DeepReg

DeepReg: a deep learning toolkit for medical image registration - Published in JOSS (2020)

Science Score: 95.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 6 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
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Committers with academic emails
10 of 20 committers (50.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

convolutional-neural-networks deep-learning deep-neural-networks deepreg image-fusion image-registration medical-image-registration neural-network tensorflow2

Scientific Fields

Mathematics Computer Science - 63% confidence

Last synced: 4 months ago · JSON representation

Repository

Medical image registration using deep learning

Basic Info

Host: GitHub
Owner: DeepRegNet
License: apache-2.0
Language: Python
Default Branch: main
Homepage:
Size: 29.7 MB

Statistics

Stars: 600
Watchers: 17
Forks: 83
Open Issues: 0
Releases: 4

Topics

convolutional-neural-networks deep-learning deep-neural-networks deepreg image-fusion image-registration medical-image-registration neural-network tensorflow2

Created over 5 years ago · Last pushed about 3 years ago

Metadata Files

Readme Changelog License Code of conduct Zenodo

README.md

deepreg_logo

Package
Documentation
Code
Papers

DeepReg

DeepReg is a freely available, community-supported open-source toolkit for research and education in medical image registration using deep learning.

TensorFlow 2-based for efficient training and rapid deployment;
Implementing major unsupervised and weakly-supervised algorithms, with their combinations and variants;
Focusing on growing and diverse clinical applications, with all DeepReg Demos using open-accessible data;
Simple built-in command line tools requiring minimal programming and scripting;
Open, permissible and research-and-education-driven, under the Apache 2.0 license.

Getting Started

Contributing

Get involved, and help make DeepReg better! We want your help - Really.

Being a contributor doesn't just mean writing code. Equally important to the open-source process is writing or proof-reading documentation, suggesting or implementing tests, or giving feedback about the project. You might see the errors and assumptions that have been glossed over. If you can write any code at all, you can contribute code to open-source. We are constantly trying out new skills, making mistakes, and learning from those mistakes. That's how we all improve, and we are happy to help others learn with us.

Code of Conduct

This project is released with a Code of Conduct. By participating in this project, you agree to abide by its terms.

Where Should I Start?

For guidance on making a contribution to DeepReg, see our Contribution Guidelines.

Have a registration application with openly accessible data? Consider contributing a DeepReg Demo.

MICCAI 2020 Educational Challenge

Our MICCAI Educational Challenge submission on DeepReg is an Award Winner!

Check it out here - you can also

Overview Video

Members of the DeepReg dev team presented "The Road to DeepReg" at the Centre for Medical Imaging Computing (CMIC) seminar series at University College London on the 4th of November 2020. You can access the talk here.

Citing DeepReg

DeepReg is research software, made by a team of academic researchers. Citations and use of our software help us justify the effort which has gone into, and will keep going into, maintaining and growing this project.

If you have used DeepReg in your research, please consider citing us:

Fu et al., (2020). DeepReg: a deep learning toolkit for medical image registration. Journal of Open Source Software, 5(55), 2705, https://doi.org/10.21105/joss.02705

Or with BibTex:

@article{Fu2020, doi = {10.21105/joss.02705}, url = {https://doi.org/10.21105/joss.02705}, year = {2020}, publisher = {The Open Journal}, volume = {5}, number = {55}, pages = {2705}, author = {Yunguan Fu and Nina Montaña Brown and Shaheer U. Saeed and Adrià Casamitjana and Zachary M. C. Baum and Rémi Delaunay and Qianye Yang and Alexander Grimwood and Zhe Min and Stefano B. Blumberg and Juan Eugenio Iglesias and Dean C. Barratt and Ester Bonmati and Daniel C. Alexander and Matthew J. Clarkson and Tom Vercauteren and Yipeng Hu}, title = {DeepReg: a deep learning toolkit for medical image registration}, journal = {Journal of Open Source Software} }

Owner

Name: DeepReg
Login: DeepRegNet
Kind: organization

Website: deepreg.net
Repositories: 4
Profile: https://github.com/DeepRegNet

JOSS Publication

DeepReg: a deep learning toolkit for medical image registration

Published

November 04, 2020

DOI

10.21105/joss.02705

Volume 5, Issue 55, Page 2705

Authors

Yunguan Fu

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK, InstaDeep, London, UK

Nina Montaña Brown

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Shaheer U. Saeed

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Adrià Casamitjana

Centre for Medical Image Computing, University College London, London, UK

Zachary M. c. Baum

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Rémi Delaunay

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Department of Surgical & Interventional Engineering, King’s College London, London, UK

Qianye Yang

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Alexander Grimwood

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Zhe Min

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK

Stefano B. Blumberg

Centre for Medical Image Computing, University College London, London, UK

Juan Eugenio Iglesias

Centre for Medical Image Computing, University College London, London, UK, Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, USA, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, USA

Dean C. Barratt

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Ester Bonmati

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Daniel C. Alexander

Centre for Medical Image Computing, University College London, London, UK

Matthew J. Clarkson

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Tom Vercauteren

Department of Surgical & Interventional Engineering, King’s College London, London, UK

Yipeng Hu

Wellcome/EPSRC Centre for Surgical and Interventional Sciences, University College London, London, UK, Centre for Medical Image Computing, University College London, London, UK

Editor

Kevin M. Moerman

GitHub Events

Total

Issues event: 4
Watch event: 34
Issue comment event: 3
Fork event: 7

Last Year

Issues event: 4
Watch event: 34
Issue comment event: 3
Fork event: 7

Committers

Last synced: 5 months ago

All Time

Total Commits: 2,037
Total Committers: 20
Avg Commits per committer: 101.85
Development Distribution Score (DDS): 0.485

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Yunguan Fu	y**8@u**k	1,050
Yipeng Hu	y**u@u**k	241
Shaheer U Saeed	s**d@g**m	181
Nina Montana Brown	n**5@u**k	146
Adria	a**a@u**k	118
ebonmati	e**i@u**k	55
Zachary Baum	z**m@h**m	54
RemiDelaunay	r**7@u**k	50
dependabot-preview[bot]	2****]	28
Qianye Yang	q**9@u**k	22
ZheMin	z**k@g**m	20
kate-sann5100	y**i@s**k	18
agrimw	a**d@u**k	14
aya	a**a@g**m	13
shannonxtreme	a**a@g**m	6
Yipeng Hu	y**u@y**n	6
agrimwood	5****d	5
DeepRegNet	d**t@g**m	5
sbb-threadrip16	s**7@u**k	4
Zhiyuan-w	w**h@g**m	1

Committer Domains (Top 20 + Academic)

ucl.ac.uk: 9 yh-xps-laptop.localdomain: 1 github.com: 1 st-annes.ox.ac.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 27
Total pull requests: 73
Average time to close issues: 3 months
Average time to close pull requests: about 1 month
Total issue authors: 19
Total pull request authors: 10
Average comments per issue: 2.26
Average comments per pull request: 2.23
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 59

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

mathpluscode (5)
codeenthusiast (2)
Zhiyuan-w (2)
urlicht (2)
IVarha (2)
omarespejel (1)
mianasbat (1)
JiYuanFeng (1)
ebonmati (1)
AmericaBG (1)
MMMMSK (1)
MichaelWerthmann (1)
pzaffino (1)
jbmcs (1)
ku294714 (1)

Pull Request Authors

dependabot-preview[bot] (48)
dependabot[bot] (11)
Zhiyuan-w (5)
mathpluscode (3)
ayoubbenc (1)
NMontanaBrown (1)
acasamitjana (1)
TrellixVulnTeam (1)
YipengHu (1)
SicongluUCL (1)

Top Labels

Issue Labels

stale (14) bug (3) refactoring (2) demo (1) feature (1)

Pull Request Labels

dependencies (59) stale (28)

Packages

Total packages: 3
Total downloads:
- pypi 45 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 10
Total maintainers: 1

proxy.golang.org: github.com/deepregnet/deepreg

Documentation: https://pkg.go.dev/github.com/deepregnet/deepreg#section-documentation
License: apache-2.0
Latest release: v0.1.2
published almost 5 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 6.4%

Average: 6.6%

Dependent repos count: 6.8%

Last synced: 4 months ago

proxy.golang.org: github.com/DeepRegNet/DeepReg

Documentation: https://pkg.go.dev/github.com/DeepRegNet/DeepReg#section-documentation
License: apache-2.0
Latest release: v0.1.2
published almost 5 years ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 6.4%

Average: 6.6%

Dependent repos count: 6.8%

Last synced: 4 months ago

pypi.org: deepreg

DeepReg is a freely available, community-supported open-source toolkit for research and education in medical image registration using deep learning.

Homepage: http://deepreg.net/
Documentation: https://deepreg.readthedocs.io/
License: apache-2.0
Latest release: 0.1.2
published almost 5 years ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 45 Last month

Rankings

Dependent packages count: 10.0%

Average: 18.3%

Dependent repos count: 21.7%

Downloads: 23.3%

Maintainers (1)

zacbaum

Last synced: 4 months ago

Dependencies

.github/workflows/pre-commit.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
pre-commit/action v2.0.0 composite

.github/workflows/python-integration-test.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/python-publish.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/python-unit-test.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
codecov/codecov-action v1 composite

Dockerfile docker

tensorflow/tensorflow 2.3.1-gpu build

environment.yml pypi

tensorflow-gpu ==2.3.1

requirements.txt pypi

GitPython ==3.1.14
argparse ==1.4.0
black ==21.5b1
flake8 ==3.9.0
h5py ==2.10.0
isort ==5.8.0
m2r2 ==0.2.7
matplotlib ==3.4.1
nibabel ==3.2.1
notebook ==6.3.0
numpy ==1.18.5
pandas ==1.2.4
pre-commit ==2.12.0
pydocstyle ==6.0.0
pydot ==1.4.2
pylint ==2.8.1
pytest ==6.2.3
pytest-cov ==2.11.1
pytest-dependency ==0.5.1
pyyaml ==5.4.1
scipy ==1.6.2
seed-isort-config ==2.2.0
sphinx ==3.5.3
sphinx-notfound-page ==0.6
sphinx-rtd-theme ==0.5.2
sphinx-tabs ==3.0.0
tabulate ==0.8.9
tensorboard_plugin_profile ==2.3.0
tensorflow ==2.3.1
testfixtures ==6.17.1
tox ==3.23.0
tqdm ==4.60.0

DeepReg

Science Score: 95.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

DeepReg

Getting Started

Contributing

Code of Conduct

Where Should I Start?

MICCAI 2020 Educational Challenge

Overview Video

Citing DeepReg

Owner

JOSS Publication

DeepReg: a deep learning toolkit for medical image registration

Authors

Editor

Tags

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/deepregnet/deepreg

Rankings

proxy.golang.org: github.com/DeepRegNet/DeepReg

Rankings

pypi.org: deepreg

Rankings

Maintainers (1)

Dependencies