论文标题

Nuclick:用于显微镜图像的交互式分割的深度学习框架

NuClick: A Deep Learning Framework for Interactive Segmentation of Microscopy Images

论文作者

Koohbanani, Navid Alemi, Jahanifar, Mostafa, Tajadin, Neda Zamani, Rajpoot, Nasir

论文摘要

对象分割是计算病理学工作流程中的重要一步。基于深度学习的模型通常需要大量的标记数据才能进行精确和可靠的预测。但是,收集标记的数据是昂贵的,因为它通常需要专家知识,尤其是在医学成像域中,标签是一个或多个人类专家进行的耗时分析的结果。作为核,细胞和腺体是计算病理/细胞学中下游分析的基本对象,在本文中,我们提出了一种基于CNN的简单方法,以加快对这些对象的收集注释,这需要从注释符中进行最小的相互作用。我们表明,对于组织学和细胞学图像中的细胞核和细胞,每个对象内部一击足以使Nuclick产生精确的注释。对于多细胞结构(例如腺体),我们提出了一种新型方法,以将核对物作为指导信号提供痕迹,从而使其能够分割腺体边界。这些监督信号与RGB通道一起作为辅助输入供应到网络。通过详细的实验,我们表明Nuclick适应了对象尺度,可与用户输入的变化进行鲁棒性,适应于新域,并提供可靠的注释。在核心产生的面具上训练的实例分割模型在Lyon19挑战中达到了第一个等级。作为框架的示例输出,我们正在释放两个数据集:1)IHC图像中淋巴细胞注释的数据集,以及2)在血液涂片图像中的分段WBC数据集。

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

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