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

• Published in: PLoS computational biology Vol. 16; no. 2; p. e1007313
• Main Authors: Stritt, Manuel, Stalder, Anna K., Vezzali, Enrico
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.02.2020; Public Library of Science (PLoS)
• Subjects: Algorithms; Biology; Biology and Life Sciences; Cable television broadcasting industry; Classification; Computer and Information Sciences; Computer networks; Deep Learning; Distributed processing; Engineering and Technology; Fibrosis; Generic drugs; Humans; Image analysis; Image processing; Image Processing, Computer-Assisted - methods; Image segmentation; Learning algorithms; Machine learning; Medicine and Health Sciences; Object recognition; Open source software; Orbit - anatomy & histology; Pathology; Pharmaceuticals; Pulmonary fibrosis; Research and Analysis Methods; Respiratory tract diseases; Segmentation; Servers (Computers); Teaching methods; Tissue analysis; User interface; User-Computer Interface; Volumetric analysis; United States; Switzerland
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1007313

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 detection in the kidney.