论文标题
H&E染色的全幻灯片图像的深度互动学习的卵巢癌分割,以研究BRCA突变的形态学模式
Deep Interactive Learning-based ovarian cancer segmentation of H&E-stained whole slide images to study morphological patterns of BRCA mutation
论文作者
论文摘要
深度学习已被广泛用于分析数字化的苏木精和曙红(H&E)染色的组织病理学全滑动图像。使用深度学习的自动化癌症分割可用于诊断恶性肿瘤并找到新的形态学模式来预测分子亚型。为了训练像素的癌症分割模型,病理学家的手动注释通常是瓶颈,因为它耗时。在本文中,我们提出了从不同的癌症类型的鉴定分段模型进行深入的互动学习,以减少手动注释时间。与其在GIGA像素整体幻灯片图像上注释癌症和非癌区区域的所有像素,这是一个迭代的过程,该过程是从分割模型中注释错误标记的区域的迭代过程,并通过附加注释训练/训练/填充模型可以减少时间。特别是,采用预验证的分割模型可以进一步减少时间,而不是从头开始注释。我们通过3.5小时的手动注释训练了精确的卵巢癌分段模型,该模型的手动注释达到了0.74,召回0.86,精度为0.84。随着自动提取的高级浆液卵巢癌斑块,我们试图训练另一个深度学习模型以预测BRCA突变。细分模型和代码已在https://github.com/mskcc-computational-pathology/dmmn-ovary上发布。
Deep learning has been widely used to analyze digitized hematoxylin and eosin (H&E)-stained histopathology whole slide images. Automated cancer segmentation using deep learning can be used to diagnose malignancy and to find novel morphological patterns to predict molecular subtypes. To train pixel-wise cancer segmentation models, manual annotation from pathologists is generally a bottleneck due to its time-consuming nature. In this paper, we propose Deep Interactive Learning with a pretrained segmentation model from a different cancer type to reduce manual annotation time. Instead of annotating all pixels from cancer and non-cancer regions on giga-pixel whole slide images, an iterative process of annotating mislabeled regions from a segmentation model and training/finetuning the model with the additional annotation can reduce the time. Especially, employing a pretrained segmentation model can further reduce the time than starting annotation from scratch. We trained an accurate ovarian cancer segmentation model with a pretrained breast segmentation model by 3.5 hours of manual annotation which achieved intersection-over-union of 0.74, recall of 0.86, and precision of 0.84. With automatically extracted high-grade serous ovarian cancer patches, we attempted to train another deep learning model to predict BRCA mutation. The segmentation model and code have been released at https://github.com/MSKCC-Computational-Pathology/DMMN-ovary.