Multi-layer pseudo-supervision for histopathology tissue semantic segmentation using patch-level classification labels
Institution:
1. Department of Radiology, Guangdong Provincial People''s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China;2. Guangdong Cardiovascular Institute, Guangzhou, Guangdong 510080, China;3. Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangdong Provincial People''s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China;4. The School of Computer Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China;5. National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China;6. Department of Pathology, Guangdong Provincial People''s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China;7. Department of Radiology, Guangzhou First People''s Hospital, The Second Affiliated Hospital of South China University of Technology, Guangzhou, Guangdong 510180, China
Abstract:
Tissue-level semantic segmentation is a vital step in computational pathology. Fully-supervised models have already achieved outstanding performance with dense pixel-level annotations. However, drawing such labels on the giga-pixel whole slide images is extremely expensive and time-consuming. In this paper, we use only patch-level classification labels to achieve tissue semantic segmentation on histopathology images, finally reducing the annotation efforts. We propose a two-step model including a classification and a segmentation phases. In the classification phase, we propose a CAM-based model to generate pseudo masks by patch-level labels. In the segmentation phase, we achieve tissue semantic segmentation by our propose Multi-Layer Pseudo-Supervision. Several technical novelties have been proposed to reduce the information gap between pixel-level and patch-level annotations. As a part of this paper, we introduce a new weakly-supervised semantic segmentation (WSSS) dataset for lung adenocarcinoma (LUAD-HistoSeg). We conduct several experiments to evaluate our proposed model on two datasets. Our proposed model outperforms five state-of-the-art WSSS approaches. Note that we can achieve comparable quantitative and qualitative results with the fully-supervised model, with only around a 2% gap for MIoU and FwIoU. By comparing with manual labeling on a randomly sampled 100 patches dataset, patch-level labeling can greatly reduce the annotation time from hours to minutes. The source code and the released datasets are available at: https://github.com/ChuHan89/WSSS-Tissue.
