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Home / Proceedings / Proceedings of the AAAI Conference on Artificial Intelligence / EAAI-20

Biomedical Image Segmentation via Representative Annotation

February 1, 2023

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Authors

Hao Zheng

University of Notre Dame


Lin Yang

University of Notre Dame


Jianxu Chen

Allen Institute for Cell Science


Jun Han

University of Notre Dame


Yizhe Zhang

University of Notre Dame


Peixian Liang

University of Notre Dame


Zhuo Zhao

University of Notre Dame


Chaoli Wang

University of Notre Dame


Danny Z. Chen

University of Notre Dame


DOI:

10.1609/aaai.v33i01.33015901


Abstract:

Deep learning has been applied successfully to many biomedical image segmentation tasks. However, due to the diversity and complexity of biomedical image data, manual annotation for training common deep learning models is very timeconsuming and labor-intensive, especially because normally only biomedical experts can annotate image data well. Human experts are often involved in a long and iterative process of annotation, as in active learning type annotation schemes. In this paper, we propose representative annotation (RA), a new deep learning framework for reducing annotation effort in biomedical image segmentation. RA uses unsupervised networks for feature extraction and selects representative image patches for annotation in the latent space of learned feature descriptors, which implicitly characterizes the underlying data while minimizing redundancy. A fully convolutional network (FCN) is then trained using the annotated selected image patches for image segmentation. Our RA scheme offers three compelling advantages: (1) It leverages the ability of deep neural networks to learn better representations of image data; (2) it performs one-shot selection for manual annotation and frees annotators from the iterative process of common active learning based annotation schemes; (3) it can be deployed to 3D images with simple extensions. We evaluate our RA approach using three datasets (two 2D and one 3D) and show our framework yields competitive segmentation results comparing with state-of-the-art methods.

Topics: AAAI

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HOW TO CITE:

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen Biomedical Image Segmentation via Representative Annotation Proceedings of the AAAI Conference on Artificial Intelligence (2019) 5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen Biomedical Image Segmentation via Representative Annotation AAAI 2019, 5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen (2019). Biomedical Image Segmentation via Representative Annotation. Proceedings of the AAAI Conference on Artificial Intelligence, 5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. Biomedical Image Segmentation via Representative Annotation. Proceedings of the AAAI Conference on Artificial Intelligence 2019 p.5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. 2019. Biomedical Image Segmentation via Representative Annotation. "Proceedings of the AAAI Conference on Artificial Intelligence". 5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. (2019) "Biomedical Image Segmentation via Representative Annotation", Proceedings of the AAAI Conference on Artificial Intelligence, p.5901-5908

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen, "Biomedical Image Segmentation via Representative Annotation", AAAI, p.5901-5908, 2019.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. "Biomedical Image Segmentation via Representative Annotation". Proceedings of the AAAI Conference on Artificial Intelligence, 2019, p.5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. "Biomedical Image Segmentation via Representative Annotation". Proceedings of the AAAI Conference on Artificial Intelligence, (2019): 5901-5908.

Hao Zheng||Lin Yang||Jianxu Chen||Jun Han||Yizhe Zhang||Peixian Liang||Zhuo Zhao||Chaoli Wang||Danny Z. Chen. Biomedical Image Segmentation via Representative Annotation. AAAI[Internet]. 2019[cited 2023]; 5901-5908.


ISSN: 2374-3468


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