Spyglass: a framework for reproducible and shareable neuroscience research
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/.
Authors
- Ji Hyun Bak (ORCID: https://orcid.org/0000-0002-5700-7823)
- Oliver Rübel (ORCID: https://orcid.org/0000-0001-9902-1984)
- Michael E. Coulter (ORCID: https://orcid.org/0000-0003-0357-351X)
- Daniel P. Gramling (ORCID: https://orcid.org/0009-0004-6136-3769)
- Alessio Paolo Buccino (ORCID: https://orcid.org/0000-0003-3661-527X)
- Sharon Chiang (ORCID: https://orcid.org/0000-0002-4548-4550)
- Jeff Soules (ORCID: https://orcid.org/0000-0002-2240-1038)
- Kyu Hyun Lee (ORCID: https://orcid.org/0000-0001-6483-9444)
- Caleb Kemere (ORCID: https://orcid.org/0000-0003-2054-0234)
- Ryan Ly (ORCID: https://orcid.org/0000-0001-9238-0642)
- Eric L. Denovellis (ORCID: https://orcid.org/0000-0003-4606-087X)
- Joshua Chu (ORCID: https://orcid.org/0000-0002-3390-2292)
- Jennifer A. Guidera (ORCID: https://orcid.org/0000-0003-4013-214X)
- Jeremy F. Magland (ORCID: https://orcid.org/0000-0002-5286-4375)
- Xulu Sun (ORCID: https://orcid.org/0000-0003-3076-0994)
- Alison E. Comrie (ORCID: https://orcid.org/0000-0002-2251-4892)
- Samuel R. Bray (ORCID: https://orcid.org/0000-0002-9696-6920)
- Rhino Nevers (ORCID: https://orcid.org/0000-0003-2144-6952)
- Emrey Broyles (ORCID: https://orcid.org/0000-0001-5559-2910)
- Loren M. Frank (ORCID: https://orcid.org/0000-0002-1752-5677)
- Samuel Garcia (ORCID: https://orcid.org/0000-0001-6389-9779)
- Chris Brozdowski
- Philip Adenekan (ORCID: https://orcid.org/0000-0002-4999-7847)
- Thinh Nguyen (ORCID: https://orcid.org/0000-0001-5964-5872)
- Andrew Tritt (ORCID: https://orcid.org/0000-0002-1617-449X)
- Cristofer Holobetz (ORCID: https://orcid.org/0009-0009-8567-3290)
- Dong‐Hoon Shin (ORCID: https://orcid.org/0009-0000-8916-7314)
- Emily Monroe (ORCID: https://orcid.org/0000-0002-5751-231X)
- Dimitri Yatsenko (ORCID: https://orcid.org/0000-0002-1844-641X)
Institutions
- Centre National de la Recherche Scientifique (FR)
- Allen Institute for Brain Science (US)
- Howard Hughes Medical Institute (US)
- Lawrence Berkeley National Laboratory (US)
- University of California, San Francisco (US)
- Sainsbury Laboratory (GB)
- Centre de Recherche en Neurosciences de Lyon (FR)
- DataJoint NEURO (United States) (US)
- Allen Institute (US)
- Flatiron Health (United States) (US)
- Flatiron Institute (US)
- University College London (GB)
- Rice University (US)
- University of Tübingen (DE)
- University of California, Berkeley (US)
Publication Details
- Journal
- eLife
- Published
- 2025-09-26
- DOI
- https://doi.org/10.7554/elife.108089
- Primary Topic
- Cell Image Analysis Techniques
- Type
- article
- Field-Weighted Citation Impact
- 0.00