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

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.

Figure 1

shows the user inter-face of Sedeen Viewer. Certain key aspects of Sedeen Viewer’s functionality will be highlighted here while further details of its use are described in the user manual. The Toolbar (1) provides access to controls for image navigation and allows the display layout (stacked, vertical, horizontal) to be customized. Screenshot, format conversion and cropping tools are also available. The File Manager panel (2) allows the order of images and their visibility to be controlled. Opacity of images and transformation parameters can also be modified which supports manual alignment. The Overlay Manager (3) provides tools for annotation and markup of images. Drawing tools include polygons, rulers, arrow, rectangles, ovals and freehand shapes. The properties of overlays (color, name and description) can be modified and reports on their relevant characteristics (e.g. area, length) can be displayed. Annotations can be exported in a human readable XML format, and can be imported into other programs and applications. The Analysis Manager (4) allows plugins generated with Pathcore SDK to be loaded into Sedeen. SDK generated plugins allow developers to collect parameters and display results of analysis in real-time.