Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/dipy/dipy

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

https://github.com/dipy/dipy

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
    30 of 172 committers (17.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary

Keywords

bundles contextual-enhancement denoising diffusion-mri dki dti machine-learning medical-imaging microstructure neuroanatomy neuroimaging patch2self python registration segmentation self-supervised-learning spherical-harmonics tracking tractography tractometry

Keywords from Contributors

3d-graphics game-engine scriptable-animations shaders brain-imaging bids fmri brain-connectivity decoding closember
Last synced: 6 months ago · JSON representation

Repository

DIPY is the paragon 3D/4D+ medical imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

Basic Info
  • Host: GitHub
  • Owner: dipy
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage: https://dipy.org
  • Size: 72.6 MB
Statistics
  • Stars: 781
  • Watchers: 54
  • Forks: 447
  • Open Issues: 142
  • Releases: 0
Topics
bundles contextual-enhancement denoising diffusion-mri dki dti machine-learning medical-imaging microstructure neuroanatomy neuroimaging patch2self python registration segmentation self-supervised-learning spherical-harmonics tracking tractography tractometry
Created about 16 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.rst 

.. image:: doc/_static/images/logos/dipy-logo.png
  :height: 180px
  :target: http://dipy.org
  :alt: DIPY - Diffusion Imaging in Python

|

.. image:: https://github.com/dipy/dipy/actions/workflows/test.yml/badge.svg?branch=master
  :target: https://github.com/dipy/dipy/actions/workflows/test.yml

.. image:: https://github.com/dipy/dipy/actions/workflows/build_docs.yml/badge.svg?branch=master
  :target: https://github.com/dipy/dipy/actions/workflows/build_docs.yml

.. image:: https://codecov.io/gh/dipy/dipy/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/dipy/dipy

.. image:: https://img.shields.io/pypi/v/dipy.svg
  :target: https://pypi.python.org/pypi/dipy

.. image:: https://anaconda.org/conda-forge/dipy/badges/platforms.svg
  :target: https://anaconda.org/conda-forge/dipy

.. image:: https://anaconda.org/conda-forge/dipy/badges/downloads.svg
  :target: https://anaconda.org/conda-forge/dipy

.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
  :target: https://github.com/dipy/dipy/blob/master/LICENSE


DIPY [DIPYREF]_ is a python library for the analysis of MR diffusion imaging.

DIPY is for research only; please contact admins@dipy.org if you plan to deploy
in clinical settings.

Website
=======

Current information can always be found from the DIPY website - http://dipy.org

Mailing Lists
=============

Please see the DIPY community list at
https://mail.python.org/mailman3/lists/dipy.python.org/

Please see the users' forum at
https://github.com/dipy/dipy/discussions

Please join the gitter chatroom `here `_.

Code
====

You can find our sources and single-click downloads:

* `Main repository`_ on Github.
* Documentation_ for all releases and current development tree.
* Download as a tar/zip file the `current trunk`_.

.. _main repository: http://github.com/dipy/dipy
.. _Documentation: http://dipy.org
.. _current trunk: http://github.com/dipy/dipy/archives/master


Installing DIPY
===============

DIPY can be installed using `pip`::

    pip install dipy

or using `conda`::

    conda install -c conda-forge dipy

For detailed installation instructions, including instructions for installing
from source, please read our `installation documentation `_.

Python versions and dependencies
--------------------------------

DIPY follows the `Scientific Python`_ `SPEC 0 — Minimum Supported Versions`_
recommendation as closely as possible, including the supported Python and
dependencies versions.

Further information can be found in `Toolchain Roadmap `_.

License
=======

DIPY is licensed under the terms of the BSD license.
Please see the `LICENSE file `_.

Contributing
============

We welcome contributions from the community. Please read our `Contributing guidelines `_.

Reference
=========

.. [DIPYREF] E. Garyfallidis, M. Brett, B. Amirbekian, A. Rokem,
    S. Van Der Walt, M. Descoteaux, I. Nimmo-Smith and DIPY contributors,
    "DIPY, a library for the analysis of diffusion MRI data",
    Frontiers in Neuroinformatics, vol. 8, p. 8, Frontiers, 2014.


.. _`Scientific Python`: https://scientific-python.org/
.. _`SPEC 0 — Minimum Supported Versions`: https://scientific-python.org/specs/spec-0000/

Owner

  • Name: DIPY
  • Login: dipy
  • Kind: organization
  • Email: dipy@python.org
  • Location: world

Scientific computing software and community-driven medical imaging organization

GitHub Events

Total
  • Create event: 8
  • Commit comment event: 2
  • Issues event: 90
  • Watch event: 64
  • Delete event: 6
  • Issue comment event: 567
  • Push event: 118
  • Gollum event: 1
  • Pull request review comment event: 317
  • Pull request event: 246
  • Pull request review event: 375
  • Fork event: 18
Last Year
  • Create event: 8
  • Commit comment event: 2
  • Issues event: 90
  • Watch event: 64
  • Delete event: 6
  • Issue comment event: 567
  • Push event: 118
  • Gollum event: 1
  • Pull request review comment event: 317
  • Pull request event: 246
  • Pull request review event: 375
  • Fork event: 18

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 12,560
  • Total Committers: 172
  • Avg Commits per committer: 73.023
  • Development Distribution Score (DDS): 0.84
Past Year
  • Commits: 431
  • Committers: 23
  • Avg Commits per committer: 18.739
  • Development Distribution Score (DDS): 0.71
Top Committers
Name Email Commits
Eleftherios Garyfallidis g****s@g****m 2,011
Ariel Rokem a****m@g****m 1,539
Serge Koudoro s****2@g****m 1,450
Rafael Neto Henriques r****1@g****m 528
Matthew Brett m****t@g****m 515
Gabriel Girard g****l@g****m 499
Jon Haitz Legarreta Gorroño j****a@g****m 483
Bago Amirbekian m****o@g****m 415
Omar Ocegueda j****g@g****m 359
Bramsh Qamar b****q@g****m 273
Francois Rheault f****t@u****e 248
Shreyas Fadnavis s****s@g****m 216
Samuel St-Jean S****n@u****a 212
Marc-Alexandre Côté m****9@g****m 186
Philippe Karan p****n@u****a 185
Javier Guaje j****g@i****u 153
Rutger Fick r****k@i****r 153
Shahnawaz Ahmed s****5@g****m 143
Mauro Zucchelli m****8@g****m 140
Maharshi Gor g****i@g****m 121
Ian Nimmo-Smith i****h@g****m 112
Matthieu Dumont m****t@u****a 110
Kesshi Jordan k****n@g****m 96
Maxime Descoteaux m****x@u****a 88
Shilpi Prasad s****d@g****m 86
Ranveer Aggarwal r****l@g****m 84
Jong Sung Park p****g@g****m 80
Riddhish Bhalodia r****b@g****m 78
Kenji Marshall k****9@g****m 76
Charles Poirier c****2@g****m 69
and 142 more...
Committer Domains (Top 20 + Academic)
usherbrooke.ca: 6 iu.edu: 6 debian.org: 3 usc.edu: 2 inria.fr: 2 imeka.ca: 2 ulg.ac.be: 1 tudelft.nl: 1 umn.edu: 1 nitk.edu.in: 1 utexas.edu: 1 lfb.rwth-aachen.de: 1 seznam.cz: 1 mailbox.org: 1 uc.cl: 1 onerussian.com: 1 cchmc.org: 1 illinois.edu: 1 cea.fr: 1 leeds.ac.uk: 1 tue.nl: 1 di.ku.dk: 1 mpimf-heidelberg.mpg.de: 1 sampras.radiology.ucsf.edu: 1 kj.luddy.indiana.edu: 1 umich.edu: 1 ic.ac.uk: 1 cern.ch: 1 iiitd.ac.in: 1 ece.ucsb.edu: 1 indiana.edu: 1 uw.edu: 1 unc.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 118
  • Total pull requests: 382
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 2 months
  • Total issue authors: 53
  • Total pull request authors: 40
  • Average comments per issue: 1.57
  • Average comments per pull request: 3.07
  • Merged pull requests: 258
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 48
  • Pull requests: 154
  • Average time to close issues: 25 days
  • Average time to close pull requests: 8 days
  • Issue authors: 20
  • Pull request authors: 21
  • Average comments per issue: 0.63
  • Average comments per pull request: 2.29
  • Merged pull requests: 101
  • Bot issues: 0
  • Bot pull requests: 4
View more stats
Top Authors
Issue Authors
  • Garyfallidis (21)
  • skoudoro (14)
  • jhlegarreta (8)
  • Atharva-Shah-2298 (6)
  • pjsjongsung (5)
  • arokem (4)
  • samcoveney (3)
  • alexrockhill (3)
  • oesteban (2)
  • KevinAquino (2)
  • ebrahimebrahim (2)
  • areeshatariq (2)
  • mattcieslak (2)
  • maharshi-gor (2)
  • zp1008611 (2)
Pull Request Authors
  • skoudoro (110)
  • jhlegarreta (108)
  • maharshi-gor (31)
  • deka27 (27)
  • arokem (13)
  • gabknight (11)
  • pjsjongsung (10)
  • dependabot[bot] (7)
  • Atharva-Shah-2298 (7)
  • mr-c (6)
  • iprajwalreddy (5)
  • samcoveney (5)
  • alexrockhill (4)
  • MRanka29 (3)
  • tanishka321 (3)
Top Labels
Issue Labels
type:Bug Fix (21) type:Enhancement (17) :notebook:type:Documentation :notebook: (10) category:visualization (9) type:Maintenance (8) Beginner-friendly (6) state: needs to check (4) :grey_question: type:Question :grey_question: (4) state: needs PR (4) type:New feature (2) type:bug (1) type:documentation (1) dependencies (1) type: Refactoring (1)
Pull Request Labels
type:Maintenance (91) :notebook:type:Documentation :notebook: (57) type:Enhancement (40) type:New feature (26) type:Bug Fix (20) category:visualization (13) type: Refactoring (10) dependencies (7) state: ready-to-be-merged (7) type:testing (6) state: needs code review (4) area:workflows (4) area:documentation (4) type:infrastructure (4) area:stats (3) github_actions (2) area:align (2) area:data (2) area:examples (2) type:Release plan (2) state: stalled (2) state: work-in-progress (2) area:tracking (2) area:reconst (1) state: needs PR (1) type:bugfix (1) :notebook:type:documentation :notebook: (1) type:style (1) area:utils (1) area:testing (1)

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 86,581 last-month
  • Total docker downloads: 4,384
  • Total dependent packages: 47
    (may contain duplicates)
  • Total dependent repositories: 255
    (may contain duplicates)
  • Total versions: 42
  • Total maintainers: 4
pypi.org: dipy

Diffusion MRI Imaging in Python

  • Documentation: https://dipy.readthedocs.io/
  • License: Unless otherwise specified by LICENSE.txt files in individual directories, or within individual files or functions, all code is: Copyright (c) 2008-2025, dipy developers All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * 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. * Neither the name of the dipy developers nor the names of any 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 OWNER 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: 1.11.0
    published 11 months ago
  • Versions: 29
  • Dependent Packages: 46
  • Dependent Repositories: 204
  • Downloads: 86,581 Last month
  • Docker Downloads: 4,384
Rankings
Dependent packages count: 0.6%
Dependent repos count: 1.1%
Average: 1.4%
Docker downloads count: 1.6%
Downloads: 2.1%
Maintainers (4)
arokem matthew.brett garyfallidis skoudoro
Last synced: 6 months ago
conda-forge.org: dipy
  • Homepage: https://dipy.org/
  • License: BSD-3-Clause
  • Latest release: 1.5.0
    published almost 4 years ago
  • Versions: 13
  • Dependent Packages: 1
  • Dependent Repositories: 51
Rankings
Dependent repos count: 5.0%
Average: 17.0%
Dependent packages count: 29.0%
Last synced: 6 months ago

Dependencies

doc/doc-requirements.txt pypi
  • cvxpy *
  • cython *
  • fury *
  • h5py *
  • matplotlib *
  • nibabel >=3.0.0
  • numpy *
  • numpydoc *
  • pandas *
  • scikit-image *
  • scikit-learn *
  • scipy *
  • sphinx *
  • statsmodels *
  • tables *
requirements.txt pypi
  • cython >=0.29.24,
  • h5py >=2.8.0
  • nibabel >=3.0.0
  • numpy >=1.14.5
  • packaging >=19.0
  • scipy >=1.1
  • tqdm >=4.30.0
.github/workflows/test_template.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v3 composite
  • conda-incubator/setup-miniconda v2 composite