Accurate colon segmentation on abdominal CT scans is crucial for various clinical applications. In this work, we propose an accurate approach to colon segmentation from abdomen CT scans. Our architecture incorporates 3D contextual information via sequential episodic training (SET). In each episode, we used two consecutive slices, in a CT scan, as support and query samples in addition to other slices that did not include colon regions as negative samples. Choosing consecutive slices is a proper assumption for support and query samples, as the anatomy of the body does not have abrupt changes. Unlike traditional few-shot segmentation (FSS) approaches, we use the episodic training strategy in a supervised manner. In addition, to improve the discriminability of the learned features of the model, an embedding space is developed using contrastive learning. To guide the contrastive learning process, we use an initial labeling that is generated by a Markov random field (MRF)-based approach. Finally, in the inference phase, we first detect the rectum, which can be accurately extracted using the MRF-based approach, and then apply the SET on the remaining slices. Experiments on our private dataset of 98 CT scans and a public dataset of 30 CT scans illustrate that the proposed FSS model achieves a remarkable validation dice coefficient (DC) of 97.3% (Jaccard index, JD 94. 5%) compared to the classical FSS approaches 82.1% (JD 70.3%). Our findings highlight the efficacy of sequential episodic training in accurate 3D medical imaging segmentation. The codes for the proposed models are available at https://github.com/Samir-Farag/ICPR2024 .

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Colon Segmentation Using Guided Sequential Episodic Training and Contrastive Learning

  • Samir Harb,
  • Asem Ali,
  • Mohamed Yousuf,
  • Salwa Elshazly,
  • Aly Farag

摘要

Accurate colon segmentation on abdominal CT scans is crucial for various clinical applications. In this work, we propose an accurate approach to colon segmentation from abdomen CT scans. Our architecture incorporates 3D contextual information via sequential episodic training (SET). In each episode, we used two consecutive slices, in a CT scan, as support and query samples in addition to other slices that did not include colon regions as negative samples. Choosing consecutive slices is a proper assumption for support and query samples, as the anatomy of the body does not have abrupt changes. Unlike traditional few-shot segmentation (FSS) approaches, we use the episodic training strategy in a supervised manner. In addition, to improve the discriminability of the learned features of the model, an embedding space is developed using contrastive learning. To guide the contrastive learning process, we use an initial labeling that is generated by a Markov random field (MRF)-based approach. Finally, in the inference phase, we first detect the rectum, which can be accurately extracted using the MRF-based approach, and then apply the SET on the remaining slices. Experiments on our private dataset of 98 CT scans and a public dataset of 30 CT scans illustrate that the proposed FSS model achieves a remarkable validation dice coefficient (DC) of 97.3% (Jaccard index, JD 94. 5%) compared to the classical FSS approaches 82.1% (JD 70.3%). Our findings highlight the efficacy of sequential episodic training in accurate 3D medical imaging segmentation. The codes for the proposed models are available at https://github.com/Samir-Farag/ICPR2024 .