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Human-Machine Interactive Tissue Prototype Learning for Label-Efficient Histopathology Image Segmentation

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Part of the Lecture Notes in Computer Science book series (LNCS,volume 13939)


Deep learning have greatly advanced histopathology image segmentation but usually require abundant annotated data. However, due to the gigapixel scale of whole slide images and pathologists’ heavy daily workload, obtaining pixel-level labels for supervised learning in clinical practice is often infeasible. Alternatively, weakly-supervised segmentation methods have been explored with less laborious image-level labels, but their performance is unsatisfactory due to the lack of dense supervision. Inspired by the recent success of self-supervised learning, we present a label-efficient tissue prototype dictionary building pipeline and propose to use the obtained prototypes to guide histopathology image segmentation. Particularly, taking advantage of self-supervised contrastive learning, an encoder is trained to project the unlabeled histopathology image patches into a discriminative embedding space where these patches are clustered to identify the tissue prototypes by efficient pathologists’ visual examination. Then, the encoder is used to map the images into the embedding space and generate pixel-level pseudo tissue masks by querying the tissue prototype dictionary. Finally, the pseudo masks are used to train a segmentation network with dense supervision for better performance. Experiments on two public datasets demonstrate that our method can achieve comparable segmentation performance as the fully-supervised baselines with less annotation burden and outperform other weakly-supervised methods. Codes are available at


  • WSI Segmentation
  • Label-efficient Learning
  • Clustering

W. Pan, J. Yan and H. Chen—contributed equally.

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This research was partly supported by the National Key R &D Program of China (Grant No. 2020AAA0108303), Shenzhen Science and Technology Project (Grant No. JCYJ20200109143041798), Shenzhen Stable Supporting Program (Grant No. WDZC20200820200655001), and Shenzhen Key Lab of next generation interactive media innovative technology (Grant No. ZDSY S20210623092001004).

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Correspondence to Jiangpeng Yan , Xiu Li or Jianhua Yao .

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Pan, W. et al. (2023). Human-Machine Interactive Tissue Prototype Learning for Label-Efficient Histopathology Image Segmentation. In: Frangi, A., de Bruijne, M., Wassermann, D., Navab, N. (eds) Information Processing in Medical Imaging. IPMI 2023. Lecture Notes in Computer Science, vol 13939. Springer, Cham.

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  • Print ISBN: 978-3-031-34047-5

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