PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation

Background and Objective: Existing deep learning platforms for medical image segmentation mainly focus on fully supervised segmentation that assumes full and accurate pixel-level annotations are available. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation, which can accelerate and simply the development of deep learning models with limited annotation budget, e.g., learning from partial, sparse or noisy annotations. Methods: Our proposed toolkit named PyMIC is a modular deep learning platform for medical image segmentation tasks. In addition to basic components that support development of high-performance models for fully supervised segmentation, it contains several advanced components that are tailored for learning from imperfect annotations, such as loading annotated and unannounced images, loss functions for unannotated, partially or inaccurately annotated images, and training procedures for co-learning between multiple networks, etc. PyMIC is built on the PyTorch framework and supports development of semi-supervised, weakly supervised and noise-robust learning methods for medical image segmentation. Results: We present four illustrative medical image segmentation tasks based on PyMIC: (1) Achieving competitive performance on fully supervised learning; (2) Semi-supervised cardiac structure segmentation with only 10% training images annotated; (3) Weakly supervised segmentation using scribble annotations; and (4) Learning from noisy labels for chest radiograph segmentation. Conclusions: The PyMIC toolkit is easy to use and facilitates efficient development of medical image segmentation models with imperfect annotations. It is modular and flexible, which enables researchers to develop high-performance models with low annotation cost. The source code is available at: https://github.com/HiLab-git/PyMIC.