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Abstract. Accurate colon segmentation on abdominal CT scans is crucial for various clinical applications. In this work, we propose an accurate AQ1 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 AQ2 an initial labeling that is generated by a Markov random field (MRF)- based approach. Finally, in the inference phase, we first detect the rec tum, 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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Fully Automated Spleen Localization And Segmentation Using Machine Learning And 3D Active Contours
Automated segmentation of the spleen in CT volumes is difficult due to variations in size, shape, and position of the spleen within the abdominal cavity as well as similarity of intensity values among organs in the abdominal cavity. In this paper we present a method for automated localization and segmentation of the spleen within axial abdominal CT volumes using trained classification models, active contours, anatomical information, and adaptive features. The results show an average Dice score of 0.873 on patients experiencing various chest, abdominal, and pelvic traumas taken at different contrast phases.
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- Award ID(s):
- 1500124
- PAR ID:
- 10298283
- Date Published:
- Journal Name:
- 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
- Page Range / eLocation ID:
- 53 to 56
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Purpose This article introduces a novel deep learning approach to substantially improve the accuracy of colon segmentation even with limited data annotation, which enhances the overall effectiveness of the CT colonography pipeline in clinical settings. Methods The proposed approach integrates 3D contextual information via guided sequential episodic training in which a query CT slice is segmented by exploiting its previous labeled CT slice (i.e., support). Segmentation starts by detecting the rectum using a Markov Random Field-based algorithm. Then, supervised sequential episodic training is applied to the remaining slices, while contrastive learning is employed to enhance feature discriminability, thereby improving segmentation accuracy. Results The proposed method, evaluated on 98 abdominal scans of prepped patients, achieved a Dice coefficient of 97.3% and a polyp information preservation accuracy of 98.28%. Statistical analysis, including 95% confidence intervals, underscores the method’s robustness and reliability. Clinically, this high level of accuracy is vital for ensuring the preservation of critical polyp details, which are essential for accurate automatic diagnostic evaluation. The proposed method performs reliably in scenarios with limited annotated data. This is demonstrated by achieving a Dice coefficient of 97.15% when the model was trained on a smaller number of annotated CT scans (e.g., 10 scans) than the testing dataset (e.g., 88 scans). Conclusions The proposed sequential segmentation approach achieves promising results in colon segmentation. A key strength of the method is its ability to generalize effectively, even with limited annotated datasets—a common challenge in medical imaging.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/EMBC.2018.8512182
