python-neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

https://github.com/neuralensemble/python-neo

Science Score: 62.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
✓
Committers with academic emails
17 of 112 committers (15.2%) from academic institutions
✓
Institutional organization owner
Organization neuralensemble has institutional domain (neuralensemble.org)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary

Keywords from Contributors

neuroscience gtk qt tk wx neuroimaging closember bids meg eeg

Last synced: 6 months ago · JSON representation ·

Repository

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

Basic Info

Host: GitHub
Owner: NeuralEnsemble
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: http://neo.readthedocs.io/en/latest/
Size: 109 MB

Statistics

Stars: 347
Watchers: 31
Forks: 259
Open Issues: 146
Releases: 13

Created almost 14 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation Authors Codemeta

README.rst

===
Neo
===

Neo is a Python package for working with electrophysiology data in Python, together
with support for reading a wide range of neurophysiology file formats, including
Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for
writing to a subset of these formats plus non-proprietary formats including HDF5.

The goal of Neo is to improve interoperability between Python tools for
analyzing, visualizing and generating electrophysiology data by providing a common,
shared object model. In order to be as lightweight a dependency as possible,
Neo is deliberately limited to represention of data, with no functions for data
analysis or visualization.

Neo is used by a number of other software tools, including
SpykeViewer_ (data analysis and visualization), Elephant_ (data analysis),
the G-node_ suite (databasing), PyNN_ (simulations), tridesclous_ (spike sorting)
and ephyviewer_ (data visualization).
OpenElectrophy_ (data analysis and visualization) uses an older version of neo.

Neo implements a hierarchical data model well adapted to intracellular and
extracellular electrophysiology and EEG data with support for multi-electrodes
(for example tetrodes). Neo's data objects build on the quantities package,
which in turn builds on NumPy by adding support for physical dimensions. Thus
Neo objects behave just like normal NumPy arrays, but with additional metadata,
checks for dimensional consistency and automatic unit conversion.

A project with similar aims but for neuroimaging file formats is `NiBabel`_.
Neo is a `NumFocus Affiliated Project`_.

Code status
-----------

.. image:: https://img.shields.io/pypi/v/neo.svg
   :target: https://pypi.python.org/pypi/neo
   :alt: PyPI Release Version
.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/core-test.yml/badge.svg?event=push&branch=master
   :target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
   :alt: Core Test Status (Github Actions)
.. image:: https://github.com/NeuralEnsemble/python-neo/actions/workflows/io-test_trigger.yml/badge.svg?event=push&branch=master
   :target: https://github.com/NeuralEnsemble/python-neo/actions?query=event%3Apush+branch%3Amaster
   :alt: IO Test Status (Github Actions)
.. image:: https://coveralls.io/repos/NeuralEnsemble/python-neo/badge.png
   :target: https://coveralls.io/r/NeuralEnsemble/python-neo
   :alt: Unit Test Coverage

More information
----------------

- Home page: http://neuralensemble.org/neo
- Mailing list: http://neuralensemble.org/community
- Documentation: http://neo.readthedocs.io/
- Bug reports: https://github.com/NeuralEnsemble/python-neo/issues

For installation instructions, see doc/source/install.rst

To cite Neo in publications, see CITATION.txt

:copyright: Copyright 2010-2025 by the Neo team, see doc/source/authors.rst.
:license: 3-Clause Revised BSD License, see LICENSE.txt for details.

Funding
-------

Development of Neo has been partially funded by the European Union Sixth Framework Program (FP6) under
grant agreement FETPI-015879 (FACETS), by the European Union Seventh Framework Program (FP7/2007-2013)
under grant agreements no. 269921 (BrainScaleS) and no. 604102 (HBP),
and by the European Union’s Horizon 2020 Framework Programme for
Research and Innovation under the Specific Grant Agreements No. 720270 (Human Brain Project SGA1),
No. 785907 (Human Brain Project SGA2) and No. 945539 (Human Brain Project SGA3),
and by the European Union's Research and Innovation Program Horizon Europe Grant Agreement No. 101147319 (EBRAINS 2.0).

.. _OpenElectrophy: https://github.com/OpenElectrophy/OpenElectrophy
.. _Elephant: http://neuralensemble.org/elephant
.. _G-node: http://www.g-node.org/
.. _Neuroshare: http://neuroshare.org/
.. _SpykeViewer: https://spyke-viewer.readthedocs.org/en/latest/
.. _NiBabel: http://nipy.sourceforge.net/nibabel/
.. _PyNN: http://neuralensemble.org/PyNN
.. _quantities: http://pypi.python.org/pypi/quantities
.. _`NeuralEnsemble mailing list`: http://neuralensemble.org/community
.. _`issue tracker`: https://github.c
.. _tridesclous: https://github.com/tridesclous/tridesclous
.. _ephyviewer: https://github.com/NeuralEnsemble/ephyviewer
.. _`NumFocus Affiliated Project`: https://numfocus.org/sponsored-projects/affiliated-projects

Owner

Name: NeuralEnsemble
Login: NeuralEnsemble
Kind: organization

Website: http://neuralensemble.org
Repositories: 25
Profile: https://github.com/NeuralEnsemble

Citation (CITATION.txt)

To cite Neo in publications, please use:

    Garcia S., Guarino D., Jaillet F., Jennings T.R., Pröpper R., Rautenberg P.L.,
    Rodgers C., Sobolev A.,Wachtler T., Yger P. and Davison A.P. (2014)
    Neo: an object model for handling electrophysiology data in multiple formats.
    Frontiers in Neuroinformatics 8:10: doi:10.3389/fninf.2014.00010

A BibTeX entry for LaTeX users is::

    @article{neo14,
        author = {Garcia S. and Guarino D. and Jaillet F. and Jennings T.R. and Pröpper R. and
                  Rautenberg P.L. and Rodgers C. and Sobolev A. and Wachtler T. and Yger P.
                  and Davison A.P.},
        doi = {10.3389/fninf.2014.00010},
        full_text = {http://www.frontiersin.org/Journal/10.3389/fninf.2014.00010/abstract},
        journal = {Frontiers in Neuroinformatics},
        month = {February},
        title = {Neo: an object model for handling electrophysiology data in multiple formats},
        volume = {8:10},
        year = {2014}
    }

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Committers

Last synced: almost 3 years ago

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Total Commits: 3,175
Total Committers: 112
Avg Commits per committer: 28.348
Development Distribution Score (DDS): 0.861

Top Committers

Name	Email	Commits
Samuel Garcia	s**e@g**m	441
Andrew Davison	a**n@u**r	318
sgarcia	s**a@a**a	259
Julia Sprenger	j**r@r**e	218
Björn Müller	b**r@f**e	199
Achilleas Koutsou	a**k@g**m	158
sprenger	j**r@u**r	152
Todd Jennings	t**n@g**m	132
Peter N. Steinmetz	P**z@s**g	124
Samuel Garcia	s**e@g**m	70
kleinjohann	a**n@f**e	68
Andrew Davison	a**n@c**r	64
apdavison	a**n@a**a	60
Jeffrey Gill	j**l@g**m	57
Alessio Buccino	a**7@g**m	55
Michael Denker	m**r@f**e	51
Mikkel Elle Lepperød	l**k@g**m	50
crodger	c**r@a**a	47
Elodie Legouée	e**e@u**r	45
Thomas Perret	t**t@i**r	35
teogale	c**d@g**m	28
Robert Pröpper	r**r@g**m	27
ygordon	y**n@a**a	26
Chadwick Boulay	c**y@g**m	26
mgr0dzicki	m**b@g**m	25
sbuergers	s**s@g**m	24
Regimantas Jurkus	r**s@g**m	22
h-mayorquin	h**n@g**m	22
amchagas	a**s@g**m	21
Chek Yin Choi	c**7@g**m	20
and 82 more...

Committer Domains (Top 20 + Academic)

fz-juelich.de: 6 unic.cnrs-gif.fr: 3 rwth-aachen.de: 2 steinmetz.org: 2 cnrs.fr: 2 blackfynn.com: 2 univ-amu.fr: 1 isc.cnrs.fr: 1 janelia.hhmi.org: 1 mike.mike: 1 sgarcia-laptop.(none): 1 live.de: 1 gerkin.org: 1 oist.jp: 1 asu.edu: 1 onerussian.com: 1 openred-13.(none): 1 meliza.org: 1 visor.udg.edu: 1 jochen.sprickerhof.de: 1 stanford.edu: 1 ufl.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 282
Total pull requests: 583
Average time to close issues: over 1 year
Average time to close pull requests: about 1 month
Total issue authors: 138
Total pull request authors: 59
Average comments per issue: 3.55
Average comments per pull request: 3.09
Merged pull requests: 425
Bot issues: 1
Bot pull requests: 60

Past Year

Issues: 56
Pull requests: 175
Average time to close issues: 12 days
Average time to close pull requests: 3 days
Issue authors: 33
Pull request authors: 26
Average comments per issue: 2.89
Average comments per pull request: 1.79
Merged pull requests: 110
Bot issues: 1
Bot pull requests: 29

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JuliaSprenger (44)
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mdenker (4)
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nikhilchandra (3)
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Pull Request Authors

zm711 (154)
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github-actions[bot] (60)
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PeterNSteinmetz (24)
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luiztauffer (8)
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nikhilchandra (7)
mahlzahn (6)
easy-electrophysiology (5)
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gkBCCN (4)

Top Labels

Issue Labels

bug (99) enhancement (49) IO (44) Documentation (16) Core (13) good-for-beginners (7) needs-input (6) question (5) continuous-integration (4) New IO Class (4) discussion (3) blocker (2) task (2)

Pull Request Labels

IO (37) enhancement (26) Documentation (18) bug (16) continuous-integration (15) Core (14) defect (9) New IO Class (8) discussion (3) task (3) needs-input (2) work-in-progress (1)

Packages

Total packages: 2
Total downloads:
- pypi 57,320 last-month
Total docker downloads: 94

Total dependent packages: 34
(may contain duplicates)
Total dependent repositories: 171
(may contain duplicates)
Total versions: 44
Total maintainers: 6

pypi.org: neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

Documentation: https://neo.readthedocs.io/
License: BSD 3-Clause License
Latest release: 0.14.2
published 8 months ago

Versions: 33
Dependent Packages: 32
Dependent Repositories: 170
Downloads: 57,320 Last month
Docker Downloads: 94

Rankings

Dependent packages count: 0.6%

Dependent repos count: 1.2%

Average: 1.4%

Downloads: 1.6%

Docker downloads count: 2.3%

Maintainers (6)

apdavison JuliaSprenger sgarcia alejoe91 mdenker zm711

Last synced: 6 months ago

conda-forge.org: python-neo

Homepage: http://neuralensemble.org/neo
License: BSD-3-Clause
Latest release: 0.11.1
published over 3 years ago

Versions: 11
Dependent Packages: 2
Dependent Repositories: 1

Rankings

Forks count: 12.2%

Dependent packages count: 19.6%

Average: 20.1%

Stargazers count: 24.4%

Dependent repos count: 24.4%

Last synced: 6 months ago

Dependencies

doc/requirements_docs.txt pypi

docutils <0.18
numpy >=1.16.1
quantities >=0.12.1

setup.py pypi

numpy >=1.18.5
packaging *
quantities >=0.12.1

.github/workflows/core-test.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/ebrains.yml actions

wei/git-sync v3 composite

.github/workflows/io-test.yml actions

actions/cache v3 composite
actions/checkout v3 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/caches_cron_job.yml actions

actions/cache v3 composite
actions/checkout v3 composite
conda-incubator/setup-miniconda v2.2.0 composite

pyproject.toml pypi

numpy >=1.19.5
packaging *
quantities >=0.14.1

ecosyste.ms

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python-neo

Science Score: 62.0%

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pypi.org: neo

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conda-forge.org: python-neo

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