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Multi-Organ Gland Segmentation Using Deep Learning

机译:利用深度学习多器官腺细分

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Clinical morphological analysis of histopathology samples is an effective method in cancer diagnosis. Computational pathology methods can be employed to automate this analysis, providing improved objectivity and scalability. More specifically, computational techniques can be used in segmenting glands, which is an essential factor in cancer diagnosis. Automatic delineation of glands is a challenging task considering a large variability in glandular morphology across tissues and pathological subtypes. A deep learning based gland segmentation method can be developed to address the above task, but it requires a large number of accurate gland annotations from several tissue slides. Such a large dataset need to be generated manually by experienced pathologists, which is laborious, time-consuming, expensive and suffers from the subjectivity of the annotator. So far, deep learning techniques have produced promising results on a few organ-specific gland segmentation tasks, however, the demand for organ-specific gland annotations hinder the extensibility of these techniques to other organs. This work investigates the idea of cross-domain (-organ type) approximation that aims at reducing the need for organ-specific annotations. Unlike parenchyma, the stromal component of tissues, that lies between the glands, is more consistent across several organs. It is hypothesized that an automatic method, that can precisely segment the stroma, would pave the way for a cross-organ gland segmentation. Two proposed Dense-U-Nets are trained on hematoxylin and eosin (H&E) stained colon adenocarcinoma samples focusing on the gland and stroma segmentation. The trained networks are evaluated on two independent datasets, they are, a H&E stained colon adenocarcinoma dataset and a H&E stained breast invasive cancer dataset. The trained network targeting the stroma segmentation performs similar to the network targeting the gland segmentation on the colon dataset. Whereas, the former approach performs significantly better compared to the latter approach on the breast dataset, showcasing the higher generalization capacity of the stroma segmentation approach. The networks are evaluated using Dice coefficient and Hausdorff distance computed between the ground truth gland masks and the predicted gland masks. The conducted experiments validate the efficacy of the proposed stoma segmentation approach towards multi-organ gland segmentation.
机译:组织病理学样本的临床形态学分析是癌症诊断的有效方法。可以采用计算病理方法来自动化该分析,提供改善的客观性和可扩展性。更具体地,可以在分段腺体中使用计算技术,这是癌症诊断的必要因素。考虑到组织和病理亚型的腺体形态的大变异性,自动描绘腺体是一个具有挑战性的任务。可以开发一种基于深度学习的Gland分段方法来解决上述任务,但它需要来自多个组织幻灯片的大量准确的腺体注释。这种大型数据集需要通过经验丰富的病理学家手动生成,这是费力,耗时,昂贵的并且遭受注释器的主体性的。到目前为止,深入学习技术已经产生了有希望的结果对一些器官特定的腺体分割任务,然而,对器官特定腺体注释的需求阻碍了这些技术对其他器官的可扩张性。这项工作调查了旨在减少对器官特定注释的需求的跨域( - organ类型)近似的思想。与薄壁组织不同,组织的基质成分在腺体之间呈现在几个器官上更一致。假设一种可以精确地分割基质的自动方法将为交叉器官腺细分铺平道路。两个提出的致密U-净训练在苏木精和曙红(H&E)上染色的结肠腺癌样品,其关注腺体和基质分割。在两个独立的数据集中评估训练网络,它们是H&E染色的结肠腺癌数据集和H&E染色的乳房侵入性癌数据集。训练的网络瞄准基质分割的网络执行类似于针对冒号数据集上的腺分段的网络。然而,与乳房数据集的后一种方法相比,前一种方法显着更好地表现出基质分割方法的较高概括能力。使用地面真实腺体掩模和预测的腺体掩模之间计算的骰子系数和Hausdorff距离进行评估网络。进行的实验验证了拟议的造口分割方法对多器官腺细分的疗效。

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