Efficient contour-based annotation by iterative deep learning for organ segmentation from volumetric medical images.

PURPOSE: Training deep neural networks usually require a large number of human-annotated data. For organ segmentation from volumetric medical images, human annotation is tedious and inefficient. To save human labour and to accelerate the training process, the strategy of annotation by iterative deep learning recently becomes popular in the research community. However, due to the lack of domain knowledge or efficient human-interaction tools, the current AID methods still suffer from long training time and high annotation burden. METHODS: We develop a contour-based annotation by iterative deep learning (AID) algorithm which uses boundary representation instead of voxel labels to incorporate high-level organ shape knowledge. We propose a contour segmentation network with a multi-scale feature extraction backbone to improve the boundary detection accuracy. We also developed a contour-based human-intervention method to facilitate easy adjustments of organ boundaries. By combining the contour-based segmentation network and the contour-adjustment intervention method, our algorithm achieves fast few-shot learning and efficient human proofreading. RESULTS: For validation, two human operators independently annotated four abdominal organs in computed tomography (CT) images using our method and two compared methods, i.e. a traditional contour-interpolation method and a state-of-the-art (SOTA) convolutional network (CNN) method based on voxel label representation. Compared to these methods, our approach considerably saved annotation time and reduced inter-rater variabilities. Our contour detection network also outperforms the SOTA nnU-Net in producing anatomically plausible organ shape with only a small training set. CONCLUSION: Taking advantage of the boundary shape prior and the contour representation, our method is more efficient, more accurate and less prone to inter-operator variability than the SOTA AID methods for organ segmentation from volumetric medical images. The good shape learning ability and flexible boundary adjustment function make it suitable for fast annotation of organ structures with regular shape.

AnatomySketch: An Extensible Open-Source Software Platform for Medical Image Analysis Algorithm Development.

The development of medical image analysis algorithm is a complex process including the multiple sub-steps of model training, data visualization, human-computer interaction and graphical user interface (GUI) construction. To accelerate the development process, algorithm developers need a software tool to assist with all the sub-steps so that they can focus on the core function implementation. Especially, for the development of deep learning (DL) algorithms, a software tool supporting training data annotation and GUI construction is highly desired. In this work, we constructed AnatomySketch, an extensible open-source software platform with a friendly GUI and a flexible plugin interface for integrating user-developed algorithm modules. Through the plugin interface, algorithm developers can quickly create a GUI-based software prototype for clinical validation. AnatomySketch supports image annotation using the stylus and multi-touch screen. It also provides efficient tools to facilitate the collaboration between human experts and artificial intelligent (AI) algorithms. We demonstrate four exemplar applications including customized MRI image diagnosis, interactive lung lobe segmentation, human-AI collaborated spine disc segmentation and Annotation-by-iterative-Deep-Learning (AID) for DL model training. Using AnatomySketch, the gap between laboratory prototyping and clinical testing is bridged and the development of MIA algorithms is accelerated. The software is opened at https://github.com/DlutMedimgGroup/AnatomySketch-Software .