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spyglass-neuro

Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF

https://github.com/lorenfranklab/spyglass

Science Score: 75.0%

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    Found .zenodo.json file
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    DOI references
    Found 5 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    11 of 34 committers (32.4%) from academic institutions
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    Institutional organization owner
    Organization lorenfranklab has institutional domain (franklab.ucsf.edu)
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    Low similarity (13.5%) to scientific vocabulary

Keywords

datajoint electrophysiology kachery neuroscience nwb python sortingview spikeinterface

Keywords from Contributors

state-space-models
Last synced: 6 months ago · JSON representation ·

Repository

Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF

Basic Info
Statistics
  • Stars: 103
  • Watchers: 10
  • Forks: 50
  • Open Issues: 87
  • Releases: 6
Topics
datajoint electrophysiology kachery neuroscience nwb python sortingview spikeinterface
Created about 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

spyglass

Tests PyPI version

Spyglass Figure

Demo | Installation | Docs | Tutorials | Citation

spyglass is a data analysis framework that facilitates the storage, analysis, visualization, and sharing of neuroscience data to support reproducible research. It is designed to be interoperable with the NWB format and integrates open-source tools into a coherent framework.

Try out a demo here!

Features of Spyglass include:

  • Standardized data storage - Spyglass uses the open-source Neurodata Without Borders: Neurophysiology (NWB:N) format to ingest and store processed data. NWB:N is a standard set by the BRAIN Initiative for neurophysiological data (Rübel et al., 2022).
  • Reproducible analysis - Spyglass uses DataJoint to ensure that all analysis is reproducible. DataJoint is a data management system that automatically tracks dependencies between data and analysis code. This ensures that all analysis is reproducible and that the results are automatically updated when the data or analysis code changes.
  • Common analysis tools - Spyglass provides easy usage of the open-source packages SpikeInterface, Ghostipy, and DeepLabCut for common analysis tasks. These packages are well-documented and have active developer communities.
  • Interactive data visualization - Spyglass uses figurl to create interactive data visualizations that can be shared with collaborators and the broader community. These visualizations are hosted on the web and can be viewed in any modern web browser. The interactivity allows users to explore the data and analysis results in detail.
  • Sharing results - Spyglass enables sharing of data and analysis results via Kachery, a decentralized content addressable data sharing platform. Kachery Cloud allows users to access the database and pull data and analysis results directly to their local machine.
  • Pipeline versioning - Processing and analysis of data in neuroscience is often dynamic, requiring new features. Spyglass uses Merge tables to ensure that analysis pipelines can be versioned. This allows users to easily use and compare results from different versions of the analysis pipeline while retaining the ability to access previously generated results.
  • Cautious Delete - Spyglass uses a cautious delete feature to ensure that data is not accidentally deleted by other users. When a user deletes data, Spyglass will first check to see if the data belongs to another team of users. This enables teams of users to work collaboratively on the same database without worrying about accidentally deleting each other's data.

Documentation can be found at - https://lorenfranklab.github.io/spyglass/

Installation

For installation instructions see - https://lorenfranklab.github.io/spyglass/latest/notebooks/00_Setup/

Typical installation time is: 5-10 minutes

Tutorials

The tutorials for spyglass are currently in the form of Jupyter Notebooks and can be found in the notebooks directory. We strongly recommend running the notebooks yourself.

Contributing

See the Developer's Note for contributing instructions found at - https://lorenfranklab.github.io/spyglass/latest/contribute/

License/Copyright

License and Copyright notice can be found at https://lorenfranklab.github.io/spyglass/latest/LICENSE/

System requirements

Spyglass has been tested on Linux Ubuntu 20.04 and MacOS 10.15. It has not been tested on Windows and likely will not work.

No specific hardware requirements are needed to run spyglass. However, the amount of data that can be stored and analyzed is limited by the available disk space and memory. GPUs are required for some of the analysis tools, such as DeepLabCut.

See pyproject.toml, environment.yml, or environment_dlc.yml for software dependencies.

See spec-file.txt for the conda environment used in the demo.

Citation

Lee, K.H.*, Denovellis, E.L.*, Ly, R., Magland, J., Soules, J., Comrie, A.E., Gramling, D.P., Guidera, J.A., Nevers, R., Adenekan, P., Brozdowski, C., Bray, S., Monroe, E., Bak, J.H., Coulter, M.E., Sun, X., Broyles, E., Shin, D., Chiang, S., Holobetz, C., Tritt, A., Rübel, O., Nguyen, T., Yatsenko, D., Chu, J., Kemere, C., Garcia, S., Buccino, A., Frank, L.M., 2024. Spyglass: a data analysis framework for reproducible and shareable neuroscience research. bioRxiv. 10.1101/2024.01.25.577295.

* Equal contribution

See paper related code here.

Owner

  • Name: Loren Frank Lab at UCSF
  • Login: LorenFrankLab
  • Kind: organization
  • Location: San Francisco, CA, USA

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: 'Spyglass: a data analysis framework for reproducible and shareable neuroscience research'
message: 'If you use this software, please cite it as below.'
type: software
authors:
  - given-names: Kyu Hyun
    family-names: Lee
    email: kyuhyun.lee@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0001-6483-9444'
  - given-names: Eric L.
    family-names: Denovellis
    email: eric.denovellis@ucsf.edu
    affiliation: Howard Hughes Medical Institute
    orcid: 'https://orcid.org/0000-0003-4606-087X'
  - given-names: Ryan
    family-names: Ly
    email: rly@lbl.gov
    affiliation: Lawrence Berkeley National Laboratory
    orcid: 'https://orcid.org/0000-0001-9238-0642'
  - given-names: Jeremy
    family-names: Magland
    email: jmagland@flatironinstitute.org
    affiliation: Flatiron Institute
    orcid: 'https://orcid.org/0000-0002-5286-4375'
  - given-names: Jeff
    family-names: Soules
    email: jsoules@flatironinstitute.org
    affiliation: Flatiron Institute
  - given-names: Alison E.
    family-names: Comrie
    orcid: 'https://orcid.org/0000-0002-2251-4892'
    email: alison.comrie@ucsf.edu
    affiliation: 'University of California, San Francisco'
  - given-names: Daniel P.
    family-names: Gramling
    orcid: 'https://orcid.org/0009-0004-6136-3769'
    affiliation: University of Tübingen
  - given-names: Jennifer A.
    family-names: Guidera
    email: jennifer.guidera@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0003-4013-214X'
  - given-names: Rhino
    family-names: Nevers
    email: rhino.nevers@ucsf.edu
    affiliation: 'University of California, San Francisco'
  - given-names: Philip
    family-names: Adenekan
    email: phil.adenekan@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0002-4999-7847'
  - given-names: Chris
    family-names: Brozdowski
    email: chris.broz@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0002-3055-6718'
  - given-names: Samuel
    family-names: Bray
    email: sam.bray@ucsf.edu
    orcid: 'https://orcid.org/0000-0002-9696-6920'
    affiliation: 'University of California, San Francisco'
  - given-names: Emily
    family-names: Monroe
    affiliation: University of California, Davis
  - given-names: Ji Hyun
    family-names: Bak
    orcid: 'https://orcid.org/0000-0002-5700-7823'
  - given-names: Michael E.
    family-names: Coulter
    email: michael.coulter@ucsf.edu
    orcid: 'https://orcid.org/0000-0003-0357-351X'
    affiliation: 'University of California, San Francisco'
  - given-names: Xulu
    family-names: Sun
    email: xulu.sun@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0003-3076-0994'
  - given-names: Broyles
    family-names: Emrey
    email: emrey.broyles@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0001-5559-2910'
  - given-names: Donghoon
    family-names: Shin
    email: donghoon.shin@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0009-0000-8916-7314'
  - given-names: Sharon
    family-names: Chiang
    email: sharon.chiang@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0002-4548-4550'
  - given-names: Cristofer
    family-names: Holobetz
    email: cristofer.holobetz.23@ucl.ac.uk
    affiliation: 'University College London'
    orcid: 'https://orcid.org/0009-0009-8567-3290'
  - given-names: Andrew
    family-names: Tritt
    email: ajtritt@lbl.gov
    affiliation: Lawrence Berkeley National Laboratory
    orcid: 'https://orcid.org/0000-0002-1617-449X'
  - given-names: Oliver
    family-names: Rübel
    email: oruebel@lbl.gov
    affiliation: Lawrence Berkeley National Laboratory
    orcid: 'https://orcid.org/0000-0001-9902-1984'
  - given-names: Thinh
    family-names: Nguyen
    affiliation: Datajoint
    email: thinh@datajoint.com
  - given-names: Dimitri
    family-names: Yatsenko
    email: dimitri@datajoint.com
    affiliation: Datajoint
    orcid: 'https://orcid.org/0000-0002-1844-641X'
  - given-names: Joshua
    family-names: Chu
    email: jpc6@rice.edu
    affiliation: Rice University
  - given-names: Caleb
    family-names: Kemere
    email: caleb.kemere@rice.edu
    affiliation: Rice University
    orcid: 'https://orcid.org/0000-0003-2054-0234'
  - given-names: Samuel
    family-names: Garcia
    email: samuel.garcia@cnrs.fr
    affiliation: 'Centre de Recherche en Neurosciences de Lyon'
    orcid: 'https://orcid.org/0000-0001-6389-9779'
  - given-names: Alessio
    family-names: Buccino
    email: alessio.buccino@alleninstitute.org
    affiliation: Allen Institute
    orcid: 'https://orcid.org/0000-0003-3661-527X'
  - given-names: Loren M.
    family-names: Frank
    email: loren.frank@ucsf.edu
    affiliation: 'University of California, San Francisco'
    orcid: 'https://orcid.org/0000-0002-1752-5677'
identifiers:
  - type: doi
    value: 10.1101/2024.01.25.577295
    description: bioRxiv preprint
repository-code: 'https://github.com/LorenFrankLab/spyglass'
url: 'https://lorenfranklab.github.io/spyglass/'
abstract: >-
  Spyglass is a data analysis framework that facilitates the
  storage, analysis, visualization, and sharing of
  neuroscience data to support reproducible research. It is
  designed to be interoperable with the NWB format and
  integrates open-source tools into a coherent framework.
keywords:
  - neuroscience
  - open science
  - electrophysiology
  - figurl
  - interactive data visualization
  - Neurodata Without Borders
  - Spike interface
  - Datajoint
  - spike sorting
  - kachery
license: MIT
version: 0.5.5
date-released: '2025-08-06'

GitHub Events

Total
  • Create event: 47
  • Release event: 2
  • Issues event: 220
  • Watch event: 8
  • Delete event: 39
  • Issue comment event: 344
  • Push event: 352
  • Pull request review comment event: 442
  • Pull request review event: 490
  • Pull request event: 139
  • Fork event: 8
Last Year
  • Create event: 47
  • Release event: 2
  • Issues event: 220
  • Watch event: 8
  • Delete event: 39
  • Issue comment event: 344
  • Push event: 352
  • Pull request review comment event: 442
  • Pull request review event: 490
  • Pull request event: 139
  • Fork event: 8

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 1,518
  • Total Committers: 34
  • Avg Commits per committer: 44.647
  • Development Distribution Score (DDS): 0.778
Past Year
  • Commits: 310
  • Committers: 23
  • Avg Commits per committer: 13.478
  • Development Distribution Score (DDS): 0.871
Top Committers
Name Email Commits
Loren Frank l****n@p****u 337
Kyu Hyun Lee k****6@g****m 298
Eric Denovellis e****o@b****u 197
Eric Denovellis e****s@g****m 184
Ryan Ly r****y@l****v 134
Eric Denovellis e****o 63
dpeg22 d****2@g****m 49
Samuel Bray s****y@u****u 39
jguides j****a@g****m 31
Chris Brozdowski C****z@u****u 24
CBroz1 C****i@y****m 19
Jeremy Magland j****d@g****m 16
MichaelCoulter 3****r 16
acomrie 4****e 16
Daniel Gramling 5****2 15
Kyu Hyun Lee k****u@t****u 12
Phil z****o@g****m 11
Jeremy Magland j****d@f****g 11
jguides 4****s 7
emilymonroe95 7****5 7
Jeremy Magland m****d 6
kyu k****e@u****u 4
Michael Coulter m****r@g****m 3
cbroz1 c****z@u****u 3
Ji Hyun Bak 3****k 3
emreybroyles 1****s 3
sharon-chiang 9****g 3
shenshan s****u@g****m 1
Xulu Sun x****9 1
cristofer-holobetz 3****z 1
and 4 more...
Committer Domains (Top 20 + Academic)
ucsf.edu: 5 cyclone.cin.ucsf.edu: 1 onerussian.com: 1 flatironinstitute.org: 1 typhoon.cin.ucsf.edu: 1 lbl.gov: 1 bu.edu: 1 phy.ucsf.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 524
  • Total pull requests: 643
  • Average time to close issues: 4 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 35
  • Total pull request authors: 28
  • Average comments per issue: 1.86
  • Average comments per pull request: 1.29
  • Merged pull requests: 525
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 157
  • Pull requests: 208
  • Average time to close issues: 16 days
  • Average time to close pull requests: 8 days
  • Issue authors: 22
  • Pull request authors: 13
  • Average comments per issue: 1.1
  • Average comments per pull request: 0.94
  • Merged pull requests: 152
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • samuelbray32 (121)
  • CBroz1 (72)
  • edeno (56)
  • MichaelCoulter (52)
  • rpswenson (24)
  • khl02007 (20)
  • lfrank (19)
  • magland (17)
  • xlsun79 (15)
  • dpeg22 (14)
  • jguides (10)
  • shijiegu (10)
  • pauladkisson (10)
  • acomrie (9)
  • zoldello (8)
Pull Request Authors
  • CBroz1 (229)
  • samuelbray32 (192)
  • edeno (82)
  • khl02007 (41)
  • dpeg22 (17)
  • MichaelCoulter (14)
  • rly (11)
  • jguides (6)
  • emreybroyles (6)
  • lfrank (6)
  • magland (6)
  • bendichter (5)
  • zoldello (4)
  • shijiegu (4)
  • acomrie (3)
Top Labels
Issue Labels
enhancement (99) bug (89) spike sorting (51) position (36) infrastructure (30) documentation (29) common (29) LFP (13) decoding (13) merge (12) Database (12) NWB ingestion (8) wontfix (6) question (5) ripple (3) invalid (1) good first issue (1)
Pull Request Labels
enhancement (19) position (16) infrastructure (16) bug (9) LFP (8) spike sorting (7) decoding (4) merge (3) documentation (2) ripple (2) question (1) common (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 185 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 28
  • Total maintainers: 4
pypi.org: spyglass-neuro

Neuroscience data analysis framework for reproducible research

  • Homepage: https://github.com/LorenFrankLab/spyglass
  • Documentation: https://spyglass-neuro.readthedocs.io/
  • License: Copyright (c) 2020-present Loren Frank Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BEsq LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  • Latest release: 0.5.5
    published 7 months ago
  • Versions: 27
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 185 Last month
Rankings
Forks count: 7.1%
Stargazers count: 9.5%
Dependent packages count: 10.1%
Average: 12.8%
Downloads: 15.9%
Dependent repos count: 21.5%
Maintainers (3)
edeno rly khl02007
Last synced: 6 months ago
pypi.org: spyndle-web-api

A non-destructive Web API for Spyglass

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 10.0%
Average: 37.9%
Dependent repos count: 65.8%
Maintainers (1)
magland
Last synced: over 1 year ago

Dependencies

.github/workflows/black.yml actions
  • actions/checkout v3 composite
  • psf/black stable composite
.github/workflows/workflow.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • conda-incubator/setup-miniconda v2 composite
  • styfle/cancel-workflow-action 0.11.0 composite
environment.yml pypi
  • black *
  • click *
  • datajoint >=0.13.6
  • figurl-jupyter *
  • ghostipy *
  • hdmf >=3.4.6
  • pubnub <6.4.0
  • pymysql *
  • pynwb >=2.2.0,<3
  • pyyaml *
  • sortingview >=0.11
requirements-dev.txt pypi
  • hither2 * development
  • kachery * development
  • kachery-client * development
  • kachery-cloud * development
  • pytest * development
  • pytest-cov * development