An Image Analysis Resource for Cancer Research: PIIP—Pathology Image Informatics Platform for Visualization, Analysis, and Management

TLDR

PIIP is an NCI/NIH‑sponsored platform that extends the free Sedeen viewer to manage, annotate, share, and quantitatively analyze digital pathology images. The project aims to embed common image‑analysis applications into Sedeen, providing a freely available resource and guidance for users to extend functionality via plugins. New plugins for out‑of‑focus detection, ROI transformation, IHC analysis, and MATLAB‑based biomarker quantification and nuclear segmentation have been integrated, and all materials, including a usage video and documentation, are freely accessible online. Published in Cancer Research 77(21):e83–86; ©2017 AACR.

Abstract

Abstract Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Thus far, new plugins have been developed and incorporated into the platform for out of focus detection, region of interest transformation, and IHC slide analysis. Our biomarker quantification and nuclear segmentation algorithms, written in MATLAB, have also been integrated into the viewer. This article describes the viewing software and the mechanism to extend functionality by plugins, brief descriptions of which are provided as examples, to guide users who want to use this platform. PIIP project materials, including a video describing its usage and applications, and links for the Sedeen Viewer, plug-ins, and user manuals are freely available through the project web page: http://pathiip.org. Cancer Res; 77(21); e83–86. ©2017 AACR.