CLAIRE
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures - Published in JOSS (2021)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
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24 of 35 committers (68.6%) from academic institutions -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
Constrained Large Deformation Diffeomorphic Image Registration (CLAIRE)
Basic Info
Statistics
- Stars: 50
- Watchers: 10
- Forks: 10
- Open Issues: 8
- Releases: 0
Topics
Metadata Files
README.md
CLAIRE
- Are you looking for examples? Check the doc/examples folder.
- Are in interested in how CLAIRE works? Check the documentation.
- Are you interested in what CLAIRE is? Read the about section.
Documentation
- News: Recent updates and news are listed in doc/README-NEWS.md
- Installation: An installation guide can be found in doc/README-INSTALL.md
- Examples: A description of how to execute and use CLAIRE on your system can be found in doc/README-RUNME.md.
- Contributing: If you have a bug report, a feature request, or you are interested in contributing to CLAIRE visit doc/CONTRIBUTING.md.
- References: If you use CLAIRE as part of your research, please refer to doc/README-REFERENCES.md for information on citing our work.
The links above point to individual markdown files. These files can be found in the doc subfolder. Basic examples for how to execute CLAIRE can be found in the doc/examples folder. The NIREP dataset used to test CLAIRE can be downloaded here.
About
CLAIRE stands for Constrained Large Deformation Diffeomorphic Image Registration. It is a C/C++ software package for velocity-based diffeomorphic image registration in three dimensions. Its performance is optimized for multi-core CPU systems (cpu branch) and multi-node, multi-GPU architectures (gpu branch; default). The CPU version uses MPI for data parallelism, and has been demonstrated to scale on several supercomputing platforms. CLAIRE can be executed on large-scale state-of-the-art computing systems as well as on local compute systems with limited resources.
Notice that the CPU version is accurate and running but new features are currently only being added to the GPU version. The GPU code is a major revision and therefore considered the default and recommended for use.
If there are any issues, you have questions, you would like to give us feedback or you have feature requests, do not hesitate to send an email to andreas@math.uh.edu.
If you plan on using CLAIRE in your research please cite the following manuscript: A. Mang, A. Gholami, C. Davatzikos & G. Biros. CLAIRE: A distributed-memory solver for constrained large deformation diffeomorphic image registration. SIAM Journal on Scientific Computing 41(5):C548--C584, 2019 [arxiv, sisc]. Additional references are listed here.
Contributors
George Biros, Malte Brunn, Amir Gholami, James Herring, Naveen Himthani, Andreas Mang, and Miriam Mehl.
If you want to contribute to CLAIRE, read the guidlines (see doc/CONTRIBUTING.md).
Code of Conduct
See doc/CODEOFCONDUCT.md.
License
Read the LICENSE file for more details.
Owner
- Name: Andreas Mang
- Login: andreasmang
- Kind: user
- Location: Houston
- Company: Department of Mathematics, University of Houston
- Website: https://www.math.uh.edu/~andreas/
- Twitter: amangmath
- Repositories: 8
- Profile: https://github.com/andreasmang
JOSS Publication
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures
Authors
Institute for Parallel and Distributed Systems, University Stuttgart
Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin
Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin
Institute for Parallel and Distributed Systems, University Stuttgart
Department of Mathematics, University of Houston
Editor
Matthew Sottile
Tags
GPUs parallel computing high performance computing large deformation diffeomorphic registration optimal control medical imagingGitHub Events
Total
- Issues event: 1
- Watch event: 3
- Issue comment event: 6
- Fork event: 1
- Create event: 1
Last Year
- Issues event: 1
- Watch event: 3
- Issue comment event: 6
- Fork event: 1
- Create event: 1
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andreas Mang | a****s@i****u | 878 |
| brunnme | m****n@i****e | 147 |
| Naveen Himthani | n****5@l****u | 47 |
| Naveen Himthani | n****b@g****m | 42 |
| brunnme | m****n@w****e | 15 |
| Naveen Himthani | n****5@l****u | 8 |
| James Herring | h****j@g****m | 4 |
| Naveen Himthani | n****5@l****u | 3 |
| Naveen Himthani | n****5@l****u | 2 |
| Naveen Himthani | n****5@l****u | 2 |
| Naveen Himthani | n****5@l****u | 2 |
| Naveen Himthani | n****5@c****u | 2 |
| Andreas Mang | a****g@l****u | 2 |
| Andreas Mang | a****g@l****u | 2 |
| Andreas Mang | a****g@l****u | 2 |
| Malte Brunn | m****n@c****l | 2 |
| Andreas Mang | a****g@c****l | 1 |
| Andreas Mang | a****g@l****u | 1 |
| Andreas Mang | a****s@c****u | 1 |
| Andreas Mang | a****s@c****u | 1 |
| James Herring | j****n@o****u | 1 |
| Malte Brunn | b****e@l****u | 1 |
| Malte Brunn | m****n@c****l | 1 |
| Malte Brunn | m****n@c****l | 1 |
| Malte Brunn | m****n@c****l | 1 |
| Naveen Himthani | n****5@c****u | 1 |
| Naveen Himthani | n****5@l****u | 1 |
| Naveen Himthani | n****5@l****u | 1 |
| Naveen Himthani | n****5@l****u | 1 |
| Naveen Himthani | n****5@l****u | 1 |
| and 5 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 14
- Total pull requests: 1
- Average time to close issues: 10 months
- Average time to close pull requests: N/A
- Total issue authors: 9
- Total pull request authors: 1
- Average comments per issue: 3.5
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tjasaki (3)
- NMontanaBrown (2)
- andreasmang (2)
- NimaMojtahedi (2)
- MalteBrunn (1)
- XuanBaiBai (1)
- LalithShiyam (1)
- ahsanjav (1)
- rohitrango (1)
Pull Request Authors
- naveenaero (1)