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neuroconv

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

https://github.com/catalystneuro/neuroconv

Science Score: 54.0%

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
    2 of 19 committers (10.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.4%) to scientific vocabulary

Keywords from Contributors

neuroscience brain eeg ieeg neuroimaging
Last synced: 6 months ago · JSON representation ·

Repository

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

Basic Info
Statistics
  • Stars: 62
  • Watchers: 3
  • Forks: 30
  • Open Issues: 129
  • Releases: 36
Created over 3 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

PyPI version Daily Tests Auto-release codecov documentation Python Code Style License

NeuroConv logo

Automatically convert neurophysiology data to NWB

Explore our documentation »

Table of Contents

About

NeuroConv is a Python package for converting neurophysiology data in a variety of proprietary formats to the Neurodata Without Borders (NWB) standard.

Features:

  • Reads data from 40 popular neurophysiology data formats and writes to NWB using best practices.
  • Extracts relevant metadata from each format.
  • Handles large data volume by reading datasets piece-wise.
  • Minimizes the size of the NWB files by automatically applying chunking and lossless compression.
  • Supports ensembles of multiple data streams, and supports common methods for temporal alignment of streams.

Installation

We always recommend installing and running Python packages in a clean environment. One way to do this is via conda environments:

shell conda create --name <give the environment a name> --python <choose a version of Python to use> conda activate <environment name>

To install the latest stable release of neuroconv though PyPI, run:

shell pip install neuroconv

To install the current unreleased main branch (requires git to be installed in your environment, such was via conda install git), run:

shell pip install git+https://github.com/catalystneuro/neuroconv.git@main

NeuroConv also supports a variety of extra dependencies that can be specified inside square brackets, such as

shell pip install "neuroconv[openephys, dandi]"

which will then install extra dependencies related to reading OpenEphys data as well as the usage of the DANDI CLI (such as automatic upload to the DANDI Archive).

You can read more about these options in the main installation guide.

Documentation

See our ReadTheDocs page for full documentation, including a gallery of all supported formats.

License

NeuroConv is distributed under the BSD3 License. See LICENSE for more information.

Owner

  • Name: CatalystNeuro
  • Login: catalystneuro
  • Kind: organization
  • Email: hello@catalystneuro.com

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Baker
    given-names: Cody
    orcid: https://orcid.org/0000-0002-0829-4790
  - family-names: Mayorquin
    given-names: Heberto
    orcid: https://orcid.org/0000-0002-5937-7537
  - family-names: Weigl
    given-names: Anna Szonja
    orcid: https://orcid.org/0000-0001-6615-1360
  - family-names: Tauffer
    given-names: Luiz
  - family-names: Buccino
    given-names: Alessio Paolo
    orcid: https://orcid.org/0000-0003-3661-527X
  - family-names: Sharda
    given-names: Saksham
  - family-names: Dichter
    given-names: Benjamin
    orcid: https://orcid.org/0000-0001-5725-6910
title: "NeuroConv"
version: 0.3.0
date-released: 2023-06-07
url: "https://github.com/catalystneuro/neuroconv.git"

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 4,131
  • Total Committers: 19
  • Avg Commits per committer: 217.421
  • Development Distribution Score (DDS): 0.784
Top Committers
Name Email Commits
Cody Baker 5****D@u****m 892
h-mayorquin h****n@g****m 692
Cody Baker c****9@n****u 587
CodyCBakerPhD c****d@g****m 459
bendichter b****r@g****m 411
luiztauffer l****r@h****m 386
weiglszonja w****a@g****m 204
pre-commit-ci[bot] 6****]@u****m 169
Saksham Sharda s****a@g****m 151
Alessio Buccino a****7@g****m 53
Cody Baker c****d@g****m 36
sbuergers s****s@g****m 31
Julia Sprenger j****r@r****e 28
Saksham Sharda 1****0@u****m 14
Steffen Bürgers 3****s@u****m 7
dependabot[bot] 4****]@u****m 5
Yaroslav Halchenko d****n@o****m 4
luiz l****r@o****m 1
wuffi 2****i@u****m 1
Committer Domains (Top 20 + Academic)
otmail.com: 1 onerussian.com: 1 rwth-aachen.de: 1 nd.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 324
  • Total pull requests: 1,298
  • Average time to close issues: 5 months
  • Average time to close pull requests: 27 days
  • Total issue authors: 65
  • Total pull request authors: 20
  • Average comments per issue: 2.38
  • Average comments per pull request: 2.43
  • Merged pull requests: 967
  • Bot issues: 0
  • Bot pull requests: 59
Past Year
  • Issues: 137
  • Pull requests: 500
  • Average time to close issues: 14 days
  • Average time to close pull requests: 9 days
  • Issue authors: 32
  • Pull request authors: 14
  • Average comments per issue: 1.04
  • Average comments per pull request: 1.8
  • Merged pull requests: 348
  • Bot issues: 0
  • Bot pull requests: 24
View more stats
Top Authors
Issue Authors
  • h-mayorquin (58)
  • bendichter (55)
  • CodyCBakerPhD (41)
  • pauladkisson (39)
  • rly (16)
  • weiglszonja (11)
  • tabedzki (8)
  • luiztauffer (6)
  • vigji (5)
  • tuanpham96 (4)
  • garrettmflynn (4)
  • magland (3)
  • Jai477 (3)
  • TheChymera (3)
  • yarikoptic (3)
Pull Request Authors
  • h-mayorquin (542)
  • CodyCBakerPhD (282)
  • bendichter (172)
  • pauladkisson (108)
  • pre-commit-ci[bot] (59)
  • weiglszonja (34)
  • Copilot (19)
  • alejoe91 (15)
  • luiztauffer (13)
  • alessandratrapani (12)
  • rly (8)
  • daphnedequatrebarbes (8)
  • garrettmflynn (7)
  • felixp8 (5)
  • magland (4)
Top Labels
Issue Labels
enhancement (127) bug (107) data interfaces (43) documentation (29) priority: low (11) new format (10) discussion (10) metadata (8) dependencies (8) question (6) testing (4) ecehys (3) code reduction (2) refactor (2) ophys (2) ecephys (2) spikeinterface (1) packaging (1) schema (1) medium priority (1) organization (1) coverage (1) Copilot (1) behavior (1) priority: medium (1) deprecation (1) priority: critical (1)
Pull Request Labels
testing (86) documentation (65) enhancement (63) data interfaces (59) bug (59) dependencies (48) metadata (34) CI (31) deprecation (24) refactor (9) packaging (7) ophys (5) regression (4) ecephys (3) ecehys (3) codex (3) pose estimation (2) schema (2) spikeinterface (2) discussion (2) priority: critical (1) performance (1) priority: low (1) behavior (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 5,150 last-month
  • Total dependent packages: 6
  • Total dependent repositories: 8
  • Total versions: 36
  • Total maintainers: 3
pypi.org: neuroconv

Convert data from proprietary formats to NWB format.

  • Homepage: https://github.com/catalystneuro/neuroconv
  • Documentation: https://neuroconv.readthedocs.io/
  • License: BSD 3-Clause License Copyright (c) 2019, Neurodata Without Borders All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.8.0
    published 7 months ago
  • Versions: 36
  • Dependent Packages: 6
  • Dependent Repositories: 8
  • Downloads: 5,150 Last month
Rankings
Dependent packages count: 2.4%
Dependent repos count: 5.2%
Downloads: 6.3%
Average: 7.0%
Forks count: 10.2%
Stargazers count: 11.3%
Maintainers (3)
h.mayorquin bendichter pauladkisson
Last synced: 6 months ago

Dependencies

requirements-minimal.txt pypi
  • PyYAML >=5.4
  • click *
  • dandi ==0.39.6
  • h5py >=2.10.0
  • hdmf >=3.2.1
  • jsonschema >=3.2.0
  • lxml >=4.6.5
  • natsort >=7.1.1
  • neo >=0.9.0
  • numpy >=1.22.0
  • numpy >=1.21.0
  • psutil >=5.8.0
  • pynwb >=1.4.0
  • pyopenephys >=1.1.2
  • roiextractors ==0.4.18
  • scipy >=1.4.1
  • spikeextractors >=0.9.10
  • tqdm >=4.60.0
requirements-rtd.txt pypi
  • Jinja2 <3.1
  • Sphinx ==5.1.1
  • myst_parser ==0.18.0
  • readthedocs-sphinx-search ==0.1.2
  • sphinx-copybutton ==0.5.0
  • sphinx-toggleprompt ==0.2.0
  • sphinx_rtd_theme ==1.0.0
requirements-testing.txt pypi
  • ndx-dandi-icephys >=0.4.0 test
  • ndx-events ==0.2.0 test
  • parameterized ==0.8.1 test
  • pytest * test
  • pytest-cov * test
pyproject.toml pypi
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setup.py pypi
src/neuroconv/datainterfaces/behavior/audio/requirements.txt pypi
  • ndx-sound >=0.2.0
src/neuroconv/datainterfaces/behavior/deeplabcut/requirements.txt pypi
  • dlc2nwb >=0.3
  • tables *
src/neuroconv/datainterfaces/behavior/fictrac/requirements.txt pypi
src/neuroconv/datainterfaces/behavior/miniscope/requirements.txt pypi
  • natsort >=8.3.1
  • ndx-miniscope >=0.5.1
src/neuroconv/datainterfaces/behavior/sleap/requirements.txt pypi
  • av >=10.0.0
  • sleap-io >=0.0.2
src/neuroconv/datainterfaces/behavior/video/requirements.txt pypi
  • opencv-python-headless >=4.5.1.48
  • opencv-python-headless >=4.5.1.48,<4.7.0.72
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src/neuroconv/datainterfaces/ecephys/cellexplorer/requirements.txt pypi
  • hdf5storage >=0.1.18
  • pymatreader >=0.0.32
src/neuroconv/datainterfaces/ecephys/edf/requirements.txt pypi
  • numpy <1.25.0
  • pyedflib >=0.1.30
src/neuroconv/datainterfaces/ecephys/intan/requirements.txt pypi
  • pyintan >=0.3.0
src/neuroconv/datainterfaces/ecephys/mearec/requirements.txt pypi
  • MEArec >=1.8.0
src/neuroconv/datainterfaces/ecephys/neuralynx/requirements.txt pypi
  • natsort >=7.1.1
src/neuroconv/datainterfaces/ecephys/neuroscope/requirements.txt pypi
  • lxml >=4.6.5
src/neuroconv/datainterfaces/ecephys/openephys/requirements.txt pypi
  • pyopenephys >=1.1.2
src/neuroconv/datainterfaces/ecephys/requirements.txt pypi
  • packaging <22.0
  • spikeinterface >=0.98.2
src/neuroconv/datainterfaces/ecephys/spike2/requirements.txt pypi
  • sonpy >=1.7.1
src/neuroconv/datainterfaces/ecephys/spikeinterface/requirements.txt pypi
  • spikeextractors *
src/neuroconv/datainterfaces/icephys/abf/requirements.txt pypi
  • ndx-dandi-icephys >=0.4.0
src/neuroconv/datainterfaces/icephys/requirements.txt pypi
  • neo >=0.9.0
src/neuroconv/datainterfaces/ophys/brukertiff/requirements.txt pypi
  • tifffile >=2023.3.21
src/neuroconv/datainterfaces/ophys/micromanagertiff/requirements.txt pypi
  • tifffile >=2023.3.21
src/neuroconv/datainterfaces/ophys/miniscope/requirements.txt pypi
  • natsort >=8.3.1
  • ndx-miniscope >=0.5.1
src/neuroconv/datainterfaces/ophys/requirements.txt pypi
  • roiextractors >=0.5.3
src/neuroconv/datainterfaces/ophys/scanimage/requirements.txt pypi
  • scanimage-tiff-reader >=1.4.1
src/neuroconv/datainterfaces/ophys/tiff/requirements.txt pypi
  • tiffile >=2018.10.18
src/neuroconv/datainterfaces/text/excel/requirements.txt pypi
  • openpyxl *
  • xlrd *
.github/workflows/dailies.yml actions
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src/neuroconv/datainterfaces/behavior/lightningpose/requirements.txt pypi
  • ndx-pose ==0.1.1
  • neuroconv *
src/neuroconv/datainterfaces/ecephys/maxwell/requirements.txt pypi
  • h5py <=3.9.0