Abstract
Semantic segmentation of multi-gigapixel whole-slide images (WSI) is fundamental to computational pathology, as segmentation of different tissue types and layers is a prerequisite for several downstream histology image analysis, such as morphometric analysis, cancer grading, and survival. Both patch-based classification and pixel-wise segmentation have been used for these tasks, where patch-based classification outputs only one label per patch while pixel-wise segmentation is more accurate and precise but it requires a large number of pixel-wise precise annotated ground truth. In this paper, we propose coarse segmentation as a new middle ground to both techniques for leveraging more context without requiring pixel-level annotations. Our proposed coarse segmentation network is a convolutional neural network (CNN) with skip connections but does not contain any decoder and utilizes sparsely annotated images during training. It takes an input patch of size \(M \times N\) and outputs a dense prediction map of size \(m \times n\), which is coarser than pixel-wise segmentation methods but denser than patch-based classification methods. We compare our proposed method with its counterparts and demonstrate its superior performance for both pixel-based segmentation and patch-based classification tasks. In addition, we also compared the impact on performance of coarse-grained and pixel-wise semantic segmentation in downstream analysis tasks and showed coarse-grained semantic segmentation has no/marginal impact on the final results.
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Bashir, R.M.S., Shaban, M., Raza, S.E.A., Khurram, S.A., Rajpoot, N. (2022). A Novel Framework for Coarse-Grained Semantic Segmentation of Whole-Slide Images. In: Yang, G., Aviles-Rivero, A., Roberts, M., Schönlieb, CB. (eds) Medical Image Understanding and Analysis. MIUA 2022. Lecture Notes in Computer Science, vol 13413. Springer, Cham. https://doi.org/10.1007/978-3-031-12053-4_32
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