Abstract

An open-source library of implementations for deep-learning based image segmentation and outcomes models is presented in this work. As oncology treatment planning becomes increasingly driven by automation, such a library of model implementations is crucial to (i) validate existing models on datasets collected at different institutions, (ii) automate segmentation, (iii) create ensembles for improving performance and (iv) incorporate validated models in the clinical workflow. The library was developed with Computational Environment for Radiological Research (CERR) software platform. CERR is a natural choice to centralize model implementations due to its comprehensiveness, popularity, and ease of use. CERR provides well-validated feature extraction for radiotherapy dosimetry and radiomics with fine control over the calculation settings. This allows users to select the appropriate feature calculation used in the model derivation. Models for automatic image segmentation are distributed via Singularity containers, with seamless i/o to and from CERR. Singularity containers allow for segmentation models to be deployed with a variety of scientific computing architectures. Deployment of models is driven by JSON configuration file, making it convenient to plug-in models. Models from the library can be called programmatically for batch evaluation. The library includes implementations for popular radiotherapy models outlined in the Quantitative Analysis of Normal Tissue Effects in the Clinic effort and recently published literature. Radiomics models include features from Image Biomarker Standardization features found to be important across multiple sites and image modalities. Deep learning-based image segmentation models include state of the art networks such as Deeplab and other problem-specific architectures. The library is distributed as GNU-copyrighted software at https://www.github.com/cerr/CERR.