Orbit Image Analysis: an open-source whole slide image analysis tool

We describe Orbit Image Analysis, an open-source whole slide image analysis tool. The tool consists of a generic tile-processing engine which allows the execution of various image analysis algorithms provided by either Orbit itself or from other open-source platforms using a tile-based map-reduce execution framework. Orbit Image Analysis is capable of sophisticated whole slide imaging analyses due to several key features. First, Orbit has machine-learning capabilities. This deep learning segmentation can be integrated with complex object detection for analysis of intricate tissues. In addition, Orbit can run locally as standalone or connect to the open-source image server OMERO. Another important characteristic is its scale-out functionality, using the Apache Spark framework for distributed computing. In this paper, we describe the use of Orbit in three different real-world applications: quantification of idiopathic lung fibrosis, nerve fibre density quantification, and glomeruli detect...

本文介绍了轨道图像分析（Orbit Image Analysis）——一款开源全切片图像分析工具。该工具配备通用切块处理引擎，可通过基于切块的映射-规约（MapReduce）执行框架，运行由Orbit自身或其他开源平台提供的各类图像分析算法。轨道图像分析凭借多项核心特性，可实现复杂精准的全切片图像分析：其一，该工具集成机器学习能力，其深度学习分割功能可与复杂目标检测功能结合，用于复杂组织的分析；此外，Orbit既可作为独立应用本地运行，也可接入开源图像服务器OMERO；另一项重要特性是其横向扩展能力，可依托Apache Spark框架实现分布式计算。本文还介绍了Orbit在三项不同实际应用场景中的应用：特发性肺纤维化量化分析、神经纤维密度量化分析，以及肾小球检测……