论文标题
快速路径:一个基于深度学习的研究和数字病理决策支持的开源平台
FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology
论文作者
论文摘要
深卷积神经网络(CNN)是组织病理学图像数字分析的当前最新。大尺寸的全坡度显微镜图像(WSIS)需要高级内存处理来读取,显示和处理这些图像。有几个用于使用WSIS的开源平台,但是CNN模型的支持部署很少。这些应用程序使用第三方解决方案进行推理,使其对用户友好且不适合高性能图像分析。为了在低端机器上部署CNNS用户友好且可行,我们使用快速框架和C ++开发了一个新的平台,快速路线。它可以最大程度地减少用于阅读和处理WSI,CNN模型的部署以及结果实时交互式可视化的内存使用量。使用不同的架构,推理引擎,硬件配置和操作系统对四个不同的用例进行了运行时实验。使用快速路径和三个现有平台测量了用于阅读,可视化,缩放和平移A WSI的内存使用量。快速路径在内存方面与其他基于C ++的应用程序相似,同时使用的是基于两个Java的平台的使用率要小得多。神经网络模型,推理引擎,硬件和处理器的选择极大地影响了运行时。因此,快速路径包括在单个应用程序中有效可视化和处理WSI所需的所有步骤,包括推理具有实时显示结果的CNN。源代码,二进制发布和测试数据可以在GitHub上在https://github.com/sintefmedtek/fast-pathology/上在线找到。
Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a new platform, FastPathology, using the FAST framework and C++. It minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results. Runtime experiments were conducted on four different use cases, using different architectures, inference engines, hardware configurations and operating systems. Memory usage for reading, visualizing, zooming and panning a WSI were measured, using FastPathology and three existing platforms. FastPathology performed similarly in terms of memory to the other C++ based application, while using considerably less than the two Java-based platforms. The choice of neural network model, inference engine, hardware and processors influenced runtime considerably. Thus, FastPathology includes all steps needed for efficient visualization and processing of WSIs in a single application, including inference of CNNs with real-time display of the results. Source code, binary releases and test data can be found online on GitHub at https://github.com/SINTEFMedtek/FAST-Pathology/.