论文标题

估价附近:组织病理学基于上下文的语义细分的记忆注意框架

Valuing Vicinity: Memory attention framework for context-based semantic segmentation in histopathology

论文作者

Ester, Oliver, Hörst, Fabian, Seibold, Constantin, Keyl, Julius, Ting, Saskia, Vasileiadis, Nikolaos, Schmitz, Jessica, Ivanyi, Philipp, Grünwald, Viktor, Bräsen, Jan Hinrich, Egger, Jan, Kleesiek, Jens

论文摘要

将组织病理学整个滑动图像分割成肿瘤和非肿瘤类型的组织是一项艰巨的任务,需要考虑局部和全球空间环境,以精确地对肿瘤区域进行分类。肿瘤组织亚型的鉴定会使问题复杂化,因为分离的清晰度降低,病理学家的推理甚至在空间环境中更加指导。但是,鉴定详细类型的组织对于提供个性化的癌症疗法至关重要。由于整个幻灯片图像的高分辨率,现有的语义分割方法仅限于孤立的图像部分,因此无法处理上下文信息。为了迈出更好的上下文理解,我们提出了一个补丁邻域注意机制,以查询相邻的组织上下文,并从嵌入记忆库中查询相邻的组织上下文,并将上下文嵌入到瓶颈隐藏的特征图中。我们的记忆注意框架(MAF)模仿病理学家的注释程序 - 缩小并考虑周围的组织环境。该框架可以集成到任何编码器分割方法中。我们使用著名的分割模型(U-NET,DEEPLABV3)评估了公共乳腺癌和内部肾癌数据集的MAF,并证明了比其他环境融合算法的优势 - 在骰子分数上可实现高达$ 17 \%$的实质性提高。该代码可公开可用:https://github.com/tio-ikim/valuing-vicinity

The segmentation of histopathological whole slide images into tumourous and non-tumourous types of tissue is a challenging task that requires the consideration of both local and global spatial contexts to classify tumourous regions precisely. The identification of subtypes of tumour tissue complicates the issue as the sharpness of separation decreases and the pathologist's reasoning is even more guided by spatial context. However, the identification of detailed types of tissue is crucial for providing personalized cancer therapies. Due to the high resolution of whole slide images, existing semantic segmentation methods, restricted to isolated image sections, are incapable of processing context information beyond. To take a step towards better context comprehension, we propose a patch neighbour attention mechanism to query the neighbouring tissue context from a patch embedding memory bank and infuse context embeddings into bottleneck hidden feature maps. Our memory attention framework (MAF) mimics a pathologist's annotation procedure -- zooming out and considering surrounding tissue context. The framework can be integrated into any encoder-decoder segmentation method. We evaluate the MAF on a public breast cancer and an internal kidney cancer data set using famous segmentation models (U-Net, DeeplabV3) and demonstrate the superiority over other context-integrating algorithms -- achieving a substantial improvement of up to $17\%$ on Dice score. The code is publicly available at: https://github.com/tio-ikim/valuing-vicinity

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