论文标题

全面学习图像细分和分析的广义深度学习框架

A Generalized Deep Learning Framework for Whole-Slide Image Segmentation and Analysis

论文作者

Khened, Mahendra, Kori, Avinash, Rajkumar, Haran, Srinivasan, Balaji, Krishnamurthi, Ganapathy

论文摘要

组织病理学组织分析被认为是癌症诊断和预后的黄金标准。鉴于这些图像的尺寸很大,并且潜在的癌症病例的数量增加,因此非常需要自动解决方案作为组织病理学家的帮助。最近,基于深度学习的技术为最先进的技术提供了多种图像分析任务,包括对数字化幻灯片的分析。但是,组织病理学任务的图像和变异性的大小和变异性使开发组织病理学图像分析的综合框架是一个挑战。我们提出了一个基于学习的基于学习的框架,用于组织病理组织分析。我们在几个开源数据集上证明了我们的框架(包括培训和推断)的普遍性,其中包括Camelyon(乳腺癌转移),Digestpath(结肠癌)和PAIP(肝癌)数据集。我们分别讨论了与数据和模型有关的多种类型的不确定性,即分别是核心和认知。同时,我们通过评估TCGA数据上的某些样本来证明跨不同数据分布的模型概括。在CamelyOn16测试数据(n = 139)中,针对病变检测任务,达到的FroC分数为0.86,在Camelyon17测试数据(n = 500)中,对于PN阶段的任务,Cohen的Kappa得分达到的任务为0.9090(在公开排行榜中为0.9090)。在DigestPath测试数据(n = 212)中,肿瘤分割任务时,骰子得分为0.782(在挑战中排名第四)。在暂停测试数据(n = 40)中,对于可行肿瘤分割的任务,达到了0.75的JACCARD指数(在挑战中排名第三),对于可行的肿瘤负担,达到了0.633的得分(在挑战赛中第二位)。我们的整个框架和相关文档可在GitHub和PYPI上免费获得。

Histopathology tissue analysis is considered the gold standard in cancer diagnosis and prognosis. Given the large size of these images and the increase in the number of potential cancer cases, an automated solution as an aid to histopathologists is highly desirable. In the recent past, deep learning-based techniques have provided state of the art results in a wide variety of image analysis tasks, including analysis of digitized slides. However, the size of images and variability in histopathology tasks makes it a challenge to develop an integrated framework for histopathology image analysis. We propose a deep learning-based framework for histopathology tissue analysis. We demonstrate the generalizability of our framework, including training and inference, on several open-source datasets, which include CAMELYON (breast cancer metastases), DigestPath (colon cancer), and PAIP (liver cancer) datasets. We discuss multiple types of uncertainties pertaining to data and model, namely aleatoric and epistemic, respectively. Simultaneously, we demonstrate our model generalization across different data distribution by evaluating some samples on TCGA data. On CAMELYON16 test data (n=139) for the task of lesion detection, the FROC score achieved was 0.86 and in the CAMELYON17 test-data (n=500) for the task of pN-staging the Cohen's kappa score achieved was 0.9090 (third in the open leaderboard). On DigestPath test data (n=212) for the task of tumor segmentation, a Dice score of 0.782 was achieved (fourth in the challenge). On PAIP test data (n=40) for the task of viable tumor segmentation, a Jaccard Index of 0.75 (third in the challenge) was achieved, and for viable tumor burden, a score of 0.633 was achieved (second in the challenge). Our entire framework and related documentation are freely available at GitHub and PyPi.

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