Multi-organ Segmentation over Partially Labeled Datasets with Multi-scale Feature Abstraction

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Publications: arXiv Add/Edit

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This paper presents a unified training strategy that enables a novel multi-scale deep neural network to be trained on multiple partially labeled datasets for multi-organ segmentation. Multi-scale contextual information is effective for pixel-level label prediction, i.e. image segmentation. However, such important information is only partially exploited by the existing methods. In this paper, we propose a new network architecture for multi-scale feature abstraction, which integrates pyramid feature analysis into an image segmentation model. To bridge the semantic gap caused by directly merging features from different scales, an equal convolutional depth mechanism is proposed. In addition, we develop a deep supervision mechanism for refining outputs in different scales. To fully leverage the segmentation features from different scales, we design an adaptive weighting layer to fuse the outputs in an automatic fashion. All these features together integrate into a pyramid-input pyramid-output network for efficient feature extraction. Last but not least, to alleviate the hunger for fully annotated data in training deep segmentation models, a unified training strategy is proposed to train one segmentation model on multiple partially labeled datasets for multi-organ segmentation with a novel target adaptive loss. Our proposed method was evaluated on four publicly available datasets, including BTCV, LiTS, KiTS and Spleen, where very promising performance has been achieved. The source code of this work is publicly shared at for others to easily reproduce the work and build their own models with the introduced mechanisms.

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Languages: Python Add/Edit

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PIPO-FAN for multi organ segmentation over partial labeled datasets using pytorch