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Open Source Science

https://github.com/alleninstitute/ipfx

computes intrinsic cell features from intracellular electrophysiology data

https://github.com/alleninstitute/ipfx

Science Score: 36.0%

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

  • ○
    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
    7 of 19 committers (36.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

computes intrinsic cell features from intracellular electrophysiology data

Basic Info
Statistics
  • Stars: 27
  • Watchers: 16
  • Forks: 38
  • Open Issues: 70
  • Releases: 7
Created over 8 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Authors

README.md

Welcome to Intrinsic Physiology Feature Extractor (IPFX)

IPFX is a Python package for computing intrinsic cell features from electrophysiology data. With this package you can:

  • Perform cell data quality control (e.g. resting potential stability)
  • Detect action potentials and their features (e.g. threshold time and voltage)
  • Calculate features of spike trains (e.g., adaptation index)
  • Calculate stimulus-specific cell features

This software is designed for use in the Allen Institute for Brain Science electrophysiology data processing pipeline.

For usage and installation instructions, see the documentation.

Quick Start

To start analyzing data now, check out the quick_start . For a more in depth guide to IPFX, see tutorial

Contributing

We welcome contributions! Please see our contribution guide for more information. Thank you!

Deprecation Warning

The 2.0.0 release of IPFX drops support for Python 3.6 which reached end of life and stopped receiving security updated on December 23, 2021. IPFX is now tested on Python 3.9 and higher.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Create event: 6
  • Issues event: 11
  • Release event: 1
  • Watch event: 1
  • Delete event: 29
  • Issue comment event: 7
  • Push event: 24
  • Pull request review event: 8
  • Pull request review comment event: 5
  • Pull request event: 14
  • Fork event: 1
Last Year
  • Create event: 6
  • Issues event: 11
  • Release event: 1
  • Watch event: 1
  • Delete event: 29
  • Issue comment event: 7
  • Push event: 24
  • Pull request review event: 8
  • Pull request review comment event: 5
  • Pull request event: 14
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 1,022
  • Total Committers: 19
  • Avg Commits per committer: 53.789
  • Development Distribution Score (DDS): 0.635
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Sergey Gratiy s****g@a****g 373
Thomas Braun t****n@b****e 202
nile graddis N****s@g****m 119
Nathan Gouwens n****g@a****g 114
David Feng d****f@a****g 88
gnayuy g****y@g****m 57
Matt Aitken m****2@g****m 28
Sherif Soliman s****n@a****g 16
Nicholas Mei n****i@a****g 4
dyf d****f 4
Tom Chartrand t****d@a****g 3
Katherine Baker k****b@l****n 3
isaak.willett@alleninstitute.org i****t@a****g 2
kasbaker 4****r 2
nicholasc n****e@g****m 2
ru57y34nn m****y@g****m 2
!git for-each-ref --format='%(refname:short)' `git symbolic-ref HEAD` b****r@g****m 1
Matthias Kastner m****r@b****e 1
isaak-willett 5****t 1
Committer Domains (Top 20 + Academic)
alleninstitute.org: 7 byte-physics.de: 2 localhost.localdomain: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 67
  • Total pull requests: 62
  • Average time to close issues: 6 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 22
  • Total pull request authors: 13
  • Average comments per issue: 2.3
  • Average comments per pull request: 0.79
  • Merged pull requests: 43
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 10
  • Pull requests: 10
  • Average time to close issues: 4 months
  • Average time to close pull requests: 9 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.1
  • Average comments per pull request: 0.1
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wbwakeman (13)
  • t-b (9)
  • tmchartrand (9)
  • ru57y34nn (8)
  • sgratiy (5)
  • gouwens (3)
  • kasbaker (2)
  • ozsat (2)
  • NileGraddis (2)
  • youngseok-seo (2)
  • gonzalobenegas (1)
  • beilouer (1)
  • sayakaminegishi (1)
  • sheriferson (1)
  • danielsf (1)
Pull Request Authors
  • MatthewAitken (17)
  • sgratiy (11)
  • t-b (9)
  • ru57y34nn (6)
  • kasbaker (4)
  • tmchartrand (4)
  • sheriferson (3)
  • gouwens (2)
  • mzabolocki (2)
  • sborde (1)
  • NileGraddis (1)
  • njmei (1)
  • bendichter (1)
Top Labels
Issue Labels
bug (22) enhancement (14) question (1) note (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 243 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 7
  • Total versions: 11
  • Total maintainers: 1
pypi.org: ipfx

Intrinsic Physiology Feature Extractor (IPFX) - tool for computing neuronal features from the intracellular electrophysiological recordings

  • Versions: 11
  • Dependent Packages: 1
  • Dependent Repositories: 7
  • Downloads: 243 Last month
Rankings
Dependent packages count: 4.8%
Dependent repos count: 5.6%
Forks count: 7.1%
Average: 8.9%
Stargazers count: 12.9%
Downloads: 14.0%
Maintainers (1)
alleninstitute
Last synced: 10 months ago

Dependencies

docs/aibs_sphinx/package.json npm
  • aibs-portal-assets 0.0.24
requirements.txt pypi
  • allensdk *
  • argschema <2.0.0
  • dictdiffer *
  • h5py ==2.10.0
  • marshmallow ==3.0.0rc6
  • matplotlib >=1.4.3
  • methodtools *
  • numpy >=1.15.4,<1.19.0
  • pandas >=0.25.1,<=0.25.3
  • pg8000 *
  • pillow *
  • pyYAML <6.0.0
  • pyabf <2.3.0
  • pynwb >=1.3.2,<2.0.0
  • scipy >=0.15.1
  • simplejson >=3.10.0
  • watchdog *
requirements_docs.txt pypi
  • m2r *
  • mistune <2
  • numpydoc >=0.6.0,<1.0.0
  • sphinx *
  • sphinx-gallery *
setup.py pypi
.github/workflows/github-actions-ci.yml actions
  • actions/checkout v3 composite
  • actions/checkout v4 composite
  • actions/setup-python v4 composite
.github/workflows/nightly-onprem.yml actions
  • actions/checkout v4 composite
requirements-test.txt pypi
  • pytest >=3.3.0 test
  • pytest-cov <3.0.0 test
  • pytest-xdist ==1.27.0 test
docker/Dockerfile docker
  • python ${PYTHON_VERSION} build