This repository contains the source code of the segmentation package. This package provides utility functions to be used for CNN-based segmentation of medical images.

• segmentation.callbacks: callbacks used during the training of the network
• segmentation.cnn: this module allows to define CNN-based models in a dynamic way
• segmentation.losses: this module allows to define loss functions to be used for segmentation tasks
• segmentation.metrics: in this module, metrics to be used during the training of the network are implemented
• segmentation.utils: utils functions used for various purposes

Submodule to preprocess dicom or Nifti files to adapt data for training and optimize memory

• segmentation.preprocess.main_preprocess: this module contains the main preprocessing functions
• segmentation.preprocess.Cycles: this module contains example functions to loop over files and call the main functions
• segmentation.preprocess.utils: utils functions used for various purposes

Current lab students working on the project: - Alberto Faglia: AlbiFag

You can install the package directly from GitHub: pip install +git https://github.com/ltebs-polimi/cnn-segmentation

You can generate your local documentation by running: make docs to update the documentation of the project. Updated documentation can be found in the docs folder. Documentation of the package can be found at the following link: https://ltebs-polimi.github.io/cnn-segmentation/