# ORMIR_XCT
**By:** [Michael T. Kuczynski](https://www.linkedin.com/in/mkuczyns/), [Nathan J. Neeteson](https://www.linkedin.com/in/nathan-neeteson/), [Kathryn S. Stok](https://www.linkedin.com/in/kstok/), [Andrew J. Burghardt](https://www.linkedin.com/in/aburghardt/), [Michelle A. Espinosa Hernandez](https://www.linkedin.com/in/michelleaespinosah/), [Jared Vicory](https://www.kitware.com/jared-vicory/), [Justin J. Tse](https://www.linkedin.com/in/justin-j-tse/), [Pholpat Durongbhan](https://www.linkedin.com/in/pholpatd/), [Serena Bonaretti](https://sbonaretti.github.io/), [Andy Kin On Wong](https://www.linkedin.com/in/andy-kin-on-wong-76408859/), [Steven K. Boyd](https://mccaig.ucalgary.ca/boyd), [Sarah L. Manske](https://www.linkedin.com/in/sarah-manske-b5402b41/), 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](https://github.com/SpectraCollab/ORMIR_XCT/tree/main/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 ORMIR_XCT package, please use the following citation:
- *Kuczynski et al., (2024). ORMIR_XCT: 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*
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"description": "# ORMIR_XCT\n\n**By:** [Michael T. Kuczynski](https://www.linkedin.com/in/mkuczyns/), [Nathan J. Neeteson](https://www.linkedin.com/in/nathan-neeteson/), [Kathryn S. Stok](https://www.linkedin.com/in/kstok/), [Andrew J. Burghardt](https://www.linkedin.com/in/aburghardt/), [Michelle A. Espinosa Hernandez](https://www.linkedin.com/in/michelleaespinosah/), [Jared Vicory](https://www.kitware.com/jared-vicory/), [Justin J. Tse](https://www.linkedin.com/in/justin-j-tse/), [Pholpat Durongbhan](https://www.linkedin.com/in/pholpatd/), [Serena Bonaretti](https://sbonaretti.github.io/), [Andy Kin On Wong](https://www.linkedin.com/in/andy-kin-on-wong-76408859/), [Steven K. Boyd](https://mccaig.ucalgary.ca/boyd), [Sarah L. Manske](https://www.linkedin.com/in/sarah-manske-b5402b41/), 2023 \n**Version:** 1.0\n\n- ORMIR_XCT is a Python package for processing high resolution peripheral computed tomography (HR-pQCT) scans. \n- Development of this project began during the \u201cBuilding the Jupyter Community in Musculoskeletal Imaging Research\u201d workshop hosted by the Open and Reproducible Musculoskeletal Imaging Research (ORMIR) group.\n\n---\n\n## Installation\n### Step 1: Install the ORMIR_XCT Anaconda Environment:\n`conda env create -f environment.yml`\n\nIf using an Apple M1, M2, or M3 processor, run the following command instead:\n`CONDA_SUBDIR=osx-64 conda env create -f environment.yml`\n\n### Step 2: Activate the Anaconda Environment:\n`conda activate ormir_xct`\n\n### Step 3: Install the Package:\n`pip install -e .`\n\n### Step 4: Run Scripts:\nThe modules in the `ormir_xct` directory can now be run. Examples for each module are provided in the `examples` directory. \n\n---\n\n## Example Jupyter Notebooks\n- Example Jupyter Notebooks demonstrating the major functionality of the ORMIR_XCT package are provided in the *[examples](https://github.com/SpectraCollab/ORMIR_XCT/tree/main/examples)* directory.\n\n---\n\n## Ways to Contribute\n### Reporting Bugs\n- 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).\n\n---\n\n### Contributing New Features\n- To add a new feature, expand existing functionality, add documentation, or other contributions, please submit a new GitHub issue outlining your contribution in detail. \n- When submitting a new pull request, ensure you outline what you have changed and why it is necessary to make this change.\n\n---\n\n## Citation\nWhen using the ORMIR_XCT package, please use the following citation:\n- *Kuczynski et al., (2024). ORMIR_XCT: 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*\n\n",
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