NuKit: A deep learning platform for fast nucleus segmentation of histopathological images.
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images.
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DOI：
10.1142/s0219720023500026
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发表时间：
2023-02
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1
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细胞核分割是组织病理学图像分析流水线的第一步，在精度和速度方面仍然是许多定量分析方法的挑战。最近，深度学习核团分割方法被证明优于以往基于强度或模式的方法。然而，深度学习的繁重计算量给人以实时滞后反应的印象，阻碍了这些模型在常规研究中的适用性。我们开发并实现了一个深度学习平台NuKit，它加速了核的分割，并向用户提供了及时的结果。NuKit平台由两个深度学习模型和一个交互式图形用户界面(GUI)组成，可提供快速、自动的核“动态”分割。这两种深度学习模型在核团分割中提供了互补的任务。全图像分割模型执行完整的图像核，而点击分割模型用用户驱动的输入来补充核分割，以编辑分割后的核。我们在一个大的公共训练数据集上训练了NuKit全图像分割模型，并在七个独立的公共图像数据集中测试了它的性能。整个图像分割模型的平均DICE=0.814，IOU=0.689。输出结果可以导出为不同的文件格式，并提供与其他图像分析工具(如QuPath)的无缝集成。NuKit可以使用个人计算机在Windows、Mac和Linux上执行。
Nucleus segmentation represents the initial step for histopathological image analysis pipelines, and it remains a challenge in many quantitative analysis methods in terms of accuracy and speed. Recently, deep learning nucleus segmentation methods have demonstrated to outperform previous intensity- or pattern-based methods. However, the heavy computation of deep learning provides impression of lagging response in real time and hampered the adoptability of these models in routine research. We developed and implemented NuKit a deep learning platform, which accelerates nucleus segmentation and provides prompt results to the users. NuKit platform consists of two deep learning models coupled with an interactive graphical user interface (GUI) to provide fast and automatic nucleus segmentation “on the fly”. Both deep learning models provide complementary tasks in nucleus segmentation. The whole image segmentation model performs whole image nucleus whereas the click segmentation model supplements the nucleus segmentation with user-driven input to edits the segmented nuclei. We trained the NuKit whole image segmentation model on a large public training data set and tested its performance in seven independent public image data sets. The whole image segmentation model achieves average DICE = 0.814 and IoU = 0.689. The outputs could be exported into different file formats, as well as provides seamless integration with other image analysis tools such as QuPath. NuKit can be executed on Windows, Mac, and Linux using personal computers.