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A shape context fully convolutional neural network for segmentation and classification of cervical nuclei in Pap smear images.
Artificial Intelligence in Medicine ( IF 6.1 ) Pub Date : 2020-06-02 , DOI: 10.1016/j.artmed.2020.101897
Elima Hussain 1 , Lipi B Mahanta 1 , Chandana Ray Das 2 , Manjula Choudhury 2 , Manish Chowdhury 3
Affiliation  

Pap smear is often employed as a screening test for diagnosing cervical pre-cancerous and cancerous lesions. Accurate identification of dysplastic changes amongst the cervical cells in a Pap smear image is thus essential for rapid diagnosis and prognosis. Manual pathological observations used in clinical practice require exhaustive analysis of thousands of cell nuclei in a whole slide image to visualize the dysplastic nuclear changes which make the process tedious and time-consuming. Automated nuclei segmentation and classification exist but are challenging to overcome issues like nuclear intra-class variability and clustered nuclei separation. To address such challenges, we put forward an application of instance segmentation and classification framework built on an Unet architecture by adding residual blocks, densely connected blocks and a fully convolutional layer as a bottleneck between encoder-decoder blocks for Pap smear images. The number of convolutional layers in the standard Unet has been replaced by densely connected blocks to ensure feature reuse-ability property while the introduction of residual blocks in the same attempts to converge the network more rapidly. The framework provides simultaneous nuclei instance segmentation and also predicts the type of nucleus class as belonging to normal and abnormal classes from the smear images. It works by assigning pixel-wise labels to individual nuclei in a whole slide image which enables identifying multiple nuclei belonging to the same or different class as individual distinct instances. Introduction of a joint loss function in the framework overcomes some trivial cell level issues on clustered nuclei separation. To increase the robustness of the overall framework, the proposed model is preceded with a stacked auto-encoder based shape representation learning model. The proposed model outperforms two state-of-the-art deep learning models Unet and Mask_RCNN with an average Zijdenbos similarity index of 97 % related to segmentation along with binary classification accuracy of 98.8 %. Experiments on hospital-based datasets using liquid-based cytology and conventional pap smear methods along with benchmark Herlev datasets proved the superiority of the proposed method than Unet and Mask_RCNN models in terms of the evaluation metrics under consideration.



中文翻译:

用于巴氏涂片图像中宫颈核的分割和分类的形状上下文全卷积神经网络。

子宫颈抹片检查通常用作诊断宫颈癌前病变和癌性病变的筛查试验。因此,在巴氏涂片图像中准确识别宫颈细胞间的发育异常变化对于快速诊断和预后至关重要。临床实践中使用的手动病理观察需要对整个幻灯片图像中的数千个细胞核进行详尽分析,以可视化发育​​不良的核变化,这使得该过程既乏味又耗时。存在自动核分割和分类,但难以克服核类内可变性和成簇核分离等问题。为了应对这些挑战,我们提出了一种基于 Unet 架构的实例分割和分类框架的应用,通过添加残差块,密集连接的块和完全卷积层作为巴氏涂片图像的编码器-解码器块之间的瓶颈。标准 Unet 中的卷积层数已被密集连接的块取代,以确保特征重用能力的特性,同时引入残差块以尝试更快地收敛网络。该框架提供同时的细胞核实例分割,并且还根据涂片图像预测细胞核类的类型属于正常类和异常类。它的工作原理是为整个幻灯片图像中的单个原子核分配像素级标签,从而能够将属于同一类或不同类的多个原子核识别为单独的不同实例。在框架中引入联合损失函数克服了关于簇核分离的一些微不足道的细胞级问题。为了增加整个框架的鲁棒性,所提出的模型之前有一个基于堆叠自动编码器的形状表示学习模型。所提出的模型优于两个最先进的深度学习模型 Unet 和 Mask_RCNN,与分割相关的平均 Zijdenbos 相似度指数为 97%,二元分类精度为 98.8%。使用基于液体的细胞学和传统巴氏涂片方法以及基准 Herlev 数据集对基于医院的数据集进行的实验证明了所提出的方法在所考虑的评估指标方面比 Unet 和 Mask_RCNN 模型优越。所提出的模型之前是基于堆叠自动编码器的形状表示学习模型。所提出的模型优于两个最先进的深度学习模型 Unet 和 Mask_RCNN,与分割相关的平均 Zijdenbos 相似度指数为 97%,二元分类精度为 98.8%。使用基于液体的细胞学和传统巴氏涂片方法以及基准 Herlev 数据集对基于医院的数据集进行的实验证明了所提出的方法在所考虑的评估指标方面比 Unet 和 Mask_RCNN 模型优越。所提出的模型之前是基于堆叠自动编码器的形状表示学习模型。所提出的模型优于两个最先进的深度学习模型 Unet 和 Mask_RCNN,与分割相关的平均 Zijdenbos 相似度指数为 97%,二元分类精度为 98.8%。使用基于液体的细胞学和传统巴氏涂片方法以及基准 Herlev 数据集对基于医院的数据集进行的实验证明了所提出的方法在所考虑的评估指标方面比 Unet 和 Mask_RCNN 模型优越。所提出的模型优于两个最先进的深度学习模型 Unet 和 Mask_RCNN,与分割相关的平均 Zijdenbos 相似度指数为 97%,二元分类精度为 98.8%。使用基于液体的细胞学和传统巴氏涂片方法以及基准 Herlev 数据集对基于医院的数据集进行的实验证明了所提出的方法在所考虑的评估指标方面比 Unet 和 Mask_RCNN 模型优越。所提出的模型优于两个最先进的深度学习模型 Unet 和 Mask_RCNN,与分割相关的平均 Zijdenbos 相似度指数为 97%,二元分类精度为 98.8%。使用基于液体的细胞学和传统巴氏涂片方法以及基准 Herlev 数据集对基于医院的数据集进行的实验证明了所提出的方法在所考虑的评估指标方面比 Unet 和 Mask_RCNN 模型优越。

更新日期:2020-06-02
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