Welcome to the LavLab Python Utils repository! This library is a collection of Python utilities developed by the LaViolette Lab to support our research in RadioPathomics and digital pathology.
LavLab Python Utils is designed to streamline common tasks in our research workflow, including data preprocessing, analysis, and visualization. Our goal is to provide a set of tools that are easy to use, well-documented, and performant.
- Data Processing: Functions to handle various data formats used in our research, including DICOM, NIfTI, and more.
- Visualization: Tools to create publication-quality plots and visualizations.
- Integration: Seamless integration with other tools and services used in our lab.
- OMERO Support: Connect to and work with OMERO servers for image data management.
- XNAT Support: Connect to and work with XNAT servers for neuroimaging data management.
You can install LavLab Python Utils via pip:
python3 -m pip install https://github.com/laviolette-lab/lavlab-python-utils/releases/latest/download/lavlab_python_utils-latest-py3-none-any.whl
# optional install targets, must install wheel from github using command above first!
python3 -m pip install 'lavlab-python-utils[all]'
# Or install specific features:
python3 -m pip install 'lavlab-python-utils[omero]' # For OMERO support
python3 -m pip install 'lavlab-python-utils[xnat]' # For XNAT support
python3 -m pip install 'lavlab-python-utils[jupyter]' # For Jupyter toolsComprehensive documentation is available on Read the Docs. This includes detailed API references, usage examples, and tutorials.
We welcome contributions from the community! If you are interested in contributing, please read our contributing guide and check out our open issues.
Thank you for using LavLab Python Utils! We hope you find it useful in your research.