pyKNEEr is an image analysis workflow for open and reproducible research on femoral knee cartilage. It is implemented in python using Jupyter notebooks as a user interface. The workflow is divided into three modules for: 1) image preprocessing; 2) segmentation of femoral knee cartilage for intersubject, multimodal, and longitudinal acquisitions; and 3) morphologic and relaxometry analysis.

Documentation: https://sbonaretti.github.io/pyKNEEr/
GitHub repository: https://github.com/sbonaretti/pyKNEEr
Preprint: https://doi.org/10.1101/556423