ],
      "name": "Daniel P Gramling"
    },
    {
      "affs": [
        0,
        2,
        6,
        7
      ],
      "name": "Jennifer A Guidera"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Rhino Nevers"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Philip Adenekan"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Chris Brozdowski"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Samuel R Bray",
      "orcid": "0000-0002-9696-6920"
    },
    {
      "affs": [
        0
      ],
      "name": "Emily Monroe"
    },
    {
      "affs": [
        0
      ],
      "name": "Ji Hyun Bak"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Michael E Coulter"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Xulu Sun",
      "orcid": "0000-0003-3076-0994"
    },
    {
      "affs": [
        0,
        2
      ],
      "name": "Emrey Broyles"
    },
    {
      "affs": [
        0,
        2,
        6
      ],
      "name": "Donghoon Shin"
    },
    {
      "affs": [
        8
      ],
      "name": "Sharon Chiang"
    },
    {
      "affs": [
        9
      ],
      "name": "Cristofer Holobetz",
      "orcid": "0009-0009-8567-3290"
    },
    {
      "affs": [
        3
      ],
      "name": "Andrew Tritt"
    },
    {
      "affs": [
        3
      ],
      "name": "Oliver Rübel"
    },
    {
      "affs": [
        10
      ],
      "name": "Thinh Nguyen"
    },
    {
      "affs": [
        10
      ],
      "name": "Dimitri Yatsenko"
    },
    {
      "affs": [
        11
      ],
      "name": "Joshua Chu"
    },
    {
      "affs": [
        11
      ],
      "name": "Caleb Kemere",
      "orcid": "0000-0003-2054-0234"
    },
    {
      "affs": [
        12
      ],
      "name": "Samuel Garcia",
      "orcid": "0000-0001-6389-9779"
    },
    {
      "affs": [
        13
      ],
      "name": "Alessio Paolo Buccino",
      "orcid": "0000-0003-3661-527X"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Loren Frank",
      "orcid": "0000-0002-1752-5677"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2gdgrm80m33df.bib",
  "cited_by": 1,
  "doi": "10.7554/elife.108089",
  "fulltext_url": "https://elifesciences.org/articles/108089",
  "id": "2gdgrm80m33df",
  "issns": [
    "2050-084X"
  ],
  "landing_url": "https://elifesciences.org/articles/108089",
  "language": "eng",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "elife",
      "neuroscience"
    ],
    [
      "openalex",
      "1802|Scientific Computing and Data Management"
    ]
  ],
  "openalex": "W4414534291",
  "pdf_url": "https://cdn.elifesciences.org/articles/108089/elife-108089-v1.pdf",
  "pmcid": "PMC13730526",
  "pmid": null,
  "published": "2026-11-03",
  "publisher": "eLife Sciences Publications",
  "ris": "https://research.draconitic.com/paper/2gdgrm80m33df.ris",
  "sources": [
    {
      "first_seen": "2026-11-04T12:20:56Z",
      "native_id": "108089",
      "source": "elife",
      "url": "https://elifesciences.org/articles/108089"
    },
    {
      "first_seen": "2026-11-04T15:20:46Z",
      "native_id": "PMC:PMC13730526",
      "source": "europepmc",
      "url": "https://europepmc.org/article/PMC/PMC13730526"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "elife:neuroscience",
      "subfield": "neuroscience"
    }
  ],
  "title": "Spyglass is a framework for reproducible and shareable neuroscience research",
  "title_text": "Spyglass is a framework for reproducible and shareable neuroscience research",
  "type": "peer-reviewed",
  "updated_at": "2026-11-04T15:20:46Z",
  "url": "https://research.draconitic.com/paper/2gdgrm80m33df",
  "venue": "eLife",
  "versions": []
}