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

We describe the open-source whole slide image analysis tool Orbit Image Analysis. It is a generic tile-processing engine which allows the execution of various image analysis algorithms provided by either Orbit itself or other open-source solutions using a tile-based map-reduce execution framework. We show its sophisticated machine-learning approach for WSI quantification, and its flexibility by integrating a deep learning segmentation method for complex object detection. It can run locally standalone or connect to the open-source image server OMERO, and provides scale-out functionality to use the Spark framework for distributed computing. We demonstrate the application of Orbit in three real-world use-cases: Idiopathic lung fibrosis, nerve fibre density quantification, and glomeruli detection in kidney.