ORMIR_XCT
ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing - Published in JOSS (2024)
Science Score: 93.0%
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○CITATION.cff file
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✓.zenodo.json file
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Found 3 DOI reference(s) in README and JOSS metadata -
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Published in Journal of Open Source Software
Scientific Fields
Mathematics
Computer Science -
84% confidence
Last synced: 6 months ago
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JSON representation
Repository
Code developed at the 2022 ORMIR workshop in Maastricht, Netherlands
Basic Info
- Host: GitHub
- Owner: SpectraCollab
- License: gpl-3.0
- Language: Jupyter Notebook
- Default Branch: main
- Size: 131 MB
Statistics
- Stars: 8
- Watchers: 1
- Forks: 2
- Open Issues: 0
- Releases: 1
Created over 3 years ago
· Last pushed 11 months ago
Metadata Files
Readme
License
README.md
ORMIR_XCT
This repository has been moved to the ORMIR-XCT organization page. Visit the new ORMIR_XCT repository here.
By: Michael T. Kuczynski, Nathan J. Neeteson, Kathryn S. Stok, Andrew J. Burghardt, Michelle A. Espinosa Hernandez, Jared Vicory, Justin J. Tse, Pholpat Durongbhan, Serena Bonaretti, Andy Kin On Wong, Steven K. Boyd, Sarah L. Manske, 2023
Version: 1.0
- ORMIR_XCT is a Python package for processing high resolution peripheral computed tomography (HR-pQCT) scans.
- Development of this project began during the “Building the Jupyter Community in Musculoskeletal Imaging Research” workshop hosted by the Open and Reproducible Musculoskeletal Imaging Research (ORMIR) group.
Installation
Step 1: Install the ORMIR_XCT Anaconda Environment:
conda env create -f environment.yml
If using an Apple M1, M2, or M3 processor, run the following command instead:
CONDA_SUBDIR=osx-64 conda env create -f environment.yml
Step 2: Activate the Anaconda Environment:
conda activate ormir_xct
Step 3: Install the Package:
pip install -e .
Step 4: Run Scripts:
The modules in the ormir_xct directory can now be run. Examples for each module are provided in the examples directory.
Example Jupyter Notebooks
- Example Jupyter Notebooks demonstrating the major functionality of the ORMIR_XCT package are provided in the examples directory.
Ways to Contribute
Reporting Bugs
- Bugs can be reported by creating a new GitHub issue in this repository. For each bug, please provide details on how to reproduce the bug and the specific error message (if possible).
Contributing New Features
- To add a new feature, expand existing functionality, add documentation, or other contributions, please submit a new GitHub issue outlining your contribution in detail.
- When submitting a new pull request, ensure you outline what you have changed and why it is necessary to make this change.
Citation
When using the ORMIRXCT package, please use the following citation: - *Kuczynski et al., (2024). ORMIRXCT: A Python package for high resolution peripheral quantitative computed tomography image processing. Journal of Open Source Software, 9(97), 6084, https://doi.org/10.21105/joss.06084*
Owner
- Name: SpectraCollab
- Login: SpectraCollab
- Kind: organization
- Repositories: 2
- Profile: https://github.com/SpectraCollab
JOSS Publication
ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing
Published
May 30, 2024
Volume 9, Issue 97, Page 6084
Authors
Michael T. Kuczynski
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, Canada
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, Canada
Nathan J. Neeteson
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, Canada
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, Calgary, Canada
Kathryn S. Stok
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
Andrew J. Burghardt
Department of Radiology and Biomedical Imaging, University of California, San Francisco, United States of America
Department of Radiology and Biomedical Imaging, University of California, San Francisco, United States of America
Michelle A. Espinosa Hernandez
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia, Rehabilitation Sciences Institute, The University of Toronto, Toronto, Canada, Joint Department of Medical Imaging, University Health Network, Toronto, Canada
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia, Rehabilitation Sciences Institute, The University of Toronto, Toronto, Canada, Joint Department of Medical Imaging, University Health Network, Toronto, Canada
Jared Vicory
Kitware, Inc., Carrboro, North Carolina, United States of America
Kitware, Inc., Carrboro, North Carolina, United States of America
Justin J. Tse
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
Pholpat Durongbhan
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
Department of Biomedical Engineering, The University of Melbourne, Parkville, Australia
Serena Bonaretti
Swiss Center for Musculoskeletal Imaging, Balgrist Campus, Zurich, Switzerland
Swiss Center for Musculoskeletal Imaging, Balgrist Campus, Zurich, Switzerland
Andy Kin On Wong
Joint Department of Medical Imaging, University Health Network, Toronto, Canada, Department of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
Joint Department of Medical Imaging, University Health Network, Toronto, Canada, Department of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
Steven K. Boyd
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
Sarah L. Manske
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Canada, Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, Canada
Editor
Prashant Jha
Tags
XtremeCT HR-pQCT bone analysisGitHub Events
Total
- Watch event: 6
- Push event: 10
- Pull request event: 6
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 6
- Push event: 10
- Pull request event: 6
- Fork event: 1
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Michael Kuczynski | m****s@u****a | 99 |
| Nathan | n****n@g****m | 55 |
| slmanske | 4****e | 1 |
| Michael Kuczynski | m****i@m****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 6
- Total pull requests: 22
- Average time to close issues: about 2 months
- Average time to close pull requests: about 23 hours
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 5.33
- Average comments per pull request: 0.05
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 3
- Average time to close issues: N/A
- Average time to close pull requests: 2 minutes
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- codeling (3)
- njneeteson (2)
- sbonaretti (1)
Pull Request Authors
- mkuczyns (34)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
requirements.txt
pypi
- itk *
- itkwidgets *
- notebook *
- numpy *
- pbr *
- pip *
- scikit-image *
- scipy *
- setuptools *
- simpleitk *
- vtk *
.github/workflows/draft-pdf.yml
actions
- actions/checkout v3 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
setup.py
pypi
environment.yml
pypi
- itk ==5.3.0
- itk-core ==5.3.0
- itk-filtering ==5.3.0
- itk-io ==5.3.0
- itk-ioscanco ==0.10.0
- itk-numerics ==5.3.0
- itk-registration ==5.3.0
- itk-segmentation ==5.3.0
- kimimaro ==3.3.0
- notebook ==6.5.2
- numba ==0.56.3