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deid

best effort anonymization for medical images using python

https://github.com/pydicom/deid

Science Score: 46.0%

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
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 22 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.9%) to scientific vocabulary

Keywords

anonymize deidentify dicom medical medical-images pydicom

Keywords from Contributors

neuroimaging mri
Last synced: 7 months ago · JSON representation

Repository

best effort anonymization for medical images using python

Basic Info
Statistics
  • Stars: 161
  • Watchers: 8
  • Forks: 51
  • Open Issues: 18
  • Releases: 3
Topics
anonymize deidentify dicom medical medical-images pydicom
Created almost 9 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing Funding License Authors Dei

README.md

Deidentify (deid)

Best effort anonymization for medical images in Python.

DOI Build Status

Please see our Documentation.

These are basic Python based tools for working with medical images and text, specifically for de-identification. The cleaning method used here mirrors the one by CTP in that we can identify images based on known locations. We are looking for collaborators to develop and validate an OCR cleaning method! Please reach out if you would like to help work on this.

Installation

Local

For the stable release, install via pip:

bash pip install deid

For the development version, install from Github:

bash pip install git+git://github.com/pydicom/deid

Docker

bash docker build -t pydicom/deid . docker run pydicom/deid --help

Issues

If you have an issue, or want to request a feature, please do so on our issues board.

Owner

  • Name: DICOM in Python
  • Login: pydicom
  • Kind: organization

development for software, modules, and containers for dicom applications that use Python

GitHub Events

Total
  • Issues event: 9
  • Watch event: 14
  • Delete event: 1
  • Issue comment event: 57
  • Push event: 6
  • Pull request review event: 37
  • Pull request review comment event: 34
  • Pull request event: 15
  • Fork event: 7
  • Create event: 1
Last Year
  • Issues event: 9
  • Watch event: 14
  • Delete event: 1
  • Issue comment event: 57
  • Push event: 6
  • Pull request review event: 37
  • Pull request review comment event: 34
  • Pull request event: 15
  • Fork event: 7
  • Create event: 1

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 376
  • Total Committers: 22
  • Avg Commits per committer: 17.091
  • Development Distribution Score (DDS): 0.154
Past Year
  • Commits: 13
  • Committers: 6
  • Avg Commits per committer: 2.167
  • Development Distribution Score (DDS): 0.462
Top Committers
Name Email Commits
vsoch v****t@s****u 318
wetzelj w****j@c****g 14
Kolowitz b****z@g****m 8
Reece Stevens r****4@g****m 7
Judd Storrs j****s@g****m 5
chenp2 c****2@c****g 4
Dimitri Papadopoulos Orfanos 3****s 4
Peter Karlsson Zetterberg p****g@a****e 2
Alexis Girault a****t@k****m 1
Brian Kolowitz k****j@u****u 1
Fernando Cossio 3****o 1
Gleb g****v@g****m 1
JJdeRidder 5****r 1
Johannes Ulén j****u 1
Michael Barrett 1****W 1
Mike Ciancibello 3****o 1
Robin Fourcade 2****d 1
Sam Maxwell 7****z 1
WillForan w****n@g****m 1
howff 3****f 1
nbelakovski-mssm 1****m 1
sjswerdloff s****f@g****m 1
Committer Domains (Top 20 + Academic)
ccf.org: 2 upmc.edu: 1 kitware.com: 1 amra.se: 1 stanford.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 48
  • Total pull requests: 92
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 23
  • Total pull request authors: 20
  • Average comments per issue: 6.25
  • Average comments per pull request: 3.65
  • Merged pull requests: 74
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 6
  • Pull requests: 19
  • Average time to close issues: 10 days
  • Average time to close pull requests: 8 days
  • Issue authors: 4
  • Pull request authors: 7
  • Average comments per issue: 1.5
  • Average comments per pull request: 2.95
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • wetzelj (12)
  • NirutaDhimal (6)
  • howff (3)
  • vsoch (3)
  • moloney (2)
  • glebsts (2)
  • WillForan (2)
  • samuelschuettler (2)
  • RobinFrcd (2)
  • sammaxwellxyz (1)
  • aawez (1)
  • travnick (1)
  • peter-kuzmak (1)
  • AlexanderBunt (1)
  • fcossio (1)
Pull Request Authors
  • vsoch (31)
  • wetzelj (16)
  • sammaxwellxyz (7)
  • jstorrs (6)
  • DimitriPapadopoulos (4)
  • glebsts (4)
  • howff (3)
  • ReeceStevens (2)
  • pvelasco (2)
  • barrettMCW (2)
  • dependabot[bot] (2)
  • Simlomb (2)
  • WillForan (2)
  • RobinFrcd (2)
  • nbelakovski-mssm (2)
Top Labels
Issue Labels
Pull Request Labels
hacktoberfest-accepted (5) dependencies (2) python (2)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 2,083 last-month
  • Total docker downloads: 132
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 118
  • Total maintainers: 1
pypi.org: deid

best effort deidentify dicom with python and pydicom

  • Versions: 83
  • Dependent Packages: 3
  • Dependent Repositories: 4
  • Downloads: 2,083 Last month
  • Docker Downloads: 132
Rankings
Docker downloads count: 2.1%
Dependent packages count: 2.4%
Average: 5.3%
Forks count: 6.3%
Stargazers count: 6.4%
Downloads: 6.8%
Dependent repos count: 7.5%
Maintainers (1)
vsochat
Last synced: 7 months ago
conda-forge.org: deid
  • Versions: 35
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.3%
Forks count: 28.8%
Stargazers count: 32.1%
Average: 34.2%
Dependent packages count: 51.6%
Last synced: 7 months ago

Dependencies

docs/Gemfile rubygems
  • jekyll-feed = 0.11.0 development
  • jekyll-seo-tag = 2.5.0 development
  • jekyll-sitemap = 1.2.0 development
  • jekyll = 3.8.4
.github/workflows/codespell.yaml actions
  • actions/checkout v3 composite
  • crate-ci/typos 592b36d23c62cb378f6097a292bc902ee73f93ef composite
.github/workflows/docs.yaml actions
  • actions/checkout v3 composite
.github/workflows/main.yaml actions
  • actions/checkout v3 composite
Dockerfile docker
  • continuumio/miniconda3 latest build
.github/dev-requirements.txt pypi
  • black * development
  • flake8 * development
  • isort * development
  • pre-commit * development
docs/api_docs/docs-requirements.txt pypi
  • Jinja2 <3.1
  • appdirs *
  • configargparse *
  • docutils ==0.12
  • recommonmark *
  • sphinx *
  • sphinx-argparse *
  • sphinx_rtd_theme *
  • sphinxcontrib-napoleon *
docs/api_docs/requirements.txt pypi
  • Jinja2 <3.1
  • appdirs *
  • configargparse *
  • deid master
  • docutils ==0.12
  • recommonmark *
  • sphinx *
  • sphinx-argparse *
  • sphinx_rtd_theme *
  • sphinxcontrib-napoleon *