Repository contains all original code we used to process MxIF data as described in ["Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients"](https://doi.org/10.1016/j.ccell.2024.02.001).
To install the package, it is recommended to use a virtual environment with Python 3.8, as newer versions may produce errors. Once the virtual environment is set up, navigate to the root directory of Cell_Atlas_MxIF and simply run the following command: pip install .
After successfully installing the package, navigate to the notebooks folder to explore the example notebooks. For tessellation and community analysis, run the code tessellation_example.ipynb and community_generation.ipynb notebooks, respectively. The data required for these examples is available in the IDR repository under the accession number idr0158.
Python 3.8+.
Dependencies are defined in:
requirements.inrequirements.txtdev-requirements.indev-requirements.txt
For community generation PyG was used. Please install it as specified here https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html.
